7YCX | pdb_00007ycx

The structure of INTAC-PEC complex

PDB DOI: https://doi.org/10.2210/pdb7YCX/pdb
NAKB: 7YCX
EM Map EMD-33741: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Homo sapiens, Sus scrofa, synthetic construct
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-07-02 Released: 2023-03-15
Deposition Author(s): Zheng, H., Jin, Q., Wang, X., Qi, Y., Liu, W., Ren, Y., Zhao, D., Chen, F.X., Cheng, J., Chen, X., Xu, Y.
Funding Organization(s): Other government

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

PubMed: 36869814 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/procel/pwad010
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 2,084.53 kDa
Atom Count: 113,089
Modeled Residue Count: 14,842
Deposited Residue Count: 18,408
Unique protein chains: 31
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 1	A	2,190	Homo sapiens	Mutation(s): 0 Gene Names: INTS1, KIAA1440, UNQ1821/PRO3434
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N201 (Homo sapiens) Explore Q8N201 Go to UniProtKB: Q8N201
PHAROS: Q8N201 GTEx: ENSG00000164880
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N201
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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 2	B	1,204	Homo sapiens	Mutation(s): 0 Gene Names: INTS2, KIAA1287
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0H0 (Homo sapiens) Explore Q9H0H0 Go to UniProtKB: Q9H0H0
PHAROS: Q9H0H0 GTEx: ENSG00000108506
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H0H0
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 4	C [auth D]	963	Homo sapiens	Mutation(s): 0 Gene Names: INTS4, MSTP093
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HW7 (Homo sapiens) Explore Q96HW7 Go to UniProtKB: Q96HW7
PHAROS: Q96HW7 GTEx: ENSG00000149262
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96HW7
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 5	D [auth E]	1,019	Homo sapiens	Mutation(s): 0 Gene Names: INTS5, KIAA1698
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Find proteins for Q6P9B9 (Homo sapiens) Explore Q6P9B9 Go to UniProtKB: Q6P9B9
PHAROS: Q6P9B9 GTEx: ENSG00000185085
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6P9B9
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 6	E [auth F]	887	Homo sapiens	Mutation(s): 0 Gene Names: INTS6, DBI1, DDX26, DDX26A
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Find proteins for Q9UL03 (Homo sapiens) Explore Q9UL03 Go to UniProtKB: Q9UL03
PHAROS: Q9UL03 GTEx: ENSG00000102786
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UniProt Group	Q9UL03
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 7	F [auth G]	962	Homo sapiens	Mutation(s): 0 Gene Names: INTS7, C1orf73
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Find proteins for Q9NVH2 (Homo sapiens) Explore Q9NVH2 Go to UniProtKB: Q9NVH2
PHAROS: Q9NVH2 GTEx: ENSG00000143493
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NVH2
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 8	G [auth H]	995	Homo sapiens	Mutation(s): 0 Gene Names: INTS8, C8orf52
UniProt & NIH Common Fund Data Resources
Find proteins for Q75QN2 (Homo sapiens) Explore Q75QN2 Go to UniProtKB: Q75QN2
PHAROS: Q75QN2 GTEx: ENSG00000164941
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q75QN2
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 9	H [auth I]	658	Homo sapiens	Mutation(s): 0 Gene Names: INTS9, RC74
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Find proteins for Q9NV88 (Homo sapiens) Explore Q9NV88 Go to UniProtKB: Q9NV88
PHAROS: Q9NV88 GTEx: ENSG00000104299
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UniProt Group	Q9NV88
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 11	I [auth K]	600	Homo sapiens	Mutation(s): 0 Gene Names: INTS11, CPSF3L, RC68 EC: 3.1.27
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Find proteins for Q5TA45 (Homo sapiens) Explore Q5TA45 Go to UniProtKB: Q5TA45
PHAROS: Q5TA45 GTEx: ENSG00000127054
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5TA45
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown2	J [auth M]	17	Homo sapiens	Mutation(s): 0

