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(-) Description

Title :  HUMAN CORE TFIIH BOUND TO DNA WITHIN THE PIC
 
Authors :  Y. He, C. Yan, J. Fang, C. Inouye, R. Tjian, I. Ivanov, E. Nogales
Date :  21 Mar 16  (Deposition) - 18 May 16  (Release) - 22 Jun 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  10.00
Chains :  Asym./Biol. Unit :  V,W,X,Y,0,1,2,3
Keywords :  Initiation, Rna Polymerase Ii, Human, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. He, C. Yan, J. Fang, C. Inouye, R. Tjian, I. Ivanov, E. Nogales
Near-Atomic Resolution Visualization Of Human Transcription Promoter Opening.
Nature V. 533 359 2016
PubMed-ID: 27193682  |  Reference-DOI: 10.1038/NATURE17970

(-) Compounds

Molecule 1 - TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX HELICASE XPB SUBUNIT
    ChainsV
    EC Number3.6.4.12
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBASIC TRANSCRIPTION FACTOR 2 89 KDA SUBUNIT, BTF2 P89, DNA EXCISION REPAIR PROTEIN ERCC-3, DNA REPAIR PROTEIN COMPLEMENTING XP-B CELLS, TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX 89 KDA SUBUNIT, TFIIH P89, XERODERMA PIGMENTOSUM GROUP B-COMPLEMENTING PROTEIN
 
Molecule 2 - TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX HELICASE XPD SUBUNIT
    ChainsW
    EC Number3.6.4.12
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBASIC TRANSCRIPTION FACTOR 2 80 KDA SUBUNIT, BTF2 P80, CXPD, DNA EXCISION REPAIR PROTEIN ERCC-2, DNA REPAIR PROTEIN COMPLEMENTING XP-D CELLS, TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX 80 KDA SUBUNIT, TFIIH P80, XERODERMA PIGMENTOSUM GROUP D-COMPLEMENTING PROTEIN
 
Molecule 3 - GENERAL TRANSCRIPTION FACTOR IIH SUBUNIT 2
    Chains0
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBASIC TRANSCRIPTION FACTOR 2 44 KDA SUBUNIT, BTF2 P44, GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 2, TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P44 SUBUNIT
 
Molecule 4 - GENERAL TRANSCRIPTION FACTOR IIH SUBUNIT 5
    Chains1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 5, TFB5 ORTHOLOG, TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX TTD-A SUBUNIT
 
Molecule 5 - GENERAL TRANSCRIPTION FACTOR IIH SUBUNIT 4
    Chains2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBASIC TRANSCRIPTION FACTOR 2 52 KDA SUBUNIT, BTF2 P52, GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 4, TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P52 SUBUNIT
 
Molecule 6 - GENERAL TRANSCRIPTION FACTOR IIH SUBUNIT 3
    Chains3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP34, BASIC TRANSCRIPTION FACTOR 2 44 KDA SUBUNIT, BTF2 P44, GENERAL TRANSCRIPTION FACTOR IIH POLYPEPTIDE 2, TFIIH BASAL TRANSCRIPTION FACTOR COMPLEX P44 SUBUNIT
 
Molecule 7 - SCP-X
    ChainsX
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES
 
Molecule 8 - SCP-Y
    ChainsY
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit VWXY0123

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5IVW)

(-) Sites  (0, 0)

(no "Site" information available for 5IVW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IVW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IVW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IVW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IVW)

(-) Exons   (0, 0)

(no "Exon" information available for 5IVW)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain 0 from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.hhhhhh......hhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeee.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.....eeeeeeee.........hhhhhhhhhhhhheeeeeeee...hhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ivw 0  54 RLGMMRHLYVVVDGSRTMEDQDLKPNRLTCTLKLLEYFVEEYFDQNPISQIGIIVTKSKRAEKLTELSGNPRKHITSLKKAVDMTCHGEPSLYNSLSIAMQTLKHMPGHTSREVLIIFSSLTTCDPSNIYDLIKTLKAAKIRVSVIGLSAEVRVCTVLARETGGTYHVILDESHYKELLTHHVSPPPA 241
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233        

Chain 1 from PDB  Type:PROTEIN  Length:62
                                                                                              
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee....hhhhhhhhhh........eee.....eeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 5ivw 1   1 MVNVLKGVLIECDPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMD  62
                                    10        20        30        40        50        60  

Chain 2 from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhh.....ee......eeee..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ivw 2  28 PGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFLKKEFSKAQEESTGLLSGLRIWHTQLLNLRIALLGGGKAWSDDTSQLGPDKHVLHFMVGSPSAAVSQDLAQLLSQAGLMKSTEPGEPPCITSAGFQFLLLDTPAQLWYFMLQYLQTAQSRGMDLVEILSFLFQLSFSTLGKDYSVEGMSDSLLNFLQHLREFGLVFQRTDQIRLWELERDRLRFTEGVLYNQFLSQVDFELLLAHARELGVLVFENSAKRLMVVTPAGHSDVKRFWKRQK 459
                                    37        47        57    ||  80        90       100||     125       135     ||162       172       182       192       202       212       222       232       242       252       262       272 ||    395       405       415       425       435       445       455    
                                                             62|                      101|                     141|                                                                                                                274|                                                                       
                                                              76                       117                      159                                                                                                                 388                                                                       

