5IYB

Human core-PIC in the open state


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

  • 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). 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 Biosciences, Northwestern University, Evanston, Illinois 60208, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,970Homo sapiensMutation(s): 0 
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,174Homo sapiensMutation(s): 0 
EC: 2.7.7.6
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GTEx:  ENSG00000047315 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102978 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4142Homo sapiensMutation(s): 0 
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PHAROS:  O15514
GTEx:  ENSG00000144231 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB5210Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099817 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB6127Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100142 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168002 
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UniProt GroupP62487
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB8150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163882 
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UniProt GroupP52434
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105258 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1067Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177700 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-a117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000005075 
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UniProt GroupP52435
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1258Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147669 
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UniProt GroupP53803
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIB316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
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GTEx:  ENSG00000137947 
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UniProt GroupQ00403
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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PHAROS:  P52655
GTEx:  ENSG00000165417 
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UniProt GroupP52655
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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GTEx:  ENSG00000140307 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding protein339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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GTEx:  ENSG00000112592 
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UniProt GroupP20226
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
UniProt & NIH Common Fund Data Resources
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PHAROS:  P29083
GTEx:  ENSG00000153767 
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UniProt GroupP29083
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit beta291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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PHAROS:  P29084
GTEx:  ENSG00000197265 
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UniProt GroupP29084
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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Find proteins for P35269 (Homo sapiens)
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GTEx:  ENSG00000125651 
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UniProt GroupP35269
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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Find proteins for P13984 (Homo sapiens)
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GTEx:  ENSG00000188342 
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UniProt GroupP13984
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor A protein 1301Homo sapiensMutation(s): 0 
Gene Names: TCEA1GTF2STFIIS
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GTEx:  ENSG00000187735 
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UniProt GroupP23193
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Entity ID: 22
MoleculeChains LengthOrganismImage
SCP-XV [auth X]75Homo sapiens
Sequence Annotations
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Entity ID: 23
MoleculeChains LengthOrganismImage
SCP-YW [auth Y]75Homo sapiens
Sequence Annotations
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth C]
CA [auth I]
DA [auth I]
EA [auth J]
AA [auth B],
BA [auth C],
CA [auth I],
DA [auth I],
EA [auth J],
FA [auth L],
GA [auth M],
HA [auth Q],
JA [auth U],
Y [auth A],
Z [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
IA [auth U],
X [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4beta

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