8YJB | pdb_00008yjb

Cryo-EM structure of the human DSS1-INTAC complex

PDB DOI: https://doi.org/10.2210/pdb8YJB/pdb
EM Map EMD-39338: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-03-01 Released: 2025-03-05
Deposition Author(s): Zheng, H., Xu, Y., Cheng, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Stabilization of Integrator/INTAC by the small but versatile DSS1 protein.

Xu, C., Zhou, Q., Zheng, H., Song, A., Zhao, W., Xiong, Y., Huang, Z., Xu, Y., Cheng, J., Chen, F.X.

To be published.

Macromolecule Content

Total Structure Weight: 1,167.34 kDa
Atom Count: 62,555
Modeled Residue Count: 8,285
Deposited Residue Count: 10,446
Unique protein chains: 12

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit DSS1	A [auth 0]	70	Homo sapiens	Mutation(s): 0 Gene Names: SHFM1, DSS1, SHFDG1
UniProt & NIH Common Fund Data Resources
Find proteins for P60896 (Homo sapiens) Explore P60896 Go to UniProtKB: P60896
PHAROS: P60896 GTEx: ENSG00000127922
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60896
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 9	B [auth I]	658	Homo sapiens	Mutation(s): 0 Gene Names: INTS9, RC74
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NV88 (Homo sapiens) Explore Q9NV88 Go to UniProtKB: Q9NV88
PHAROS: Q9NV88 GTEx: ENSG00000104299
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NV88
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 11	C [auth K]	600	Homo sapiens	Mutation(s): 0 Gene Names: INTS11, CPSF3L, RC68 EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TA45 (Homo sapiens) Explore Q5TA45 Go to UniProtKB: Q5TA45
PHAROS: Q5TA45 GTEx: ENSG00000127054
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5TA45
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 2	D [auth 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H0H0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 4	E [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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96HW7
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Reference Sequence

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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
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVH2 (Homo sapiens) Explore Q9NVH2 Go to UniProtKB: Q9NVH2
PHAROS: Q9NVH2 GTEx: ENSG00000143493
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NVH2
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	G [auth P]	589	Homo sapiens	Mutation(s): 0 Gene Names: PPP2R1A
UniProt & NIH Common Fund Data Resources
Find proteins for P30153 (Homo sapiens) Explore P30153 Go to UniProtKB: P30153
PHAROS: P30153 GTEx: ENSG00000105568
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30153
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	H [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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P67775
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 1	I [auth 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N201
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 5	J [auth E]	1,019	Homo sapiens	Mutation(s): 0 Gene Names: INTS5, KIAA1698
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P9B9 (Homo sapiens) Explore Q6P9B9 Go to UniProtKB: Q6P9B9
PHAROS: Q6P9B9 GTEx: ENSG00000185085
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6P9B9
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 6	K [auth F]	887	Homo sapiens	Mutation(s): 0 Gene Names: INTS6, DBI1, DDX26, DDX26A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL03 (Homo sapiens) Explore Q9UL03 Go to UniProtKB: Q9UL03
PHAROS: Q9UL03 GTEx: ENSG00000102786
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UL03
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrator complex subunit 8	L [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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q75QN2
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Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain N [auth K] SDF format, chain M [auth K] MOL2 format, chain N [auth K] MOL2 format, chain M [auth K] mmCIF format, chain N [auth K] mmCIF format, chain M [auth K]	M [auth K], N [auth K]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth K] Focus chain N [auth K] Interactions & Density Focus chain M [auth K] Focus chain N [auth K]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain P [auth Q] SDF format, chain O [auth Q] MOL2 format, chain P [auth Q] MOL2 format, chain O [auth Q] mmCIF format, chain P [auth Q] mmCIF format, chain O [auth Q]	O [auth Q], P [auth Q]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain O [auth Q] Focus chain P [auth Q] Interactions & Density Focus chain O [auth Q] Focus chain P [auth Q]