1I50,1I3Q,1I6H


Conserved Protein Domain Family
RNAP_II_Rpb1_C

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cd02584: RNAP_II_Rpb1_C 
Click on image for an interactive view with Cn3D
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain
RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Statistics
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PSSM-Id: 132720
View PSSM: cd02584
Aligned: 37 rows
Threshold Bit Score: 474.001
Threshold Setting Gi: 161899215
Created: 9-Jun-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:Rpb1 - Rpb2 interaction site [polypeptide binding site]
Evidence:
  • Comment:The two largest subunits, Rpb1 and Rpb2, form distinct masses with a deep cleft between them. Each of the small subunits occurs in a single copy, arrayed around the periphery.
  • Structure:1I50; Interface between Rpb1 (1I50_A) and Rpb2 (1I50_B) subunits in Saccharomyces cerevisiae RNAP II; defined using 3.5A contacts
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                     #  #                                                
1I50_A       1035 YRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVaSKKVTSGVPRLKEILNVAKNMKTP 1114 baker's yeast
Q8SSC4       1020 HRLNTEAFNWVVEVIDAKILKAKITPNEMVGTLAAQSVGEPATQMTLNTFHLAGV-ASTVTMGVPRLKEIFNVTKNLKTP 1098 Encephalitozo...
AAD12604     1020 YKLSLEAYNWILKEIKFKILKSIISPNEMVGTLAAQSVGEPATQMTLNTFHLAGV-SANITMGVPRLKEIINVAKNIKTP 1098 Vairimorpha n...
AAD12605      998 YRISTLGVEWIANEIKKKFVRGIISTNEMVGTLAAQSIGEPATQMTLNTFHYAGV-AQAITQGVPRLKEIINVAKNIRTP 1076 Antonospora l...
AAK00313      951 ERLSKDAFNWILGEIKSRFDQALVNPGEMVGSIGAQSMGEPATQMTLNTFHFAGVsAKNVTLGVPRLKEIINVAKNIKTP 1030 Stylonychia m...
XP_001712625 1036 YKFSKVAFLWVLNEICTQYRKSIASPGEMVGTISAQSIGQPATQMTLNTFHYAGVsAKNVTLGVPRLKEIINVLQTVKTP 1115 Hemiselmis an...
XP_001713319 1029 FNLNQHALNWIVNEICLSIRKSLIQPGEMVGTISAQSIGQPATQMTLNTFHFAGVsAKNVTLGVPRLKEIIDIQKNIKSP 1108 Guillardia theta
AAB50025     1055 YRLNEQAFKYILGSIKDRFYRSIVAPGEMVGTIAGQSIGEPSTQMTLNTFHFAGIsAHDVTLGVPRLNELMNLAKHIRTP 1134 Trichomonas v...
AAT40981     1050 HHLSKESFDDLMDRIKNIYERSFINPGEMVGSIAAQSIGAPATQMTLNTFHHAGIsSASVTEGVPRLKELLNVSKTPKTP 1129 Entamoeba his...
XP_001007918 1086 HKLSMEVFDKLTKEIFDKFKKAISHPGETIGAISAQSVGEPTTQMTLNTFHFAGVsDRNVTLGVPRLQEILDASKNVKTP 1165 Tetrahymena t...
Feature 1                                                                                         
1I50_A       1115 SLTVYLEpgh-----------------aaDQEQAKLIRSAIEHTTLk----SVTIASEIYYDPDPRstVIPEDEEIIQLH 1173 baker's yeast
Q8SSC4       1099 SMKIYLDreh-----------------gkSIEAAKTIQNEIECLTVk----DLCLFSEIYYDPEITgtEISDDKDFVEAY 1157 Encephalitozo...
AAD12604     1099 CMKIYLKdpf-----------------nkTLEMAKKIQSELEFSDIk----SLCEFSEIYYDPVIEdtSIKEDKDFVQEY 1157 Vairimorpha n...
AAD12605     1077 SHKIYLKpg-------------------sTIEQAKKVASEIEYINIe----MVCSEIKIIYDPKVDttIINEDRDFVEAY 1133 Antonospora l...
AAK00313     1031 SMKIFLKdkd-----------------kqDERIATIIGGRIEHTTLc----HVVKSSAIYYDPDPErtIVREDEELIRLY 1089 Stylonychia m...
XP_001712625 1116 SLTIYFRkef-----------------ssSLSKIKQFQQTLEFITLk----SMIKKKTVFYDPDPYktILKNDQIILENY 1174 Hemiselmis an...
XP_001713319 1109 SLTIFLHkkc-----------------snDPRKVKKIQESIESVRLn----RISNYFEIIYDPDFFfsISKCNRILVKNY 1167 Guillardia theta
AAB50025     1135 SVTVEFErdv-----------------akDEEIVKAVRAQIESASFk----KFVIKAEIYYDPNPEetIIEPDTKWINTR 1193 Trichomonas v...