Chain 3 from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...hhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeee.hhhhhhhhhhhhhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.......hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhh..eee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ivw 3   5 EDELNLLVIVVDANPIWWGKQTLSKCIDAVMVLGNSHLFMNRSNKLAVIASHIQESRFLYPKYELLTSANEVIVEEIKDLMTKSDIKGQHTETLLAGSLAKALCYIHRMNKEVKDNQEMKSRILVIKAAEDSALQYMNFMNVIFAAQKQNILIDACVLDSDSGLLQQACDITGGLYLKVPQMPSLLQYLLWVF 231
                                    14        24||      41        51        61        71||     108       118       128       138       148       158       168       178       188       198       208       218       228   
                                               25|                                     72|                                                                                                                                   
                                                33                                     100                                                                                                                                   

Chain V from PDB  Type:PROTEIN  Length:475
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeee.................eeee.hhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhh.eee.....hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh.......ee..........ee...eeee...........................eeeee.hhhh....hhhhhhh....eeeeee........hhhhhhhhh..eee...hhhhh.......eeeeeeee....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhh..ee....hhhhhhhhhhhhhhh....eeee.hhhh.........eeee......hhhhhhhhhhhhh............eeeeeeee..hhhhhhhhhhhhhhhhh...eeee....hhhhh.....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ivw V 244 IPMDLFDFYEQMDKDEEEEEETQTVSFEVKQEMIEELQKRCIHLEYPLLAEYDFRNDSVNPDINIDLKPTAVLRPYQEKSLRKMFGNGRARSGVIVLPCGAGKSLVGVTAACTVRKRCLVLGNSAVSVEQWKAQFKMWSTIDDSQICRFTSDAKDKPIGCSVAISTYSMLGHTTKRSWEAERVMEWLKTQEWGLMILDEVHTIPAKMFRRVLTIVQAHCKLGLTATLVREDDKIVDLNFLIGPKLYEANWMELQNNGYIAKVQCAEVWCPMSPEFYREYVAIKTKKRILLYTMNPNKFRACQFLIKFHERRNDKIIVFADNVFALKEYAIRLNKPYIYGPTSQGERMQILQNFKHNPKINTIFISKVGDTSFDLPEANVLIQISSHGGSRRQEAQRLGRVLRAKKGMVAEEYNAFFYSLVSQDTQEMAYSTKRQRFLVDQGYSFKVITKLAGMEEEDLAFSTKEEQQQLLQKVLA 718
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713     

Chain W from PDB  Type:PROTEIN  Length:665
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh..........eeeeee.hhhhhhhhhhhhhhhhh.............eee..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhheeehhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh......eeeee............eeeee..hhhhhhhhhh...eeeeee.......hhhhhhhh...eeee.....hhh.ee..ee.................hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh.......................hhhhhhhhhhhhhhh........eeee..hhhhhh.........eeeee.........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhh......hhhhh.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ivw W  15 DYIYPEQFSYMRELKRTLDAKGHGVLEMPSGTGKTVSLLALIMAYQRAYPLEVTKLIYCSRTVPEIEKVIEELRKLLNFYEKQEGEKLPFLGLALSSRKNLCIHPEVTPLRFGKDVDGKCHSLTASYVRAQYQHDTSLPHCRFYEEFDAHGREVPLPAGIYNLDDLKALGRRQGWCPYFLARYSILHANVVVYSYHYLLDPKIADLVSKELARKAVVVFDEAHNIDNVCIDSMSVNLTRRTLDRCQGNLETLQKTVLRIKETDEQRLRDEYRRLVEGLREASAARETDAHLANPVLPDEVLQEAVPGSIRTAEHFLGFLRRLLEYVKWRLRVFSPLTLLANFATLVSTYAKGFTIIIEPFDDRTPTIANPILHFSCMDASLAIKPVFERFQSVIITSGTLSPLDIYPKILDFHPVTMATFTMTLARVCLCPMIIGRGNDQVAISSKFETREDIAVIRNYGNLLLEMSAVVPDGIVAFFTSYQYMESTVASWYEQGILENIQRNKLLFIETQDGAETSVALEKYQEACENGRGAILLSVARGKVSEGIDFVHHYGRAVIMFGVPYVYTQSRILKARLEYLRDQFQIRENDFLTFDAMRHAAQCVGRAIRGKTDYGLMVFADKRFARGDKRGKLPRWIQEHLTDANLNLTVDEGVQVAKYFLRQMAQ 726
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344 ||    401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721     
                                                                                                                                                                                                                                                                                                                                                                     346|                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                      394                                                                                                                                                                                                                                                                                                                                            

Chain X from PDB  Type:DNA  Length:19
                                                   
                 5ivw X   1 ATTGCCGAAGACGAAAAAA  19
                                    10         

Chain Y from PDB  Type:DNA  Length:20
                                                    
                 5ivw Y   1 TTTTTTTCGTCTTCGGCAAT  20
                                    10        20

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5IVW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IVW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IVW)

(-) Gene Ontology  (99, 266)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ERCC2_HUMAN | P180745iy6 5iy7 5iy8 5iy9
        ERCC3_HUMAN | P194474ern 5iy6 5iy7 5iy8 5iy9
        TF2H2_HUMAN | Q138881z60 5iy6 5iy7 5iy8 5iy9
        TF2H3_HUMAN | Q138895iy6 5iy7 5iy8 5iy9
        TF2H4_HUMAN | Q927595iy6 5iy7 5iy8 5iy9
        TF2H5_HUMAN | Q6ZYL41ydl 2jnj 5iy6 5iy7 5iy8 5iy9

(-) Related Entries Specified in the PDB File

5iy6 5iy7 5iy8 5iy9 5iya 5iyb 5iyc 5iyd