8GRM | pdb_00008grm

Cryo-EM structure of PRC1 bound to H2AK119-UbcH5b-Ub nucleosome

PDB DOI: https://doi.org/10.2210/pdb8GRM/pdb
NAKB: 8GRM
EM Map EMD-34207: EMDB EMDataResource

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-02 Released: 2023-04-12
Deposition Author(s): Ai, H.S., Zebin, T., Zhihend, D., Jiakun, T., Liying, Z., Jia-Bin, L., Man, P., Liu, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.05 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

Synthetic E2-Ub-nucleosome conjugates for studying nucleosome ubiquitination.

Ai, H.S., Tong, Z., Deng, Z., Tian, J., Zhang, L., Sun, M., Du, Y., Xu, Z., Shi, Q., Liang, L., Zheng, Q., Li, J.B., Pan, M., Liu, L.

(2023) Chem

DOI: https://doi.org/10.1016/j.chempr.2023.01.012

Macromolecule Content

Total Structure Weight: 225.89 kDa
Atom Count: 15,415
Modeled Residue Count: 1,484
Deposited Residue Count: 1,488
Unique protein chains: 9
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	98	Homo sapiens	Mutation(s): 0 Gene Names: LOC102839401, LOC102825049, LOC102826576
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68431
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	85	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805 Go to UniProtKB: P62805
PHAROS: P62805 GTEx: ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62805
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	109	Homo sapiens	Mutation(s): 0 Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908 Go to UniProtKB: P04908
PHAROS: P04908 GTEx: ENSG00000277075 ENSG00000278463
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04908
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	D	96	Homo sapiens	Mutation(s): 0 Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814 Go to UniProtKB: O60814
PHAROS: O60814 GTEx: ENSG00000197903
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60814
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	H	95	Homo sapiens	Mutation(s): 0 Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814 Go to UniProtKB: O60814
PHAROS: O60814 GTEx: ENSG00000197903
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60814
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
COMMD3 protein	I [auth M]	101	Homo sapiens	Mutation(s): 0 Gene Names: COMMD3
UniProt & NIH Common Fund Data Resources
Find proteins for P35226 (Homo sapiens) Explore P35226 Go to UniProtKB: P35226
PHAROS: P35226 GTEx: ENSG00000168283
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35226
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Ring1B	J [auth N]	101	Homo sapiens	Mutation(s): 0 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q99496 (Homo sapiens) Explore Q99496 Go to UniProtKB: Q99496
PHAROS: Q99496 GTEx: ENSG00000121481
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99496
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	M [auth O]	76	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG47
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
UbcH5b	N [auth P]	146	Homo sapiens	Mutation(s): 0 EC: 2.3.2.24 (UniProt), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens) Explore P62837 Go to UniProtKB: P62837
PHAROS: P62837 GTEx: ENSG00000131508
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62837
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 8
DNA (144-MER)	K [auth I]	144	Homo sapiens
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 9
DNA (145-MER)	L [auth J]	145	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain R [auth N] SDF format, chain Q [auth N] SDF format, chain P [auth M] SDF format, chain O [auth M] MOL2 format, chain R [auth N] MOL2 format, chain Q [auth N] MOL2 format, chain P [auth M] MOL2 format, chain O [auth M] mmCIF format, chain R [auth N] mmCIF format, chain Q [auth N] mmCIF format, chain P [auth M] mmCIF format, chain O [auth M]	O [auth M], P [auth M], Q [auth N], R [auth N]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth N] Focus chain R [auth N] Interactions & Density Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth N] Focus chain R [auth N]