5IYD

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  

  • 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. ...

    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

    Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1
A
1970Homo sapiensMutation(s): 0 
Gene Names: POLR2A (POLR2)
EC: 2.7.7.6
Find proteins for P24928 (Homo sapiens)
Go to Gene View: POLR2A
Go to UniProtKB:  P24928
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2
B
1174Homo sapiensMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for P30876 (Homo sapiens)
Go to Gene View: POLR2B
Go to UniProtKB:  P30876
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3
C
275Homo sapiensMutation(s): 0 
Gene Names: POLR2C
Find proteins for P19387 (Homo sapiens)
Go to Gene View: POLR2C
Go to UniProtKB:  P19387
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB4
D
142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
Find proteins for O15514 (Homo sapiens)
Go to Gene View: POLR2D
Go to UniProtKB:  O15514
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB5
E
210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
Find proteins for P19388 (Homo sapiens)
Go to Gene View: POLR2E
Go to UniProtKB:  P19388
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB6
F
127Homo sapiensMutation(s): 0 
Gene Names: POLR2F (POLRF)
Find proteins for P61218 (Homo sapiens)
Go to Gene View: POLR2F
Go to UniProtKB:  P61218
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7
G
172Homo sapiensMutation(s): 0 
Gene Names: POLR2G (RPB7)
Find proteins for P62487 (Homo sapiens)
Go to Gene View: POLR2G
Go to UniProtKB:  P62487
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB8
H
150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
Find proteins for P52434 (Homo sapiens)
Go to Gene View: POLR2H
Go to UniProtKB:  P52434
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9
I
125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
Find proteins for P36954 (Homo sapiens)
Go to Gene View: POLR2I
Go to UniProtKB:  P36954
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB10
J
67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
Find proteins for P62875 (Homo sapiens)
Go to Gene View: POLR2L
Go to UniProtKB:  P62875
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11-a
K
117Homo sapiensMutation(s): 0 
Gene Names: POLR2J (POLR2J1)
Find proteins for P52435 (Homo sapiens)
Go to Gene View: POLR2J
Go to UniProtKB:  P52435
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB12
L
58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
Find proteins for P53803 (Homo sapiens)
Go to Gene View: POLR2K
Go to UniProtKB:  P53803
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIB
M
316Homo sapiensMutation(s): 0 
Gene Names: GTF2B (TF2B, TFIIB)
EC: 2.3.1.48
Find proteins for Q00403 (Homo sapiens)
Go to Gene View: GTF2B
Go to UniProtKB:  Q00403
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 1
N
376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1 (TF2A1)
Find proteins for P52655 (Homo sapiens)
Go to Gene View: GTF2A1
Go to UniProtKB:  P52655
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 2
O
109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2 (TF2A2)
Find proteins for P52657 (Homo sapiens)
Go to Gene View: GTF2A2
Go to UniProtKB:  P52657
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding protein
P
339Homo sapiensMutation(s): 0 
Gene Names: TBP (GTF2D1, TF2D, TFIID)
Find proteins for P20226 (Homo sapiens)
Go to Gene View: TBP
Go to UniProtKB:  P20226
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIE subunit 1
Q
439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1 (TF2E1)
Find proteins for P29083 (Homo sapiens)
Go to Gene View: GTF2E1
Go to UniProtKB:  P29083
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit beta
R
291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2 (TF2E2)
Find proteins for P29084 (Homo sapiens)
Go to Gene View: GTF2E2
Go to UniProtKB:  P29084
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIF subunit 1
S
517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1 (RAP74)
Find proteins for P35269 (Homo sapiens)
Go to Gene View: GTF2F1
Go to UniProtKB:  P35269
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
General transcription factor IIF subunit 2
T
249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2 (RAP30)
EC: 3.6.4.12
Find proteins for P13984 (Homo sapiens)
Go to Gene View: GTF2F2
Go to UniProtKB:  P13984
Entity ID: 21
MoleculeChainsLengthOrganism
SCP-XX80Homo sapiens
Entity ID: 22
MoleculeChainsLengthOrganism
SCP-YY80Homo sapiens
Entity ID: 23
MoleculeChainsLengthOrganism
RNAZ6Homo sapiens
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, I, J, L, M, Q
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.9 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM63072
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM110387
National Science Foundation (United States)United StatesMCB-1149521
Howard Hughes Medical InstituteUnited States--

Revision History 

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