Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 14-mer - ABCDEFGHIJKLMN 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy, gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 694730.50 
• Atom Count: 37988 
• Residue Count: 5927 
• Unique protein chains: 14
• Unique nucleic acid chains: 3

5OIK

Structure of an RNA polymerase II-DSIF transcription elongation complex

• DOI: 10.2210/pdb5OIK/pdb
• EMDataResource: EMD-3817

• Classification: TRANSCRIPTION
• Organism(s): Bos taurus, synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2017-07-18 Released: 2017-09-13 
• Deposition Author(s): Bernecky, C., Plitzko, J.M., Cramer, P.
• Funding Organization(s): German Research Foundation; European Research Council; Volkswagen Foundation 

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.

Bernecky, C., Plitzko, J.M., Cramer, P.

(2017) Nat. Struct. Mol. Biol. 24: 809-815

• PubMed: 28892040 
• DOI: 10.1038/nsmb.3465
• Primary Citation of Related Structures:  
  5OHQ, 5OHO


• PubMed Abstract: 
  

During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4 Å. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.

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Organizational Affiliation: 

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB1	A	1970	Bos taurus	Mutation(s): 0  Gene Names: POLR2A EC: 2.7.7.6
Find proteins for G3MZY8 (Bos taurus) Go to Gene View: POLR2A Go to UniProtKB:  G3MZY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase subunit beta	B	1174	Bos taurus	Mutation(s): 0  Gene Names: POLR2B EC: 2.7.7.6
Find proteins for A5PJW8 (Bos taurus) Go to Gene View: POLR2B Go to UniProtKB:  A5PJW8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB3	C	275	Bos taurus	Mutation(s): 0  Gene Names: POLR2C
Find proteins for Q3T0Q3 (Bos taurus) Go to Gene View: POLR2C Go to UniProtKB:  Q3T0Q3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Polymerase (RNA) II (DNA directed) polypeptide D	D	142	Bos taurus	Mutation(s): 0  Gene Names: POLR2D
Find proteins for Q1JQ91 (Bos taurus) Go to Gene View: POLR2D Go to UniProtKB:  Q1JQ91

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	210	Bos taurus	Mutation(s): 0  Gene Names: POLR2E
Find proteins for Q2T9T3 (Bos taurus) Go to Gene View: POLR2E Go to UniProtKB:  Q2T9T3

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	127	Bos taurus	Mutation(s): 0  Gene Names: POLR2F
Find proteins for Q32PE0 (Bos taurus) Go to Gene View: POLR2F Go to UniProtKB:  Q32PE0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB7	G	172	Bos taurus	Mutation(s): 0  Gene Names: POLR2G
Find proteins for Q5E9B8 (Bos taurus) Go to Gene View: POLR2G Go to UniProtKB:  Q5E9B8

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
Uncharacterized protein	H	150	Bos taurus	Mutation(s): 0  Gene Names: POLR2H
Find proteins for F2Z4H3 (Bos taurus) Go to Gene View: POLR2H Go to UniProtKB:  F2Z4H3

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB9	I	125	Bos taurus	Mutation(s): 0  Gene Names: POLR2I
Find proteins for Q32P73 (Bos taurus) Go to Gene View: POLR2I Go to UniProtKB:  Q32P73

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	67	Bos taurus	Mutation(s): 0  Gene Names: POLR2L
Find proteins for Q32P78 (Bos taurus) Go to Gene View: POLR2L Go to UniProtKB:  Q32P78

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerase II subunit RPB11	K	117	Bos taurus	Mutation(s): 0  Gene Names: POLR2J
Find proteins for Q32P79 (Bos taurus) Go to Gene View: POLR2J Go to UniProtKB:  Q32P79

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	58	Bos taurus	Mutation(s): 0  Gene Names: POLR2K
Find proteins for Q3ZBC0 (Bos taurus) Go to Gene View: POLR2K Go to UniProtKB:  Q3ZBC0

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
Transcription elongation factor SPT4	Y	117	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: 17
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: 13
Molecule	Chains	Length	Organism
DNA (43-MER)	N	43	synthetic construct

Entity ID: 14
Molecule	Chains	Length	Organism
RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')	P	50	synthetic construct

Entity ID: 15
Molecule	Chains	Length	Organism
DNA (43-MER)	T	43	synthetic construct

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.7 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: 2017-07-18 
• Released Date: 2017-09-13 
• Deposition Author(s): Bernecky, C., Plitzko, J.M., Cramer, P.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB860, SPP1935
European Research Council	Germany	TRANSREGULON
Volkswagen Foundation	Germany	--

Revision History 

• Version 1.0: 2017-09-13
  Type: Initial release
• Version 1.1: 2017-10-18
  Type: Database references
• Version 1.2: 2018-01-24
  Type: Source and taxonomy