5IY6

Human holo-PIC in the closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Near-atomic resolution visualization of human transcription promoter opening.

He, Y.Yan, C.Fang, J.Inouye, C.Tjian, R.Ivanov, I.Nogales, E.

(2016) Nature 533: 359-365

  • DOI: 10.1038/nature17970
  • Primary Citation of Related Structures:  
    5IVW, 5IYB, 5IYA, 5IYD, 5IYC, 5IY6, 5IY8, 5IY7, 5IY9

  • PubMed Abstract: 
  • In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here ...

    In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1 A1970Homo sapiensMutation(s): 0 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
Find proteins for P24928 (Homo sapiens)
Explore P24928 
Go to UniProtKB:  P24928
NIH Common Fund Data Resources
PHAROS:  P24928
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2 B1174Homo sapiensMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for P30876 (Homo sapiens)
Explore P30876 
Go to UniProtKB:  P30876
NIH Common Fund Data Resources
PHAROS:  P30876
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3 C275Homo sapiensMutation(s): 0 
Gene Names: POLR2CA-152E5.7
Find proteins for P19387 (Homo sapiens)
Explore P19387 
Go to UniProtKB:  P19387
NIH Common Fund Data Resources
PHAROS:  P19387
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4 D142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
Find proteins for O15514 (Homo sapiens)
Explore O15514 
Go to UniProtKB:  O15514
NIH Common Fund Data Resources
PHAROS:  O15514
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB5 E210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
Find proteins for P19388 (Homo sapiens)
Explore P19388 
Go to UniProtKB:  P19388
NIH Common Fund Data Resources
PHAROS:  P19388
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB6 F127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
Find proteins for P61218 (Homo sapiens)
Explore P61218 
Go to UniProtKB:  P61218
NIH Common Fund Data Resources
PHAROS:  P61218
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7 G172Homo sapiensMutation(s): 0 
Gene Names: POLR2GRPB7
Find proteins for P62487 (Homo sapiens)
Explore P62487 
Go to UniProtKB:  P62487
NIH Common Fund Data Resources
PHAROS:  P62487
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB8 H150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
Find proteins for P52434 (Homo sapiens)
Explore P52434 
Go to UniProtKB:  P52434
NIH Common Fund Data Resources
PHAROS:  P52434
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9 I125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
Find proteins for P36954 (Homo sapiens)
Explore P36954 
Go to UniProtKB:  P36954
NIH Common Fund Data Resources
PHAROS:  P36954
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB10 J67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
Find proteins for P62875 (Homo sapiens)
Explore P62875 
Go to UniProtKB:  P62875
NIH Common Fund Data Resources
PHAROS:  P62875
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-a K117Homo sapiensMutation(s): 0 
Gene Names: POLR2JPOLR2J1
Find proteins for P52435 (Homo sapiens)
Explore P52435 
Go to UniProtKB:  P52435
NIH Common Fund Data Resources
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB12 L58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
Find proteins for P53803 (Homo sapiens)
Explore P53803 
Go to UniProtKB:  P53803
NIH Common Fund Data Resources
PHAROS:  P53803
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIB M316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
Find proteins for Q00403 (Homo sapiens)
Explore Q00403 
Go to UniProtKB:  Q00403
NIH Common Fund Data Resources
PHAROS:  Q00403
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1 N376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
Find proteins for P52655 (Homo sapiens)
Explore P52655 
Go to UniProtKB:  P52655
NIH Common Fund Data Resources
PHAROS:  P52655
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2 O109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
Find proteins for P52657 (Homo sapiens)
Explore P52657 
Go to UniProtKB:  P52657
NIH Common Fund Data Resources
PHAROS:  P52657
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding protein P339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
NIH Common Fund Data Resources
PHAROS:  P20226
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1 Q439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
Find proteins for P29083 (Homo sapiens)
Explore P29083 
Go to UniProtKB:  P29083
NIH Common Fund Data Resources
PHAROS:  P29083
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit beta R291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
Find proteins for P29084 (Homo sapiens)
Explore P29084 
Go to UniProtKB:  P29084
NIH Common Fund Data Resources
PHAROS:  P29084
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1 S517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
Find proteins for P35269 (Homo sapiens)
Explore P35269 
Go to UniProtKB:  P35269
NIH Common Fund Data Resources
PHAROS:  P35269
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2 T249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
Find proteins for P13984 (Homo sapiens)
Explore P13984 
Go to UniProtKB:  P13984
NIH Common Fund Data Resources
PHAROS:  P13984
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor A protein 1 U301Homo sapiensMutation(s): 0 
Gene Names: TCEA1GTF2STFIIS
Find proteins for P23193 (Homo sapiens)
Explore P23193 
Go to UniProtKB:  P23193
NIH Common Fund Data Resources
PHAROS:  P23193
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPB subunit V782Homo sapiensMutation(s): 0 
Gene Names: ERCC3XPBXPBC
EC: 3.6.4.12
Find proteins for P19447 (Homo sapiens)
Explore P19447 
Go to UniProtKB:  P19447
NIH Common Fund Data Resources
PHAROS:  P19447
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPD subunit W760Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
Find proteins for P18074 (Homo sapiens)
Explore P18074 
Go to UniProtKB:  P18074
NIH Common Fund Data Resources
PHAROS:  P18074
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2 0395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
Find proteins for Q13888 (Homo sapiens)
Explore Q13888 
Go to UniProtKB:  Q13888
NIH Common Fund Data Resources
PHAROS:  Q13888
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5 171Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
Find proteins for Q6ZYL4 (Homo sapiens)
Explore Q6ZYL4 
Go to UniProtKB:  Q6ZYL4
NIH Common Fund Data Resources
PHAROS:  Q6ZYL4
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4 2462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
Find proteins for Q92759 (Homo sapiens)
Explore Q92759 
Go to UniProtKB:  Q92759
NIH Common Fund Data Resources
PHAROS:  Q92759
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3 3308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
Find proteins for Q13889 (Homo sapiens)
Explore Q13889 
Go to UniProtKB:  Q13889
NIH Common Fund Data Resources
PHAROS:  Q13889
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 28
MoleculeChainsLengthOrganismImage
SCP-XX65Homo sapiens
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 29
MoleculeChainsLengthOrganismImage
SCP-YY65Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM63072
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110387
National Science Foundation (NSF, United States)United StatesMCB-1149521
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2016-06-22
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence