5IYD

Human core-PIC in the initial transcribing state (no IIS)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 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 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) ...

    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 RPB1A1970Homo sapiensMutation(s): 0 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens)
Explore P24928 
Go to UniProtKB:  P24928
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 RPB2B1174Homo sapiensMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
UniProt & NIH Common Fund Data Resources
Find proteins for P30876 (Homo sapiens)
Explore P30876 
Go to UniProtKB:  P30876
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 RPB3C275Homo sapiensMutation(s): 0 
Gene Names: POLR2CA-152E5.7
UniProt & NIH Common Fund Data Resources
Find proteins for P19387 (Homo sapiens)
Explore P19387 
Go to UniProtKB:  P19387
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 RPB4D142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
UniProt & NIH Common Fund Data Resources
Find proteins for O15514 (Homo sapiens)
Explore O15514 
Go to UniProtKB:  O15514
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 RPB5E210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
UniProt & NIH Common Fund Data Resources
Find proteins for P19388 (Homo sapiens)
Explore P19388 
Go to UniProtKB:  P19388
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 RPB6F127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
UniProt & NIH Common Fund Data Resources
Find proteins for P61218 (Homo sapiens)
Explore P61218 
Go to UniProtKB:  P61218
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 RPB7G172Homo sapiensMutation(s): 0 
Gene Names: POLR2GRPB7
UniProt & NIH Common Fund Data Resources
Find proteins for P62487 (Homo sapiens)
Explore P62487 
Go to UniProtKB:  P62487
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 RPB8H150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
UniProt & NIH Common Fund Data Resources
Find proteins for P52434 (Homo sapiens)
Explore P52434 
Go to UniProtKB:  P52434
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 RPB9I125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
UniProt & NIH Common Fund Data Resources
Find proteins for P36954 (Homo sapiens)
Explore P36954 
Go to UniProtKB:  P36954
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 RPB10J67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
UniProt & NIH Common Fund Data Resources
Find proteins for P62875 (Homo sapiens)
Explore P62875 
Go to UniProtKB:  P62875
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-aK117Homo sapiensMutation(s): 0 
Gene Names: POLR2JPOLR2J1
UniProt & NIH Common Fund Data Resources
Find proteins for P52435 (Homo sapiens)
Explore P52435 
Go to UniProtKB:  P52435
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 RPB12L58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
UniProt & NIH Common Fund Data Resources
Find proteins for P53803 (Homo sapiens)
Explore P53803 
Go to UniProtKB:  P53803
PHAROS:  P53803
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBM316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q00403 (Homo sapiens)
Explore Q00403 
Go to UniProtKB:  Q00403
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 1N376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
UniProt & NIH Common Fund Data Resources
Find proteins for P52655 (Homo sapiens)
Explore P52655 
Go to UniProtKB:  P52655
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 2O109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
UniProt & NIH Common Fund Data Resources
Find proteins for P52657 (Homo sapiens)
Explore P52657 
Go to UniProtKB:  P52657
PHAROS:  P52657
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinP339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
UniProt & NIH Common Fund Data Resources
Find proteins for P20226 (Homo sapiens)
Explore P20226 
Go to UniProtKB:  P20226
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 1Q439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
UniProt & NIH Common Fund Data Resources
Find proteins for P29083 (Homo sapiens)
Explore P29083 
Go to UniProtKB:  P29083
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 betaR291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
UniProt & NIH Common Fund Data Resources
Find proteins for P29084 (Homo sapiens)
Explore P29084 
Go to UniProtKB:  P29084
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 1S517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
UniProt & NIH Common Fund Data Resources
Find proteins for P35269 (Homo sapiens)
Explore P35269 
Go to UniProtKB:  P35269
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 2T249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P13984 (Homo sapiens)
Explore P13984 
Go to UniProtKB:  P13984
PHAROS:  P13984
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 21
MoleculeChainsLengthOrganismImage
SCP-XU [auth X]80Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsLengthOrganismImage
SCP-YV [auth Y]80Homo sapiens
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 23
    MoleculeChainsLengthOrganismImage
    RNAW [auth Z]6Homo sapiens
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 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  (Full details and data files)

    • 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