1I50


Conserved Protein Domain Family
RNAP_II_RPB3

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cd07031: RNAP_II_RPB3 
Click on image for an interactive view with Cn3D
RPB3 subunit of Eukaryotic RNA polymerase II
The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Statistics
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PSSM-Id: 132909
View PSSM: cd07031
Aligned: 38 rows
Threshold Bit Score: 308.379
Threshold Setting Gi: 67471071
Created: 19-Dec-2008
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
  next features
Conserved site includes 22 residues -Click on image for an interactive view with Cn3D
Feature 1:RPB3 - RPB11 heterodimer interface [polypeptide binding site]
Evidence:
  • Comment:The yeast RNAP II RPB11/RPB3 heterodimer, together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, stabilizing their association.
  • Structure:1I50_C; Interface between the Saccharomyces cerevisiae RNAP II RPB3 and RPB11 (1I50_K) subunits; defined at 3.5A contacts.
    View structure with Cn3D
  • Comment:RPB3 associates with RPB11 through its RPB11-like subdomain.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1        ###    ##       #   # ##  #  #                                                  
1I50_C         6 PQVKIREASkDNVDFILSNvDLAMANSLRRVMIAeiPTLAIDSVEVETNTtVLADEFIAHRLGLIPLQSMDieqleys-- 83  baker's yeast
CAQ39273      13 HEVEITKLTkDEMTFVLHNsNTGMANALRRIMLSeiPTLAIDVVNVYENTsPFHDEFLAHRLGLIPIDSRNvknfefr-- 90  Plasmodium know...
XP_001471367   4 IKLTLTNLEeFKCEFTLENcDISLANSLRRILLAeiETIAIHNVKVYENTsSLPDEYIAHRLGLIPLNSAKvddynyi-- 81  Tetrahymena the...
XP_765556     10 PSIEIVDLRkDRMDFILLNsDVSTANAIRRVILSeiPSLAIEIVTVLENTsVLHDEYISHRLGLLPIDSTLasefefr-- 87  Theileria parva...
XP_001439135  12 HRIEILELSdEKCKFSFEG-DLSIANAIRRVMIAevPVMAIHFVDIIENTsPLSDEFLAQRLAKCMIGKLMqi------- 83  Paramecium tetr...
CAL52099       9 SHVSVTRLEdQSITFSLKGvDVSLANALRRVMIAdvPTLAIDLVEVVENSsVLCDEFLAHRLGLIPLSSKKvselfkp-- 86  Ostreococcus tauri
EEA99370     151 PSIVVKEVSqNKVKFLLENcDVSIANGLRRVMISevPSLAIDLVTVYENTsVLHDEYISHRLGLLPIDSTRvaefvnr-- 228 Toxoplasma gond...
EEC47062       7 PRVEILSIQpQEIKFILSEsDTSVANTLRRIMIAevPTLAIDLVEFHENStVLNDEYIAHRMGLIPVRYQPaeslkgsdc 86  Phaeodactylum t...
XP_002142225   9 PHIEITEFSpSVIKFILSNtDVSMANALRRIMLAeiPTLAIDLVTIIDNTsVLHDEFIVHRLGLLPIDSRQirdfnfk-- 86  Cryptosporidium...
XP_651491     10 PIITNVECKeEKLSFHIERtDTSMVNGLRRVIMAetPTIAIQLVRVYANSsYLCDEFIAHRLGLIPIDSTQih------- 82  Entamoeba histo...
Feature 1                                                                                        
1I50_C        84 -rdcfcedHCDKCSVVLTLQAFGeseSTTNVYSKDLVIvsn-----------lmGRNIGHPIIQdke---------gnGV 142 baker's yeast
CAQ39273      91 -ekckckeTCSKCTIQYLIQVKCnnvSKIDVTHYDIESve-------------hEPNVPMPVPFedrnnk---maqsnAI 153 Plasmodium know...
XP_001471367  82 -wncncqgECDRCTIHFDLRVSNftnEVLEVTSLDLKQrqd-----------htDEDAVRPIKVysilrdeygnkrevGI 149 Tetrahymena the...
XP_765556     88 -drcqctdKCAKCTVDYTLDVSCkdsDSRVVTHFDIVPddths-------ksiyGKNLPMPIPRadvtnf---ngatdGI 156 Theileria parva...
XP_001439135  84 ------plDDQKTKVVFTLRQKNlndAPLEITSQHLEPefg-----------qvGEMAIRPVRMfspin-----gkevGI 141 Paramecium tetr...
CAL52099      87 --yeymgeDDSATDVHLELNVRClteQAMDVTSEDMVS----------------YDERVKPITFqgtvsd---aakpgGI 145 Ostreococcus tauri
EEA99370     229 -ddcdcadHCSRCSVQYALDVVCe-rDSLLVTHRDIVAdnargaslasagfldlGCPMPVPLLRemqe------kemdGI 300 Toxoplasma gond...
EEC47062      87 sdaflphrECVCYEHCMRCSVEFeldITYKVTGEEDVLapltvt----skdlvsNNELVQPAHFlsqdeq--deaqdeGV 160 Phaeodactylum t...
