7YCX

The structure of INTAC-PEC complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of INTAC-regulated transcription.

Zheng, H., Jin, Q., Wang, X., Qi, Y., Liu, W., Ren, Y., Zhao, D., Xavier Chen, F., Cheng, J., Chen, X., Xu, Y.

(2023) Protein Cell 14: 698-702

  • DOI: https://doi.org/10.1093/procel/pwad010
  • Primary Citation of Related Structures:  
    7YCX
    • Organizational Affiliation: 

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 12,190Homo sapiensMutation(s): 0 
Gene Names: INTS1, KIAA1440, UNQ1821/PRO3434
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PHAROS:  Q8N201
GTEx:  ENSG00000164880 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 21,204Homo sapiensMutation(s): 0 
Gene Names: INTS2, KIAA1287
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PHAROS:  Q9H0H0
GTEx:  ENSG00000108506 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 4C [auth D]963Homo sapiensMutation(s): 0 
Gene Names: INTS4, MSTP093
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GTEx:  ENSG00000149262 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 5D [auth E]1,019Homo sapiensMutation(s): 0 
Gene Names: INTS5, KIAA1698
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GTEx:  ENSG00000185085 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 6E [auth F]887Homo sapiensMutation(s): 0 
Gene Names: INTS6, DBI1, DDX26, DDX26A
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GTEx:  ENSG00000102786 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 7F [auth G]962Homo sapiensMutation(s): 0 
Gene Names: INTS7, C1orf73
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GTEx:  ENSG00000143493 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 8G [auth H]995Homo sapiensMutation(s): 0 
Gene Names: INTS8, C8orf52
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GTEx:  ENSG00000164941 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 9H [auth I]658Homo sapiensMutation(s): 0 
Gene Names: INTS9, RC74
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GTEx:  ENSG00000104299 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 11I [auth K]600Homo sapiensMutation(s): 0 
Gene Names: INTS11, CPSF3L, RC68
EC: 3.1.27
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GTEx:  ENSG00000127054 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown2J [auth M]17Homo sapiensMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoformK [auth P]589Homo sapiensMutation(s): 0 
Gene Names: PPP2R1A
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GTEx:  ENSG00000105568 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoformL [auth Q]309Homo sapiensMutation(s): 0 
Gene Names: PPP2CA
EC: 3.1.3.16
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GTEx:  ENSG00000113575 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
UnknownM [auth U]27Homo sapiensMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1,DNA-directed RNA polymerase II subunit RPB1, CTD1, CTD2, CTD3, CTD4N [auth 1]1,970Homo sapiensMutation(s): 0 
Gene Names: POLR2A, POLR2
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (PDB Primary Data), 3.1.13 (UniProt)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaO [auth 2]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3P [auth 3]271Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCH3 (Sus scrofa)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EQ [auth 4]210Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LSI7 (Sus scrofa)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FR [auth 5]127Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3S [auth 6]150Sus scrofaMutation(s): 0 
UniProt
Find proteins for I3LCB2 (Sus scrofa)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9T [auth 7]125Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5U [auth 8]67Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinV [auth 9]117Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
RPB12W [auth a]58Sus scrofaMutation(s): 0 
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor AAA [auth e]528Homo sapiensMutation(s): 0 
Gene Names: NELFA, WHSC2, P/OKcl.15
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Find proteins for Q9H3P2 (Homo sapiens)
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GTEx:  ENSG00000185049 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor BBA [auth f]580Homo sapiensMutation(s): 0 
Gene Names: NELFB, COBRA1, KIAA1182
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Find proteins for Q8WX92 (Homo sapiens)
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GTEx:  ENSG00000188986 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor C/DCA [auth g]590Homo sapiensMutation(s): 0 
Gene Names: NELFCD, NELFD, TH1, TH1L, HSPC130
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GTEx:  ENSG00000101158 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor EDA [auth h]380Homo sapiensMutation(s): 0 
Gene Names: NELFE, RD, RDBP
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GTEx:  ENSG00000204356 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4EA [auth i]121Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1, SPT4H, SUPT4H
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GTEx:  ENSG00000213246 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5FA [auth j]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5H, SPT5, SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7GA [auth k]172Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4HA [auth l]142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains LengthOrganismImage
non-template DNAX [auth b]48synthetic construct
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Entity ID: 25
MoleculeChains LengthOrganismImage
RNAY [auth c]23synthetic construct
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Entity ID: 26
MoleculeChains LengthOrganismImage
template DNAZ [auth d]48synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
IA [auth K]
JA [auth K]
NA [auth 1]
OA [auth 1]
PA [auth 2]
IA [auth K],
JA [auth K],
NA [auth 1],
OA [auth 1],
PA [auth 2],
QA [auth 3],
RA [auth 7],
SA [auth 7],
TA [auth 8],
UA [auth a]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN
Query on MN
Download Ideal Coordinates CCD File 
KA [auth Q],
LA [auth Q]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
MA [auth 1]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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

Deposition Data

Funding OrganizationLocationGrant Number
Other governmentChinathe National key R&D program of China(2016YFA0500700)
Other governmentChinathe National Natural Science Foundation of China(32030055, 31830107, 31821002)
Other governmentChinathe Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)
Other governmentChinaShanghai Municipal Science and Technology Commission(19JC1411500)
Other governmentChinathe National Ten-Thousand Talent Program
Other governmentChinathe Strategic Priority Research Program of the Chinese Academy of Sciences(XDB08000000)

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-03-22
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references