RNAP3D

PDB Method Taxonomy Organism Name Reference_pub Resolution Stage  Contents   Ligands 
1DOQ XRD Prokaryote Thermus Thermophilus The C-terminal domain of the RNA polymerase alpha subunit from thermus thermophilus 10821859 Subunit RNA polymerase alpha subunit
1IW7 XRD Prokaryote Thermus Thermophilus Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6 angstrom resolution 12000971 2.60 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma-70 subunit PB MG
1SMY XRD Prokaryote Thermus Thermophilus Structural basis for transcription regulation by alarmone ppGpp 15109491 2.70 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma-70 subunit G4P[ GUANOSINE-5',3'-TETRAPHOSPHATE ],ZN,MG
2BE5 XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNA polymerase holoenzyme in complex with inhibitor tagetitoxin 16273103 2.40 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor RpoD subunit TGT[ TAGETITOXIN ],ZN,MG
2PPB XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNAP polymerase elongation complex with the NTP substrate analog and antibiotic streptolydigin 17581591 3.00 Å EC RNA polymerase alpha/beta/beta'/omega subunit STD[ STREPTOLYDIGIN ],APC[DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER ],ZN,MG
3EQL XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNA polymerase holoenzyme in complex with antibiotic myxopyronin 18946472 2.70 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor RpoD subunit MXP[ Myxopyronin B ],ZN,MG
4Q4Z XRD Prokaryote Thermus Thermophilus Thermus thermophilus RNA polymerase de novo transcription initiation complex 24973216 2.90 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor sigA subunit 2TM[ 5'-O-S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphory]cytidine ],ATP,ZN,MG
4Q5S XRD Prokaryote Thermus Thermophilus Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA 24973216 3.00 Å IC alpha/beta/beta'/omega/sigma factor sigA subunit ATP ZN MG
4WQS XRD Prokaryote Thermus Thermophilus Thermus thermophilus RNA polymerase backtracked complex 25601758 4.31 Å EC RNA polymerase alpha/beta/beta'/omega subunit ZN
4WQT XRD Prokaryote Thermus Thermophilus Thermus thermophilus RNA polymerase complexed with an RNA cleavage stimulating factor (a grea/gfh1 chimeric protein) 25601758 4.40 Å EC RNA polymerase alpha/beta/beta'/omega subunit,GreA/Gfh1 chimeric protein ZN MG
5D4C XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus product complex for transcription initiation with ATP and CTP 27383794 3.28 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit C[ CYTIDINE-5'-MONOPHOSPHATE ],ATP,CTP,ZN,MG
5D4D XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP 27383794 3.00 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit NAD,CTP,A[ ADENOSINE-5'-MONOPHOSPHATE ],C[ CYTIDINE-5'-MONOPHOSPHATE ],ZN,MG
5D4E XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus product complex for transcription initiation with 3'-dephosphate-COA and CTP 27383794 3.08 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit COD[ DEPHOSPHO COENZYME A ], C[ CYTIDINE-5'-MONOPHOSPHATE ], DPO[ DIPHOSPHATE ],ZN,MG
5E+017 XRD Prokaryote Thermus Thermophilus T. Thermophilus transcription initiation complex having a rrr discriminator sequence and a nontemplate-strand length corresponding to tss selection at position 7 (Rpo-ggg-7) 26941320 3.20 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
5E+018 SOLUTION NMR Prokaryote Thermus Thermophilus T. Thermophilus transcription initiation complex having a yyy discriminator sequence and a nontemplate-strand length corresponding to tss selection at position 8 (Rpo-ccc-8) 26941320 3.30 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
5I2D XRD Prokaryote Thermus Thermophilus Crystal structure of t. Thermophilus tthb099 Classification II transcription activation complex: tap-Rpo 27284196 4.41 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit,Crp family ZN MG
5TMC XRD Prokaryote Thermus Thermophilus Re-refinement of thermus thermopiles DNA-directed RNA polymerase structure 25352397 2.71 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit G4P[ GUANOSINE-5',3'-TETRAPHOSPHATE],PO4,ZN,MG
5TMF XRD Prokaryote Thermus Thermophilus Re-refinement of Thermus thermophilus RNA polymerase 25352397 3.00 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit NE6[ methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate ],PO4,ZN,MG
5VO8 XRD Prokaryote Thermus Thermophilus X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter 28652344 3.30 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit POP[ PYROPHOSPHATE 2- ],ZN,MG
5VOI XRD Prokaryote Thermus Thermophilus X-ray crystal structure of bacterial RNA polymerase and pyrg promoter complex 28652344 2.80 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
5X21 XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex with Gpa and pseudouridimycin (pum) 28622509 3.32 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit PUM[ (1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol ],ZN,MG
5X22 XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex with Gpa and cmpcpp 28622509 3.35 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit 2TM[ 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine ],ZN,MG
5XJ0 XRD Prokaryote Thermus Thermophilus T. Thermophilus RNA polymerase holoenzyme bound with gp39 and gp76 29165680 4.00 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit,gp39,gp76 ZN