XP_002142225  87 -drcgcqeRCNKCSVDYTLDLKCegpTVRNVTHLDIYStlp-----------vpNIPLPVPRKEdvtd------pnneGI 148 Cryptosporidium...
XP_651491     83 -------nFEDTDDAILELKEENnsnQLVVVTSNDLVSig-------------dKRVAPVNYKNdv-----------dPI 131 Entamoeba histo...
Feature 1                              ##                                                        
1I50_C       143 LICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPwn----kLKHTDYWYEqds--------------------- 197 baker's yeast
CAQ39273     154 PIVTLSKNQTLHMKLIATKGIGKMHAKWIPANVSYRIDHKv-----sIKHHLINSLspehklllanslnkdcyv------ 222 Plasmodium know...
XP_001471367 150 PIIKLSKGQQIHFECEAQKGIGKMHSKWNPVCISTFSVEPeiifdqeIQNLDIEQKkalvnacptkvfg----------- 218 Tetrahymena the...
XP_765556    157 PIVKLKRGHSINMKLTASKGLGKFHAKWIVANVNYKMEPRf-----sFNSSLMEQLsseekagiaascprnvfkytgvrs 231 Theileria parva...
XP_001439135 142 PITRLGKNQSVHVRCHALKGFGKMHAKWTPINIATFRHEAel----nFDHSQTQSLslfekqsirdscpmn--------- 208 Paramecium tetr...
CAL52099     146 LIVKLRNKQQLLLKCIARKGTGKDHAKWSPVATAVFKHDPvv----hVNQELLKTLsgsdkraivesdpsqmfky----- 216 Ostreococcus tauri
EEA99370     301 PIVKLRKNQSVNMRMTATKGIGKVHAKWSPVATASYKFEPei----aFEEDLLARApaevkrqiaascprevfs------ 370 Toxoplasma gond...
EEC47062     161 AIVKLGPGQRLKLKAIARMGISKEHAKWCPVAVATYRFWPei----hINDEQMATLtleqkqelvdtcpdrileld---- 232 Phaeodactylum t...
XP_002142225 149 LIAKLGPGQSLTARMTATKGIGKFHAKWIPVATATFTNEAdi----rINQSSMTNVslkhrreivnscpknvfglsasks 224 Cryptosporidium...
XP_651491    132 VITQLGPRQNIHMVCYVKKGTGKFHAKWNPTCQCVFQTLAdi----rINDEKMISLtpeqkrtfceqcpqkl-------- 199 Entamoeba histo...
Feature 1                                                                              #   #  ## 
1I50_C       198 -----------------------akEWPQSKNCEyedppn----egdpfDYKAQADTFYMNVESVGsiPVDQVVVRGIDT 250 baker's yeast
CAQ39273     223 -------lknaeahdrdmslrlnenMSVVMAESCievlnel--gykdvvKIIYDETKFHFKVESVGsmPPEQVVEMAIEI 293 Plasmodium know...
XP_001471367 219 ------------inphtntlevqdhMKCMYCEECvykcaed-fqkpkliKIDHKKDKFFFKVETTGvmKPVEVLRRGFST 285 Tetrahymena the...
XP_765556    232 eapsflgpsdktfkldaaglhvvdkLACIYCDECinycrel--ghkdliRIQPDESKFHFTIESTGaiPPEKILEIALVV 309 Theileria parva...
XP_001439135 209 ----------vfamdanqdlivnaiEKCVFCEECircaesm--kkprliKMQHKKNKYIFTVESAGqlKAADIVQKALIV 276 Paramecium tetr...
CAL52099     217 ------dadldtisltstgsctfdgEIVKKVNEMgkh---------gliDIRPCFDSFTFHVESTGvlDAEEIVLQAVHI 281 Ostreococcus tauri
EEA99370     371 -------fiddtatggtgvlrvenkMNCIFCDQCkvkaqel--gfrrlvRVEPNERKFHFTVESTGvmPAEQIVEMAFDI 441 Toxoplasma gond...
EEC47062     233 ------evtgdiravdnawdictytEDLKFAQAAmkkrpe----dddfvTVTQSKDRFIFNVETTGamDADEILLSAIRV 302 Phaeodactylum t...
XP_002142225 225 --efgmfdkpvekstnipdievlnsSDCIFCNECvntcrnlgyinppliRVDTKPDKFHFVVESTGamPAEQIIEMALEI 302 Cryptosporidium...
XP_651491    200 ----------fdyqevgekvfirgeENCIFCNECtvyardi--gqrnlvTVTPKTDQFVFKVEGTGvyPPKQIIELGLEE 267 Entamoeba histo...
Feature 1         #     ##  #  #
1I50_C       251 LQKKVASILLALTQM 265 baker's yeast
CAQ39273     294 LENKLKTLEPQIKSS 308 Plasmodium knowlesi strain H
XP_001471367 286 LRQKLDFMREQIQEN 300 Tetrahymena thermophila SB210
XP_765556    310 LEKKLQDLQSNFTEA 324 Theileria parva strain Muguga
XP_001439135 277 LRKKVDEISQDLSFA 291 Paramecium tetraurelia strain d4-2
CAL52099     282 LQTKLDTVGGELDMI 296 Ostreococcus tauri
EEA99370     442 LLNKVTELEGLVSQA 456 Toxoplasma gondii ME49
EEC47062     303 LRNRLNYLAQELENL 317 Phaeodactylum tricornutum CCAP 1055/1
XP_002142225 303 LQEKLQNLGRSVARA 317 Cryptosporidium muris RN66
XP_651491    268 MKKKFVNLKKALNES 282 Entamoeba histolytica HM-1:IMSS

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