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	K [auth P]	589	Homo sapiens	Mutation(s): 0 Gene Names: PPP2R1A
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Find proteins for P30153 (Homo sapiens) Explore P30153 Go to UniProtKB: P30153
PHAROS: P30153 GTEx: ENSG00000105568
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30153
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	L [auth Q]	309	Homo sapiens	Mutation(s): 0 Gene Names: PPP2CA EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P67775 (Homo sapiens) Explore P67775 Go to UniProtKB: P67775
PHAROS: P67775 GTEx: ENSG00000113575
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P67775
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Unknown	M [auth U]	27	Homo sapiens	Mutation(s): 0

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1,DNA-directed RNA polymerase II subunit RPB1, CTD1, CTD2, CTD3, CTD4	N [auth 1]	1,970	Homo sapiens	Mutation(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)
UniProt & NIH Common Fund Data Resources
Find proteins for P24928 (Homo sapiens) Explore P24928 Go to UniProtKB: P24928
PHAROS: P24928
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P24928
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	O [auth 2]	1,174	Sus scrofa	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa) Explore I3LGP4 Go to UniProtKB: I3LGP4
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UniProt Group	I3LGP4
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	P [auth 3]	271	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3LCH3 (Sus scrofa) Explore I3LCH3 Go to UniProtKB: I3LCH3
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3LCH3
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit E	Q [auth 4]	210	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3LSI7 (Sus scrofa) Explore I3LSI7 Go to UniProtKB: I3LSI7
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3LSI7
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit F	R [auth 5]	127	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa) Explore A0A4X1VEK9 Go to UniProtKB: A0A4X1VEK9
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UniProt Group	A0A4X1VEK9
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	S [auth 6]	150	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3LCB2 (Sus scrofa) Explore I3LCB2 Go to UniProtKB: I3LCB2
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UniProt Group	I3LCB2
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	T [auth 7]	125	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P60899 (Sus scrofa) Explore P60899 Go to UniProtKB: P60899
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60899
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	U [auth 8]	67	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa) Explore A0A8W4F9W9 Go to UniProtKB: A0A8W4F9W9
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8W4F9W9
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA_pol_L_2 domain-containing protein	V [auth 9]	117	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1RKE4 (Sus scrofa) Explore F1RKE4 Go to UniProtKB: F1RKE4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1RKE4
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
RPB12	W [auth a]	58	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa) Explore A0A4X1TRS6 Go to UniProtKB: A0A4X1TRS6
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UniProt Group	A0A4X1TRS6
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative elongation factor A	AA [auth e]	528	Homo sapiens	Mutation(s): 0 Gene Names: NELFA, WHSC2, P/OKcl.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3P2 (Homo sapiens) Explore Q9H3P2 Go to UniProtKB: Q9H3P2
PHAROS: Q9H3P2 GTEx: ENSG00000185049
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UniProt Group	Q9H3P2
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative elongation factor B	BA [auth f]	580	Homo sapiens	Mutation(s): 0 Gene Names: NELFB, COBRA1, KIAA1182
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WX92 (Homo sapiens) Explore Q8WX92 Go to UniProtKB: Q8WX92
PHAROS: Q8WX92 GTEx: ENSG00000188986
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UniProt Group	Q8WX92
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative elongation factor C/D	CA [auth g]	590	Homo sapiens	Mutation(s): 0 Gene Names: NELFCD, NELFD, TH1, TH1L, HSPC130
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXH7 (Homo sapiens) Explore Q8IXH7 Go to UniProtKB: Q8IXH7
PHAROS: Q8IXH7 GTEx: ENSG00000101158
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UniProt Group	Q8IXH7
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative elongation factor E	DA [auth h]	380	Homo sapiens	Mutation(s): 0 Gene Names: NELFE, RD, RDBP
UniProt & NIH Common Fund Data Resources
Find proteins for P18615 (Homo sapiens) Explore P18615 Go to UniProtKB: P18615
PHAROS: P18615 GTEx: ENSG00000204356
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P18615
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT4	EA [auth i]	121	Homo sapiens	Mutation(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
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UniProt Group	P63272
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT5	FA [auth j]	1,087	Homo sapiens	Mutation(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
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UniProt Group	O00267
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	GA [auth k]	172	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa) Explore A0A4X1VKG7 Go to UniProtKB: A0A4X1VKG7
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UniProt Group	A0A4X1VKG7
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	HA [auth l]	142	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VM56 (Sus scrofa) Explore A0A4X1VM56 Go to UniProtKB: A0A4X1VM56
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UniProt Group	A0A4X1VM56
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 24
non-template DNA	X [auth b]	48	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 25
RNA	Y [auth c]	23	synthetic construct
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Molecule	Chains	Length	Organism
Entity ID: 26
template DNA	Z [auth d]	48	synthetic construct
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain UA [auth a] SDF format, chain TA [auth 8] SDF format, chain SA [auth 7] SDF format, chain RA [auth 7] SDF format, chain QA [auth 3] SDF format, chain PA [auth 2] SDF format, chain OA [auth 1] SDF format, chain NA [auth 1] SDF format, chain JA [auth K] SDF format, chain IA [auth K] MOL2 format, chain UA [auth a] MOL2 format, chain TA [auth 8] MOL2 format, chain SA [auth 7] MOL2 format, chain RA [auth 7] MOL2 format, chain QA [auth 3] MOL2 format, chain PA [auth 2] MOL2 format, chain OA [auth 1] MOL2 format, chain NA [auth 1] MOL2 format, chain JA [auth K] MOL2 format, chain IA [auth K] mmCIF format, chain UA [auth a] mmCIF format, chain TA [auth 8] mmCIF format, chain SA [auth 7] mmCIF format, chain RA [auth 7] mmCIF format, chain QA [auth 3] mmCIF format, chain PA [auth 2] mmCIF format, chain OA [auth 1] mmCIF format, chain NA [auth 1] mmCIF format, chain JA [auth K] mmCIF format, chain IA [auth K]	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		Interactions Focus chain IA [auth K] Focus chain JA [auth K] Focus chain NA [auth 1] Focus chain OA [auth 1] Focus chain PA [auth 2] Focus chain QA [auth 3] Focus chain RA [auth 7] Focus chain SA [auth 7] Focus chain TA [auth 8] Focus chain UA [auth a] Interactions & Density Focus chain IA [auth K] Focus chain JA [auth K] Focus chain NA [auth 1] Focus chain OA [auth 1] Focus chain PA [auth 2] Focus chain QA [auth 3] Focus chain RA [auth 7] Focus chain SA [auth 7] Focus chain TA [auth 8] Focus chain UA [auth a]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain LA [auth Q] SDF format, chain KA [auth Q] MOL2 format, chain LA [auth Q] MOL2 format, chain KA [auth Q] mmCIF format, chain LA [auth Q] mmCIF format, chain KA [auth Q]	KA [auth Q], LA [auth Q]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain KA [auth Q] Focus chain LA [auth Q] Interactions & Density Focus chain KA [auth Q] Focus chain LA [auth Q]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain MA [auth 1] MOL2 format, chain MA [auth 1] mmCIF format, chain MA [auth 1]	MA [auth 1]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain MA [auth 1] Interactions & Density Focus chain MA [auth 1]

Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	the National key R&D program of China(2016YFA0500700)
Other government	China	the National Natural Science Foundation of China(32030055, 31830107, 31821002)
Other government	China	the Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)
Other government	China	Shanghai Municipal Science and Technology Commission(19JC1411500)
Other government	China	the National Ten-Thousand Talent Program
Other government	China	the 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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7YCX | pdb_00007ycx

The structure of INTAC-PEC complex

Literature

Structural basis of INTAC-regulated transcription.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 4

UniProt & NIH Common Fund Data Resources

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Entity ID: 5

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Entity ID: 6

UniProt & NIH Common Fund Data Resources

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Entity ID: 7

UniProt & NIH Common Fund Data Resources

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Entity ID: 8

UniProt & NIH Common Fund Data Resources

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Entity ID: 9

UniProt & NIH Common Fund Data Resources

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Entity ID: 10

Entity ID: 11

UniProt & NIH Common Fund Data Resources

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Entity ID: 12

UniProt & NIH Common Fund Data Resources

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Entity ID: 13

Entity ID: 14

UniProt & NIH Common Fund Data Resources

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Entity ID: 15

UniProt

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Entity ID: 16

UniProt

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Entity ID: 17

UniProt

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Entity ID: 18

UniProt

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Entity ID: 19

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Entity ID: 20

UniProt

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