AAT40981     1130 SMNVYLTndt----------------resMVDLDKELNKTIPYTKLk----DLIDNVEIWFDPDIAnsVIEEDREFINDF 1189 Entamoeba his...
XP_001007918 1166 EMTVFFEnglrkkifrkdmmsnydaesfkREYDEIVSQERQEILRLkqeieYQTISYYINQTRIVY--KSKDDEDFQQQD 1243 Tetrahymena t...
Feature 1                                                                                         
1I50_A       1174 FSLLDEeaeqsfdqqSPWLLRLELDRAAMNDKDLTMGQVg--ERIKQTFKNDLFVIWSEDNde----kLIIRCRVVRpks 1247 baker's yeast
Q8SSC4       1158 FEFPDEdvdf--sclSPFLMRLVVDRAKLVGRGINLEYVa--MFIRKELGGGAHVICSDENav----nMVVRVRTTKs-- 1227 Encephalitozo...
AAD12604     1158 FDFPDEhldf--skmPKFIIRLKIDRIKLVSKNLKLENIv--KSLHEAFPNIFHIIRSDENsq----nLIIRIRCISsln 1229 Vairimorpha n...
AAD12605     1134 FEFPDEyvsl--dtlNPWLLRLVVARDRLISNNLDFEFIa--QKIKKVFHQDIFLLHSDANae----eLVIRIRVLGms- 1204 Antonospora l...
AAK00313     1090 NEVRLFeter--rrtSPWVLRFELDNDKVQFKDLSMQLIe--QKINDIFRDQIDVVKSDENae----kLVLRLRVNDied 1161 Stylonychia m...
XP_001712625 1175 FEIPDWasei--sciGTWTTKIGLEKDEFIDKKLSTIQIv-eKMKKKIKPLPLFIVNSDENsq----nLFFRLKLIWpni 1247 Hemiselmis an...
XP_001713319 1168 MEIPDEdinf--lqaSSWILKLKLLTEEFVEKGLFSNYIi-eTIKKKIKPIPFLIIASDENsg----sIEFLVRFIWp-- 1238 Guillardia theta
AAB50025     1194 IRYGGVedre-lqdlAPWVLRFEINREEMIASNIESISDi-vQKIKGMYGDKFFVIGDDDAr-----iIRMQARLKDeqa 1266 Trichomonas v...
AAT40981     1190 IEVEEIkpe----dyCKWTIRLVFGYNKMVSMGVDSDSDilrVKIKELFKDALVIPSDSNNivngtvkIVVHIRFRVgsi 1265 Entamoeba his...
XP_001007918 1244 NIFDDDnisd--dleDPIVLIIYFDTQKTTIDTFELLNAk-iRKIADDSKKWGNLIVEKKQfe----kGQIHVKFDStq- 1315 Tetrahymena t...
Feature 1                                     #   #                                               
1I50_A       1248 ldaete-----------aeedhmlkKIENTMLENITLRGven-------------ieRVVMMKYDRKVps---------- 1293 baker's yeast
Q8SSC4       1228 -------------------------EDESLNFYTTALNSll--------------rlQLGGYKNVKKVy----------- 1257 Encephalitozo...
AAD12604     1230 -----------------------nnVEYYNLQYKNILNL------------------KIMGYNKIKKVf----------- 1257 Vairimorpha n...
AAD12605     1205 -----------------------anEEFYRRLLNTILGI------------------HLKGITNIRRI------------ 1231 Antonospora l...
AAK00313     1162 deedr-------------tvcmylkGFQDELFNDLALKGl-----------------HEISKVTFTKYndeif------- 1204 Stylonychia m...
XP_001712625 1248 dwtknskktvknpnfnffnferkylNRTTYFLSNINLKSygts----------kikkAFIRKSSQIIFes---------- 1307 Hemiselmis an...
XP_001713319 1239 -------------------------EFINNYNSEKIEKLfsrsn--------antffEYIKRANQKVSenlflepnyfkk 1285 Guillardia theta
AAB50025     1267 efam---------------dvkflrETEQQMYKSFTLKGipg------------isrVKINSAAEKMFlnp--------- 1310 Trichomonas v...
AAT40981     1266 -----------------------seCSNIDHLTDEVDKSveavayykskldellrtvVISGIEGITKViipqkpkn---- 1318 Entamoeba his...
XP_001007918 1316 -----------------------lgQGQQNPDSQMNAYSslllfe------sefkdaYIGGIQKIQKVyptqkkefrpwv 1366 Tetrahymena t...
Feature 1                                                                                         
1I50_A       1294 ----------------------------------ptGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVL 1339 baker's yeast
Q8SSC4       1258 -----------------------------------iSEDKDRKEWYLQTDGICLSQILGNPAVNSRLTISNDLVEIAETL 1302 Encephalitozo...
AAD12604     1258 -----------------------------------iSEDKDKDEWYLQTDGVCIREIFSHPNVEGHLVTSNDLNEIVEVL 1302 Vairimorpha n...
