9MLC | pdb_00009mlc

Pol II-DSIF-SPT6-PAF1c-TFIIS-IWS1-ELOF1-LEDGF-nucleosome activated elongation complex Composite map T

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structure and function of IWS1 in transcription elongation

Syau, D., Farnung, L.

To be published.

Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,984Sus scrofaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,300Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
Explore I3LGP4 
Go to UniProtKB:  I3LGP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LGP4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A481DF93 (Sus scrofa)
Explore A0A481DF93 
Go to UniProtKB:  A0A481DF93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A481DF93
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RPOL4c domain-containing protein184Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1GCS3 (Sus scrofa)
Explore A0A8D1GCS3 
Go to UniProtKB:  A0A8D1GCS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D1GCS3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VTX4 (Sus scrofa)
Explore A0A4X1VTX4 
Go to UniProtKB:  A0A4X1VTX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1VTX4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2127Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa)
Explore A0A4X1VEK9 
Go to UniProtKB:  A0A4X1VEK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1VEK9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa)
Explore A0A4X1VKG7 
Go to UniProtKB:  A0A4X1VKG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1VKG7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D1AQR7 (Sus scrofa)
Explore A0A8D1AQR7 
Go to UniProtKB:  A0A8D1AQR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D1AQR7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofaMutation(s): 0 
UniProt
Find proteins for P60899 (Sus scrofa)
Explore P60899 
Go to UniProtKB:  P60899
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60899
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa)
Explore A0A8W4F9W9 
Go to UniProtKB:  A0A8W4F9W9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8W4F9W9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit J117Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8D0TE17 (Sus scrofa)
Explore A0A8D0TE17 
Go to UniProtKB:  A0A8D0TE17
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8D0TE17
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa)
Explore A0A4X1TRS6 
Go to UniProtKB:  A0A4X1TRS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1TRS6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT61,726Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor 1 homolog83Homo sapiensMutation(s): 0 
Gene Names: ELOF1
UniProt & NIH Common Fund Data Resources
Find proteins for P60002 (Homo sapiens)
Explore P60002 
Go to UniProtKB:  P60002
PHAROS:  P60002
GTEx:  ENSG00000130165 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60002
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein CTR9 homolog1,173Homo sapiensMutation(s): 0 
Gene Names: CTR9, KIAA0155, SH2BP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PD62 (Homo sapiens)
Explore Q6PD62 
Go to UniProtKB:  Q6PD62
PHAROS:  Q6PD62
GTEx:  ENSG00000198730 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PD62
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein RTF1 homolog710Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor A protein 1301Homo sapiensMutation(s): 0 
Gene Names: TCEA1, GTF2S, TFIIS
UniProt & NIH Common Fund Data Resources
Find proteins for P23193 (Homo sapiens)
Explore P23193 
Go to UniProtKB:  P23193
PHAROS:  P23193
GTEx:  ENSG00000187735 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23193
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase-associated protein LEO1666Homo sapiensMutation(s): 0 
Gene Names: LEO1, RDL
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WVC0 (Homo sapiens)
Explore Q8WVC0 
Go to UniProtKB:  Q8WVC0
PHAROS:  Q8WVC0
GTEx:  ENSG00000166477 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WVC0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II-associated factor 1 homolog531Homo sapiensMutation(s): 0 
Gene Names: PAF1, PD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N7H5 (Homo sapiens)
Explore Q8N7H5 
Go to UniProtKB:  Q8N7H5
PHAROS:  Q8N7H5
GTEx:  ENSG00000006712 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N7H5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
WDR61305Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZS3 (Homo sapiens)
Explore Q9GZS3 
Go to UniProtKB:  Q9GZS3
PHAROS:  Q9GZS3
GTEx:  ENSG00000140395 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZS3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Parafibromin531Homo sapiensMutation(s): 0 
Gene Names: CDC73, C1orf28, HRPT2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P1J9 (Homo sapiens)
Explore Q6P1J9 
Go to UniProtKB:  Q6P1J9
PHAROS:  Q6P1J9
GTEx:  ENSG00000134371 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P1J9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1, SPT4H, SUPT4H
UniProt & NIH Common Fund Data Resources
Find proteins for P63272 (Homo sapiens)
Explore P63272 
Go to UniProtKB:  P63272
PHAROS:  P63272
GTEx:  ENSG00000213246 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63272
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT51,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5H, SPT5, SPT5H
UniProt & NIH Common Fund Data Resources
Find proteins for O00267 (Homo sapiens)
Explore O00267 
Go to UniProtKB:  O00267
PHAROS:  O00267
GTEx:  ENSG00000196235 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00267
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Protein IWS1 homologAA [auth i]819Homo sapiensMutation(s): 0 
Gene Names: IWS1, IWS1L
UniProt & NIH Common Fund Data Resources
Find proteins for Q96ST2 (Homo sapiens)
Explore Q96ST2 
Go to UniProtKB:  Q96ST2
PHAROS:  Q96ST2
GTEx:  ENSG00000163166 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96ST2
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains LengthOrganismImage
DNA (194-MER)206synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*UP*UP*GP*GP*UP*GP*UP*GP*UP*CP*UP*GP*GP*GP*UP*GP*GP*UP*G)-3')39synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains LengthOrganismImage
DNA (194-MER)215synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BA [auth A]
CA [auth A]
EA [auth B]
FA [auth C]
GA [auth I]
BA [auth A],
CA [auth A],
EA [auth B],
FA [auth C],
GA [auth I],
HA [auth I],
IA [auth J],
JA [auth L],
KA [auth S],
LA [auth Y]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
DA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2.0
RECONSTRUCTIONWarp
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Richard and Susan Smith Family FoundationUnited States--
Damon Runyon Cancer Research FoundationUnited States--
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesDP2-ES036404

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-21
    Type: Initial release