8TB9

PRC2-J119-450 monomer bound to H1-nucleosome

PDB DOI: https://doi.org/10.2210/pdb8TB9/pdb
EM Map EMD-41146: EMDB EMDataResource
NAKB: 8TB9

Classification: GENE REGULATION
Organism(s): Homo sapiens, synthetic construct, Xenopus laevis
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): No

Deposited: 2023-06-28 Released: 2024-09-25
Deposition Author(s): Sauer, P.V., Cookis, T., Pavlenko, E., Nogales, E., Poepsel, S.
Funding Organization(s): Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Activation of automethylated PRC2 by dimerization on chromatin

Sauer, P.V., Pavlenko, E., Cookis, T., Zirden, L.C., Renn, J., Singhal, A., Hunold, P., Hoehne-Wiechmann, M.N., van Ray, O., Kaschani, F., Kaiser, M., Hansel-Hertsch, R., Sanbonmatsu, K.Y., Nogales, E., Poepsel, S.

(2024) Mol Cell

DOI: https://doi.org/10.1016/j.molcel.2024.08.025

Macromolecule Content

Total Structure Weight: 591.04 kDa
Atom Count: 30,224
Modelled Residue Count: 3,175
Deposited Residue Count: 4,498
Unique protein chains: 11
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H1.0	A	197	Homo sapiens	Mutation(s): 0 Gene Names: H1-0, H1F0, H1FV
UniProt & NIH Common Fund Data Resources
Find proteins for P07305 (Homo sapiens) Explore P07305 Go to UniProtKB: P07305
PHAROS: P07305 GTEx: ENSG00000189060
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07305
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Jumonji	B	334	Homo sapiens	Mutation(s): 0 Gene Names: JARID2, JMJ
UniProt & NIH Common Fund Data Resources
Find proteins for Q92833 (Homo sapiens) Explore Q92833 Go to UniProtKB: Q92833
PHAROS: Q92833 GTEx: ENSG00000008083
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92833
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein SUZ12	C [auth D]	619	Homo sapiens	Mutation(s): 0 Gene Names: SUZ12, CHET9, JJAZ1, KIAA0160
UniProt & NIH Common Fund Data Resources
Find proteins for Q15022 (Homo sapiens) Explore Q15022 Go to UniProtKB: Q15022
PHAROS: Q15022 GTEx: ENSG00000178691
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15022
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase EZH2	D [auth E]	753	Homo sapiens	Mutation(s): 0 Gene Names: EZH2, KMT6 EC: 2.1.1.356
UniProt & NIH Common Fund Data Resources
Find proteins for Q15910 (Homo sapiens) Explore Q15910 Go to UniProtKB: Q15910
PHAROS: Q15910 GTEx: ENSG00000106462
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15910
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein EED	E [auth G]	441	Homo sapiens	Mutation(s): 0 Gene Names: EED
UniProt & NIH Common Fund Data Resources
Find proteins for O75530 (Homo sapiens) Explore O75530 Go to UniProtKB: O75530
PHAROS: O75530 GTEx: ENSG00000074266
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75530
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	G [auth I], O [auth W]	136	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84233
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	H [auth J], P [auth X]	106	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62799
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-binding protein RBBP4	I [auth O]	425	Homo sapiens	Mutation(s): 0 Gene Names: RBBP4, RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens) Explore Q09028 Go to UniProtKB: Q09028
PHAROS: Q09028 GTEx: ENSG00000162521
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09028
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	J [auth R], M [auth U]	133	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06897
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	K [auth S], N [auth V]	123	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02281
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger protein AEBP2	Q [auth Y]	303	Homo sapiens	Mutation(s): 0 Gene Names: AEBP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZN18 (Homo sapiens) Explore Q6ZN18 Go to UniProtKB: Q6ZN18
PHAROS: Q6ZN18 GTEx: ENSG00000139154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6ZN18
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (226-MER)	F [auth H]	215	synthetic construct
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Length	Organism	Image
DNA (226-MER)	L [auth T]	215	synthetic construct
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain R [auth E] MOL2 format, chain R [auth E]	R [auth E]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain R [auth E] Interactions & Density Focus chain R [auth E]