6ASG XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus RNA polymerase core enzyme 29606590 3.80 Å RNAP RNA polymerase alpha/beta/beta'/omega subunit ZN MG
6KQD XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-OH RNA of 3 nt 32127479 3.30 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit DG[ 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE ],ZN,MG
6KQE XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-OH RNA of 4 nt 32127479 3.30 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6KQF XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-OH RNA of 5 nt 32127479 2.45 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6KQG XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-OH RNA of 6 nt 32127479 2.78 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6KQH XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-OH RNA of 7 nt 32127479 3.18 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6KQL XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 4 nt 32127479 2.89 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6KQM XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 5 nt 32127479 3.20 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6KQN XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 6 nt 32127479 3.49 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6L74 XRD Prokaryote Thermus Thermophilus Thermus thermophilus initial transcription complex comprising sigma a and 5'-triphosphate RNA of 2 nt 32127479 3.12 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6LTS XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex comprising a truncated sigma finger 32127479 3.45 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6OVR XRD Prokaryote Thermus Thermophilus X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter variant -1g 31965171 2.84 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit POP[ PYROPHOSPHATE 4- ],ZN,MG
6OVY XRD Prokaryote Thermus Thermophilus X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter variant -1c 31965171 3.00 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit POP[ PYROPHOSPHATE 4- ],ZN,MG
6OW3 XRD Prokaryote Thermus Thermophilus X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter variant -1t 31965171 2.77 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit POP[ PYROPHOSPHATE 4- ],ZN,MG
6OY5 XRD Prokaryote Thermus Thermophilus X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter at 3 min 31965171 3.10 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit GTP ZN MG
6OY6 XRD Prokaryote Thermus Thermophilus X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter at 5 min 31965171 3.10 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit GTP ZN MG
6OY7 XRD Prokaryote Thermus Thermophilus X-ray crystal structure of a bacterial reiterative transcription complex of pyrg promoter at 7 min 31965171 3.04 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit POP[ PYROPHOSPHATE 4- ],ZN,MG
6P70 XRD Prokaryote Thermus Thermophilus X-ray crystal structure of bacterial RNA polymerase and pyrbi promoter complex 31965171 3.05 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit ZN MG
6P71 XRD Prokaryote Thermus Thermophilus X-ray crystal structure of a bacterial reiterative transcription complex of pyrbi promoter 31965171 2.92 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit UTP ZN MG
6WOX XRD Prokaryote Thermus Thermophilus Thermus thermophilus RNA polymerase initially transcribing complex with 2'dCTP 33542236 3.14 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit DCP[ 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE ],ZN,MG,NA
6WOY XRD Prokaryote Thermus Thermophilus Thermus thermophilus RNA polymerase initially transcribing complex with 3'dCTP 33542236 3.00 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit CH1[ 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE ],ZN,MG
1ZYR XRD Prokaryote Thermus Thermophilus Structure of Thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin 16122422 3.00 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor SigA subunit,antibiotic streptolydigin STD[ STREPTOLYDIGIN ],ZN,MG
2A68 XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifabutin 16096056 2.50 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor RpoD subunit RBT[ RIFABUTIN ],ZN,MG
2A69 XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNA polymerase holoenzyme in complex with antibiotic rifapentin 16096056 2.50 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor RpoD subunit RPT[ RIFAPENTINE ],ZN,MG
2A6E XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNA polymerase holoenzyme 16096056 2.80 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor RpoD subunit ZN MG
2A6H XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNA polymerase holoenzyme in complex with antibiotic sterptolydigin 16167380 2.40 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor RpoD subunit STD[ STREPTOLYDIGIN ],MG,ZN
2CW0 XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus RNA polymerase holoenzyme at 3.3 angstroms resolution 16122422 3.30 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor RpoD subunit ZN MG
2O5I XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNA polymerase elongation complex 17581590 2.50 Å EC RNA polymerase alpha/beta/beta'/omega subunit ZN MG
