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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8BVW

RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W)

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
10General transcription and DNA repair factor IIH helicase subunit XPBpolymer77288090.11UniProt (P19447)
Pfam (PF13625)
Pfam (PF04851)
Pfam (PF16203)
In PDB		Homo sapiens (human)TFIIH subunit XPB,Basic 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 89 kDa subunit,TFIIH p89,Xeroderma pigmentosum group B-complementing protein
21TFIIH basal transcription factor complex helicase XPD subunitpolymer76087021.11UniProt (P18074)
Pfam (PF06733)
Pfam (PF06777)
Pfam (PF13307)
In PDB		Homo sapiens (human)Basic 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
32General transcription factor IIH subunit 1polymer54862116.51UniProt (P32780)
Pfam (PF08567)
Pfam (PF03909)
In PDB		Homo sapiens (human)Basic transcription factor 2 62 kDa subunit,BTF2 p62,General transcription factor IIH polypeptide 1,TFIIH basal transcription factor complex p62 subunit
43General transcription factor IIH subunit 4polymer46252245.21UniProt (Q92759)
Pfam (PF18307)
Pfam (PF03849)
In PDB		Homo sapiens (human)Basic transcription factor 2 52 kDa subunit,BTF2 p52,General transcription factor IIH polypeptide 4,TFIIH basal transcription factor complex p52 subunit
54General transcription factor IIH subunit 2polymer39544482.01UniProt (Q13888)
Pfam (PF04056)
Pfam (PF07975)
In PDB		Homo sapiens (human)Basic transcription factor 2 44 kDa subunit,BTF2 p44,General transcription factor IIH polypeptide 2,TFIIH basal transcription factor complex p44 subunit
65General transcription factor IIH subunit 3polymer30834416.01UniProt (Q13889)
Pfam (PF03850)
In PDB		Homo sapiens (human)Basic transcription factor 2 34 kDa subunit,BTF2 p34,General transcription factor IIH polypeptide 3,TFIIH basal transcription factor complex p34 subunit
76General transcription factor IIH subunit 5polymer718060.41UniProt (Q6ZYL4)
Pfam (PF06331)
In PDB		Homo sapiens (human)General transcription factor IIH polypeptide 5,TFB5 ortholog,TFIIH basal transcription factor complex TTD-A subunit
87CDK-activating kinase assembly factor MAT1polymer30935874.01UniProt (P51948)
Pfam (PF17121)
Pfam (PF06391)
In PDB		Homo sapiens (human)CDK7/cyclin-H assembly factor,Cyclin-G1-interacting protein,Menage a trois,RING finger protein 66,RING finger protein MAT1,p35,p36
98Cyclin-dependent kinase 7polymer34639090.31UniProt (P50613)
Pfam (PF00069)
In PDB		Homo sapiens (human)39 kDa protein kinase,p39 Mo15,CDK-activating kinase 1,Cell division protein kinase 7,Serine/threonine-protein kinase 1,TFIIH basal transcription factor complex kinase subunit
109Cyclin-Hpolymer32337695.51UniProt (P51946)
Pfam (PF00134)
Pfam (PF16899)
In PDB		Homo sapiens (human)MO15-associated protein,p34,p37
11ADNA-directed RNA polymerase subunitpolymer1970217450.11UniProt (A0A7M4DUC2)
Pfam (PF04997)
Pfam (PF00623)
Pfam (PF04983)
Pfam (PF05000)
Pfam (PF04998)
Pfam (PF04992)
Pfam (PF04990)
Pfam (PF05001)
In PDB		Sus scrofa (pig)
12BDNA-directed RNA polymerase subunit betapolymer1174134041.41UniProt (I3LGP4)
Pfam (PF04563)
Pfam (PF04561)
Pfam (PF04565)
Pfam (PF04566)
Pfam (PF04567)
Pfam (PF00562)
Pfam (PF04560)
In PDB		Sus scrofa (pig)
13CDNA-directed RNA polymerase II subunit RPB3polymer27531439.11UniProt (I3LCH3)
Pfam (PF01193)
Pfam (PF01000)
In PDB		Sus scrofa (pig)
14DRNA polymerase II subunit Dpolymer14216331.31UniProt (A0A287ADR4)
Pfam (PF03874)
In PDB		Sus scrofa (pig)
15EDNA-directed RNA polymerase II subunit Epolymer21024644.31UniProt (I3LSI7)
Pfam (PF03871)
Pfam (PF01191)
In PDB		Sus scrofa (pig)RPB5 homolog
16FDNA-directed RNA polymerase II subunit Fpolymer12714477.01UniProt (F1SKN8)
Pfam (PF01192)
UniProt (by SIFTS) (A0A4X1VEK9)
In PDB		Sus scrofa (pig)DNA-directed RNA polymerases I,II,and III subunit RPABC2,RPB6 homolog
17GDNA-directed RNA polymerase II subunit RPB7polymer17219314.31UniProt (A0A4X1VKG7)
Pfam (PF03876)
Pfam (PF00575)
In PDB		Sus scrofa (pig)
18HDNA-directed RNA polymerases I, II, and III subunit RPABC3polymer15017162.31UniProt (I3LCB2)
Pfam (PF03870)
In PDB		Sus scrofa (pig)
19IDNA-directed RNA polymerase II subunit RPB9polymer12514541.21UniProt (P60899)
Pfam (PF02150)
Pfam (PF01096)
