6GML

Structure of paused transcription complex Pol II-DSIF-NELF


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structure of paused transcription complex Pol II-DSIF-NELF.

Vos, S.M.Farnung, L.Urlaub, H.Cramer, P.

(2018) Nature 560: 601-606


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit
A
1970Sus scrofaMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
Find proteins for I3LJR4 (Sus scrofa)
Go to Gene View: POLR2A
Go to UniProtKB:  I3LJR4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
B
1174Sus scrofaMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for I3LGP4 (Sus scrofa)
Go to Gene View: POLR2B
Go to UniProtKB:  I3LGP4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit C
C
271Sus scrofaMutation(s): 0 
Gene Names: POLR2C
Find proteins for I3LCH3 (Sus scrofa)
Go to Gene View: POLR2C
Go to UniProtKB:  I3LCH3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit E
E
210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
Find proteins for I3LSI7 (Sus scrofa)
Go to Gene View: POLR2E
Go to UniProtKB:  I3LSI7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit F
F
127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
Find proteins for F1SKN8 (Sus scrofa)
Go to Gene View: POLR2F
Go to UniProtKB:  F1SKN8
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H
150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
Find proteins for I3LCB2 (Sus scrofa)
Go to Gene View: POLR2H
Go to UniProtKB:  I3LCB2
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9
I
125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
Find proteins for P60899 (Sus scrofa)
Go to Gene View: POLR2I
Go to UniProtKB:  P60899
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
J
67Sus scrofaMutation(s): 0 
Gene Names: POLR2L
Find proteins for A0A287B432 (Sus scrofa)
Go to Gene View: POLR2L
Go to UniProtKB:  A0A287B432
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
K
117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
Find proteins for F1RKE4 (Sus scrofa)
Go to Gene View: POLR2J
Go to UniProtKB:  F1RKE4
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
L
58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
Find proteins for I3LN51 (Sus scrofa)
Go to Gene View: POLR2K
Go to UniProtKB:  I3LN51
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Negative elongation factor A
U
528Homo sapiensMutation(s): 0 
Gene Names: NELFA (WHSC2)
Find proteins for Q9H3P2 (Homo sapiens)
Go to Gene View: NELFA
Go to UniProtKB:  Q9H3P2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Negative elongation factor B,Negative elongation factor B
V
577Homo sapiensMutation(s): 0 
Gene Names: NELFB (COBRA1, KIAA1182)
Find proteins for Q8WX92 (Homo sapiens)
Go to Gene View: NELFB
Go to UniProtKB:  Q8WX92
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Negative elongation factor C/D
W
584Homo sapiensMutation(s): 0 
Gene Names: NELFCD (NELFD, TH1, TH1L)
Find proteins for Q8IXH7 (Homo sapiens)
Go to Gene View: NELFCD
Go to UniProtKB:  Q8IXH7
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Negative elongation factor E,Negative elongation factor E
X
404Homo sapiensMutation(s): 0 
Gene Names: NELFE (RD, RDBP)
Find proteins for P18615 (Homo sapiens)
Go to Gene View: NELFE
Go to UniProtKB:  P18615
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT4
Y
121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1 (SPT4H, SUPT4H)
Find proteins for P63272 (Homo sapiens)
Go to Gene View: SUPT4H1
Go to UniProtKB:  P63272
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT5
Z
1087Homo sapiensMutation(s): 0 
Gene Names: SUPT5H (SPT5, SPT5H)
Find proteins for O00267 (Homo sapiens)
Go to Gene View: SUPT5H
Go to UniProtKB:  O00267
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit D
D
142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
Find proteins for A0A287ADR4 (Sus scrofa)
Go to Gene View: POLR2D
Go to UniProtKB:  A0A287ADR4
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II subunit G
G
172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
Find proteins for I3LJZ9 (Sus scrofa)
Go to Gene View: POLR2G
Go to UniProtKB:  I3LJZ9
Entity ID: 11
MoleculeChainsLengthOrganism
Non-template DNAN48Human immunodeficiency virus 1
Entity ID: 12
MoleculeChainsLengthOrganism
TAR RNAP46Human immunodeficiency virus 1
Entity ID: 13
MoleculeChainsLengthOrganism
Template DNAT48Human immunodeficiency virus 1
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, Y
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
V, W, X
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationGermanyALTF-725-2014
German Research FoundationGermanyDFG SFB860
European Research CouncilGermany693023

Revision History 

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-12
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Experimental preparation
  • Version 2.0: 2019-01-23
    Type: Advisory, Data collection, Database references, Polymer sequence, Source and taxonomy, Structure summary