2O5J XRD Prokaryote Thermus Thermophilus Crystal structure of the t. Thermophilus RNAP polymerase elongation complex with the NTP substrate analog 17581591 3.00 Å EC RNA polymerase alpha/beta/beta'/omega subunit APC[ DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER ],ZN,MG
3AOH XRD Prokaryote Thermus Thermophilus RNA polymerase-GFH1 complex (crystal type 1) 21124318 4.10 Å RNAP RNA polymerase alpha/beta/beta'/omega subunit,TF Gfh1 ZN MG
3AOI XRD Prokaryote Thermus Thermophilus RNA polymerase-GFH1 complex (crystal type 2) 21124318 4.30 Å RNAP RNA polymerase alpha/beta/beta'/omega subunit,TF Gfh1 ZN MG
3DXJ XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic myxopyronin 18957204 3.00 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor RpoD subunit NE6[ methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate ],MPD[ (4S)-2-METHYL-2,4-PENTANEDIOL ],PO4,ZN,MG
3WOD XRD Prokaryote Thermus Thermophilus RNA polymerase-GP39 complex 24589779 3.60 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor subunit ZN
4G7H XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex 23086998 2.90 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor subunit ZN MG
4G7O XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex containing 2 nt of RNA 23086998 2.99 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor subunit ZN MG
4G7Z XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex containing 5-bru at template-strand position +1 23086998 3.81 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor subunit ZN MG
4GZY XRD Prokaryote Thermus Thermophilus Crystal structures of bacterial RNA polymerase paused elongation complexes 23374340 3.51 Å EC RNA polymerase alpha/beta/beta'/omega subunit ZN MG
4GZZ XRD Prokaryote Thermus Thermophilus Crystal structures of bacterial RNA polymerase paused elongation complexes 23374340 4.29 Å EC RNA polymerase alpha/beta/beta'/omega subunit ZN MG
4MQ9 XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus RNA polymerase holoenzyme in complex with ge23077 24755292 3.35 Å RNAP RNA polymerase alpha/beta/beta'/omega/sigma factor subunit,GE23077 MB8[ (2Z)-2-methylbut-2-enoic acid ],ZN,MG
4Oin XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex soaked with ge23077 24755292 2.80 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor sigA subunit,GE23077 MB8[ (2Z)-2-methylbut-2-enoic acid ],ZN,MG
4OIO XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation 24755292 3.10 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor sigA subunit ATP,2TM[5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine ],ZN,MG
4OIP XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex soaked with ge23077, ATP, and cmpcpp 24755292 3.40 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor sigA subunit,GE23077 ATP,MB8[ (2Z)-2-methylbut-2-enoic acid ],ZN,MG
4OIQ XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus transcription initiation complex soaked with ge23077 and rifampicin 24755292 3.62 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor sigA subunit,GE23077 MB8[ (2Z)-2-methylbut-2-enoic acid ],ZN,MG
4OIR XRD Prokaryote Thermus Thermophilus Crystal structure of Thermus thermophilus RNA polymerase transcription initiation complex soaked with ge23077 and rifamycin sv 24755292 3.10 Å IC RNA polymerase alpha/beta/beta'/omega/sigma factor sigA subunit,GE23077 RFV[ rifamycin SV ],MB8[ (2Z)-2-methylbut-2-enoic acid ],ZN,MG
6CUU XRD Prokaryote Thermus Thermophilus Thermus thermophiles RNA polymerase in complex with promoter DNA and antibiotic kanglemycin A 30244835 2.99 Å RNAP DNA-directed RNA polymerase subunit alpha/beta/beta'/omega/sigma factor SigA KNG[ Kanglemycin A ],ZN,MG
6M6B XRD Prokaryote Thermus Thermophilus Cryo-EM structure of Thermus thermophilus Mfd in complex with RNA polymerase and ATP-gamma-S 33068413 4.10 Å RNAP DNA-directed RNA polymerase subunit alpha/beta/beta'/omega,Transcription-repair-coupling factor AGS[ PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER ],ZN,MG
6M6A XRD Prokaryote Thermus Thermophilus Cryo-EM structure of Thermus thermophilus Mfd in complex with RNA polymerase 33068413 5.00 Å RNAP DNA-directed RNA polymerase subunit alpha/beta/beta'/omega,Transcription-repair-coupling factor ZN MG
6M6C EM Prokaryote Thermus Thermophilus Cryo-EM structure of Thermus thermophilus RNA polymerase elongation complex 33068413 3.10 Å EC DNA-directed RNA polymerase subunit alpha/beta/beta'/omega ZN MG
3WOE XRD Prokaryote Thermus Thermophilus Crystal structure of P23-45 gp39 (6-109) bound to Thermus thermophilus RNA polymerase beta-flap domain 24589779 2.35 Å Subunit DNA-directed RNA polymerase subunit beta,Putative uncharacterized protein
3WOF XRD Prokaryote Thermus Thermophilus Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermophilus RNA polymerase beta-flap domain 24589779 3.30 Å Subunit DNA-directed RNA polymerase subunit beta,Putative uncharacterized protein
7EH0 XRD Prokaryote Thermus thermophilus Thermus thermophilus RNA polymerase transcription initiation complex containing a template-strand purine at position TSS-2, UpA RNA primer and CMPcPP 34187896 2.81Å IC 2TM,ZN,MG
7EH2 XRD Prokaryote Thermus thermophilus Thermus thermophilus RNA polymerase transcription initiation complex containing a template-strand purine at position TSS-2, UpA RNA primer and CMPcPP 34187896 2.81Å IC RNAP 2TM,ZN,MG