Macromolecule Content

Total Structure Weight: 265.26 kDa
Atom Count: 14,067
Modelled Residue Count: 1,238
Deposited Residue Count: 1,743
Unique protein chains: 5
Unique nucleic acid chains: 2

8G8B

Nucleosome with human nMatn1 sequence in complex with Human Oct4

PDB DOI: https://doi.org/10.2210/pdb8G8B/pdb
EM Map EMD-29845: EMDB EMDataResource

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

Deposited: 2023-02-17 Released: 2023-03-22
Deposition Author(s): Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Histone modifications regulate pioneer transcription factor cooperativity

Sinha, K.K., Bilokapic, S., Du, Y., Malik, D., Halic, M.

(2023) Nature

DOI: https://doi.org/10.1038/s41586-023-06112-6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	135	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	102	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	C, G	129	Xenopus laevis	Mutation(s): 0 Gene Names: hist1h2aj, h2ac14, LOC494591, XELAEV_18003602mg, h2ac14.L, hist1h2aj.L
UniProt
Find proteins for Q6AZJ8 (Xenopus laevis) Explore Q6AZJ8 Go to UniProtKB: Q6AZJ8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6AZJ8
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	122	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
POU domain, class 5, transcription factor 1	K [auth X]	395	Homo sapiens	Mutation(s): 0 Gene Names: POU5F1, OCT3, OCT4, OTF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q01860 (Homo sapiens) Explore Q01860 Go to UniProtKB: Q01860
PHAROS: Q01860
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q01860
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Length	Organism	Image
nMatn1 DNA (top strand,168-MER)	I	186	Homo sapiens
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Length	Organism	Image
nMatn1 DNA (bottom strand, 168-MER)	J	186	Homo sapiens
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Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM135599-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM141694-01