In PDB		Sus scrofa (pig)RNA polymerase II subunit B9,DNA-directed RNA polymerase II subunit I,RNA polymerase II 14.5 kDa subunit,RPB14.5
20JDNA-directed RNA polymerases I, II, and III subunit RPABC5polymer677655.11UniProt (A0A4X1VYD0)
Pfam (PF01194)
In PDB		Sus scrofa (pig)
21KDNA-directed RNA polymerase II subunit RPB11-apolymer11713310.31UniProt (F1RKE4)
Pfam (PF13656)
In PDB		Sus scrofa (pig)
22LRNA polymerase II subunit Kpolymer587018.21UniProt (I3LN51)
Pfam (PF03604)
UniProt (by SIFTS) (A0A4X1TRS6)
In PDB		Sus scrofa (pig)
23MTranscription initiation factor IIBpolymer31634877.91UniProt (Q00403)
Pfam (PF08271)
Pfam (PF00382)
In PDB		Homo sapiens (human)General transcription factor TFIIB,S300-II
24NNon-template DNApolymer21867222.71unidentified adenovirus
25OTATA-box-binding proteinpolymer33937729.91UniProt (P20226)
Pfam (PF00352)
In PDB		Homo sapiens (human)TATA sequence-binding protein,TATA-binding factor,TATA-box factor,Transcription initiation factor TFIID TBP subunit
26QGeneral transcription factor IIF subunit 1polymer51758343.61UniProt (P35269)
Pfam (PF05793)
In PDB		Homo sapiens (human)General transcription factor IIF 74 kDa subunit,Transcription initiation factor IIF subunit alpha,TFIIF-alpha,Transcription initiation factor RAP74
27RGeneral transcription factor IIF subunit 2polymer24928427.31UniProt (P13984)
Pfam (PF17683)
Pfam (PF02270)
In PDB		Homo sapiens (human)ATP-dependent helicase GTF2F2,General transcription factor IIF 30 kDa subunit,Transcription initiation factor IIF subunit beta,TFIIF-beta,Transcription initiation factor RAP30
28TTemplate DNApolymer21867405.91unidentified adenovirus
29UTranscription initiation factor IIA subunit 1polymer37641544.61UniProt (P52655)
Pfam (PF03153)
In PDB		Homo sapiens (human)General transcription factor IIA subunit 1,TFIIAL,Transcription initiation factor TFIIA 42 kDa subunit,TFIIA-42
30VTranscription initiation factor IIA subunit 2polymer10912469.11UniProt (P52657)
Pfam (PF02268)
Pfam (PF02751)
In PDB		Homo sapiens (human)General transcription factor IIA subunit 2,TFIIA p12 subunit,TFIIA-12,TFIIAS,Transcription initiation factor IIA gamma chain,TFIIA-gamma
31WGeneral transcription factor IIE subunit 1polymer43949516.11UniProt (P29083)
Pfam (PF02002)
Pfam (PF08271)
Pfam (PF11521)
In PDB		Homo sapiens (human)General transcription factor IIE 56 kDa subunit,Transcription initiation factor IIE subunit alpha,TFIIE-alpha
32XTranscription initiation factor IIE subunit betapolymer29133106.81UniProt (P29084)
Pfam (PF02186)
Pfam (PF18121)
In PDB		Homo sapiens (human)TFIIE-beta,General transcription factor IIE subunit 2
33YUnassigned peptide, likely XPBpolymer8698.91Homo sapiens (human)
34ZUnassigned peptide, likely TFIIE-betapolymer191635.01Homo sapiens (human)
35a, eHistone H3.2polymer13615435.12UniProt (P84233)
Pfam (PF00125)
In PDB		Xenopus laevis (African clawed frog)
36b, fHistone H4polymer10311394.42UniProt (P62799)
Pfam (PF15511)
In PDB		Xenopus laevis (African clawed frog)
37c, gHistone H2A type 1polymer13014093.42UniProt (P06897)
Pfam (PF16211)
Pfam (PF00125)
In PDB		Xenopus laevis (African clawed frog)
38d, hHistone H2B 1.1polymer12613965.32UniProt (P02281)
Pfam (PF00125)
In PDB		Xenopus laevis (African clawed frog)H2B1.1
391IRON/SULFUR CLUSTERnon-polymer351.61Chemie (SF4)
40B, C, I, J, L...ZINC IONnon-polymer65.417Chemie (ZN)
41AMAGNESIUM IONnon-polymer24.31Chemie (MG)
Sequence modifications
A: 1 - 1970 (UniProt: A0A7M4DUC2)
PDBExternal DatabaseDetails
-Tyr 1636deletion
-Ser 1637deletion
-Pro 1638deletion
-Thr 1639deletion
-Ser 1640deletion
-Pro 1641deletion
-Ser 1642deletion
-Tyr 1643deletion
-Ser 1644deletion
-Pro 1645deletion
-Thr 1646deletion
-Ser 1647deletion
-Pro 1648deletion
-Ser 1649deletion
W: 1 - 273 (UniProt: P29083)
W: 274 - 439 (UniProt: P29083)
a, e: 1 - 136 (UniProt: P84233)
PDBExternal DatabaseDetails
Ala 103Gly 103engineered mutation
c, g: 1 - 130 (UniProt: P06897)
PDBExternal DatabaseDetails
Arg 100Gly 100engineered mutation
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains42
Total formula weight1549229.8
Non-Polymers*Number of molecules19
Total formula weight1487.9
All*Total formula weight1550717.7
*Water molecules are not included.

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PDB entries from 2024-07-24

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