AAD12605     1232 ------------------------------------YLLREREEWILQTDGKNLKQLLLVEDILANKVYCNDLLEVYEVL 1275 Antonospora l...
AAK00313     1205 -------------------------------dvetgECKQDKECWLIETDGVALQKVLGLEGINYKKTVSNDIIEILRVL 1253 Stylonychia m...
XP_001712625 1308 ----------------------------------isGSIKNNEEYVLDTEGVDLRYILNYSGIDYTRCSSNDILEIYKIL 1353 Hemiselmis an...
XP_001713319 1286 ikhyfynynlkpygsqkltklyprridiiepepnqsGKLKNNFEFVLETEGVDLRFVMNYNGIDYSRCTTNDLLESLKVL 1365 Guillardia theta
AAB50025     1311 ----------------------------------etHGFDKEKVSCLYTEGTAFREILSLDHVDTVHTITNDIYQVCDVL 1356 Trichomonas v...
AAT40981     1319 ----------------------------aivvdpetKMLRDQLQWVVFTEGSNMAGLAECDNVDFYKTVTNNVYETFLYL 1370 Entamoeba his...
XP_001007918 1367 en---------------------eciceapkpgaafFTERKPQEHIFNTSGSNLKEVLKVDKVDATRTYSNDIQEIITIL 1425 Tetrahymena t...
Feature 1                                                                                #        
1I50_A       1340 GIEAGRAALYKEVYNVIAsdGSYVNYRHMALLVDVMTTQGgLTSVTRHGFNRSN-TGALMRCSFEETVEILFEAGASAEL 1418 baker's yeast
Q8SSC4       1303 GIEAARESILRELTIVIDgnGSYVNYRHMSLLADVMTMRGyLCGITRHGVNKVG-AGALKRSSFEETVEILLDAALVSEK 1381 Encephalitozo...
AAD12604     1303 GIEAARETILNELTLVIDgnGSYVNHRHISLLADVMTMKGyLTGITRHGVNKVG-FGCTKRASFEETVDILLDAALVAEK 1381 Vairimorpha n...
AAD12605     1276 GIEAVRECILRELRNVIEaeGSYVNFRHLYLLCDVMTLKG-LRGITRHGANRAA-TGALKRCSFEETVEILLEASCFAER 1353 Antonospora l...
AAK00313     1254 GIEAVRMSLINELRFVLSsyGIYVNYRHLSTLCDVMTQRGiLTAITRHGINRVD-SSPLRKCSFEETVEILLEAAVFAET 1332 Stylonychia m...
XP_001712625 1354 GIEAVRKILIQELRNLISfdGSYVNSRHLSLLVDVMTHKGkLMSITRHGINRTD-IGPIAKCSFEETIEVLYQAAAFGVC 1432 Hemiselmis an...
XP_001713319 1366 GIEATRKILIQELRNLISfdGSYVNYRHLCTLVDLITFRGsLMSINRHGINKCN-SGPIAKSTFEETVDIFYESAVFGLN 1444 Guillardia theta
AAB50025     1357 GIEAARHSLSYEMMLIMEkaGAALNRRHLDLLADTMTQYGvLYPVSRHGINKTP-TGTLMRASYEMTNDVFFDAAVFSEI 1435 Trichomonas v...
AAT40981     1371 GIEAGRTQLEAELIKTLS--GSYVNFRHLALMADVMTFTGrIQPFNRMGLSRGR-AGVITRASFEQTLEQFRRAAAFSES 1447 Entamoeba his...
XP_001007918 1426 GIEAGRRSIVNQIRVVIEpyGIYINYRHLAILAEWMTVRGrLTPINRNGINRIPgLSCLRKSSFEETVDILNTAAIFFEK 1505 Tetrahymena t...
Feature 1          ###     ## # #    #        
1I50_A       1419 DDCRGVSENVILGQMAPIGTGAFDVMID 1446 baker's yeast
Q8SSC4       1382 NICRGITENIMMGQLAPMGTGNIEIMLD 1409 Encephalitozoon cuniculi
AAD12604     1382 YVTKGYTENIMMGHLAPLGTGIGNLLLD 1409 Vairimorpha necatrix
AAD12605     1354 NYCRGVTENIMLGQLAPIGTGNTICILD 1381 Antonospora locustae
AAK00313     1333 DPLKGITENIIMGQLAPFGTGCFEITID 1360 Stylonychia mytilus
XP_001712625 1433 DNLKGVSGSILVGQVSSLGTGKIDLFLC 1460 Hemiselmis andersenii
XP_001713319 1445 DNLRGVSAQIMTGMVPKIGTGKIDLFVN 1472 Guillardia theta
AAB50025     1436 DYMRDVSSNIIAGKPSRAGTGIVEVLIN 1463 Trichomonas vaginalis
AAT40981     1448 DILNGISQNILMGQRTVAGTGAFTVLLD 1475 Entamoeba histolytica
XP_001007918 1506 DDLKGVTENIIFGQNCDIGTGCFDLLVD 1533 Tetrahymena thermophila SB210

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