9DG3

ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome

PDB DOI: https://doi.org/10.2210/pdb9DG3/pdb
EM Map EMD-46822: EMDB EMDataResource

Classification: NUCLEAR PROTEIN/DNA
Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-09-01 Released: 2024-11-20
Deposition Author(s): Godinez-Lopez, V., Valencia-Sanchez, M.I., Armache, J.P., Armache, K.-J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), The Mark Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

ncPRC1RYBP Delta-linker mutant bound to singly modified H2AK119Ub nucleosome

Godinez-Lopez, V., Valencia-Sanchez, M.I., Armache, K.-J.

To be published.

Macromolecule Content

Total Structure Weight: 258.8 kDa
Atom Count: 12,553
Modelled Residue Count: 1,152
Deposited Residue Count: 1,668
Unique protein chains: 7
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	136	Xenopus laevis	Mutation(s): 1
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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C	130	Xenopus laevis	Mutation(s): 1
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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	D, H	126	Xenopus laevis	Mutation(s): 1
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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	G	130	Xenopus laevis	Mutation(s): 2
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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
RING1 and YY1-binding protein	K [auth M]	228	Homo sapiens	Mutation(s): 0 Gene Names: RYBP, DEDAF, YEAF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N488 (Homo sapiens) Explore Q8N488 Go to UniProtKB: Q8N488
PHAROS: Q8N488 GTEx: ENSG00000163602
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N488
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	L [auth N]	76	Homo sapiens	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG47
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (187-MER)	I	187	synthetic construct
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA (187-MER)	J	187	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain M MOL2 format, chain M mmCIF format, chain M	M	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M Interactions & Density Focus chain M

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-20

Deposition Author(s):

Godinez-Lopez, V.

Valencia-Sanchez, M.I.

Armache, J.P.

Armache, K.-J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM115882
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01CA266978
The Mark Foundation	United States	--