Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 18-mer - ABCDEFGHIJKLMNOPQR 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 928515.88 
• Atom Count: 44827 
• Residue Count: 8026 
• Unique protein chains: 18
• Unique nucleic acid chains: 3

6GML

Structure of paused transcription complex Pol II-DSIF-NELF

• DOI: 10.2210/pdb6GML/pdb
• EMDataBank: EMD-0038

• Classification: TRANSCRIPTION
• Organism(s): Sus scrofa, Homo sapiens, Human immunodeficiency virus 1
• Expression System: Trichoplusia ni, Escherichia coli BL21(DE3)


• Deposited: 2018-05-27 Released: 2018-09-05 
• Deposition Author(s): Vos, S.M., Farnung, L., Urlaub, H., Cramer, P.
• Funding Organization(s): European Molecular Biology Organization; German Research Foundation; European Research Council 

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Experimental Data Snapshot

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

Literature

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

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

(2018) Nature 560: 601-606

• PubMed: 30135580 

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit	A	1970	Sus scrofa	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit beta	B	1174	Sus scrofa	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit C	C	271	Sus scrofa	Mutation(s): 0  Gene Names: POLR2C
Find proteins for I3LCH3 (Sus scrofa) Go to Gene View: POLR2C Go to UniProtKB:  I3LCH3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit E	E	210	Sus scrofa	Mutation(s): 0  Gene Names: POLR2E
Find proteins for I3LSI7 (Sus scrofa) Go to Gene View: POLR2E Go to UniProtKB:  I3LSI7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit F	F	127	Sus scrofa	Mutation(s): 0  Gene Names: POLR2F
Find proteins for F1SKN8 (Sus scrofa) Go to Gene View: POLR2F Go to UniProtKB:  F1SKN8

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	150	Sus scrofa	Mutation(s): 0  Gene Names: POLR2H
Find proteins for I3LCB2 (Sus scrofa) Go to Gene View: POLR2H Go to UniProtKB:  I3LCB2

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB9	I	125	Sus scrofa	Mutation(s): 0  Gene Names: POLR2I
Find proteins for P60899 (Sus scrofa) Go to Gene View: POLR2I Go to UniProtKB:  P60899

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Uncharacterized protein	J	67	Sus scrofa	Mutation(s): 0  Gene Names: POLR2L
Find proteins for A0A287B432 (Sus scrofa) Go to Gene View: POLR2L Go to UniProtKB:  A0A287B432

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
Uncharacterized protein	K	117	Sus scrofa	Mutation(s): 0  Gene Names: POLR2J
Find proteins for F1RKE4 (Sus scrofa) Go to Gene View: POLR2J Go to UniProtKB:  F1RKE4

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
Uncharacterized protein	L	58	Sus scrofa	Mutation(s): 0  Gene Names: POLR2K
Find proteins for I3LN51 (Sus scrofa) Go to Gene View: POLR2K Go to UniProtKB:  I3LN51

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
Negative elongation factor A	U	528	Homo sapiens	Mutation(s): 0  Gene Names: NELFA (WHSC2)
Find proteins for Q9H3P2 (Homo sapiens) Go to Gene View: NELFA Go to UniProtKB:  Q9H3P2

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
Negative elongation factor B,Negative elongation factor B	V	577	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Negative elongation factor C/D	W	584	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Negative elongation factor E,Negative elongation factor E	X	404	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Transcription elongation factor SPT4	Y	121	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Transcription elongation factor SPT5	Z	1087	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit D	D	142	Sus scrofa	Mutation(s): 0  Gene Names: POLR2D
Find proteins for A0A287ADR4 (Sus scrofa) Go to Gene View: POLR2D Go to UniProtKB:  A0A287ADR4

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
RNA polymerase II subunit G	G	172	Sus scrofa	Mutation(s): 0  Gene Names: POLR2G
Find proteins for I3LJZ9 (Sus scrofa) Go to Gene View: POLR2G Go to UniProtKB:  I3LJZ9

Entity ID: 11
Molecule	Chains	Length	Organism
Non-template DNA	N	48	Human immunodeficiency virus 1

Entity ID: 12
Molecule	Chains	Length	Organism
TAR RNA	P	46	Human immunodeficiency virus 1

Entity ID: 13
Molecule	Chains	Length	Organism
Template DNA	T	48	Human immunodeficiency virus 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B, C, I, J, L, Y	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	V, W, X	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

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

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-27 
• Released Date: 2018-09-05 
• Deposition Author(s): Vos, S.M., Farnung, L., Urlaub, H., Cramer, P.

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Funding Organization	Location	Grant Number
European Molecular Biology Organization	Germany	ALTF-725-2014
German Research Foundation	Germany	DFG SFB860
European Research Council	Germany	693023

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