5B40 | pdb_00005b40

The nucleosome structure containing H2B-K120 and H4-K31 monoubiquitinations

PDB DOI: https://doi.org/10.2210/pdb5B40/pdb
NAKB: 5B40

Classification: STRUCTURAL PROTEIN/DNA
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): Yes

Deposited: 2016-03-22 Released: 2016-06-22
Deposition Author(s): Machida, S., Sekine, S., Nishiyama, Y., Horikoshi, N., Kurumizaka, H.
Funding Organization(s): MEXT KAKENHI, JSPS KAKENHI

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.33 Å
R-Value Free:
0.263 (Depositor), 0.264 (DCC)
R-Value Work:
0.201 (Depositor), 0.208 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Monoubiquitination of histones H2B and H4 changes the nucleosome stability without affecting the nucleosome structure

Machida, S., Sekine, S., Nishiyama, Y., Horikoshi, N., Kurumizaka, H.

To be published.

Macromolecule Content

Total Structure Weight: 202.03 kDa
Atom Count: 11,817
Modeled Residue Count: 1,031
Deposited Residue Count: 1,306
Unique protein chains: 4
Unique nucleic acid chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	139	Homo sapiens	Mutation(s): 1 Gene Names: HIST2H3A, HIST2H3C, H3F2, H3FM, HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3 Go to UniProtKB: Q71DI3
PHAROS: Q71DI3 GTEx: ENSG00000183598 ENSG00000203811 ENSG00000203852
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q71DI3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	106	Homo sapiens	Mutation(s): 1 Gene Names: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D... HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	C, G	133	Homo sapiens	Mutation(s): 0 Gene Names: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	129	Homo sapiens	Mutation(s): 1 Gene Names: HIST1H2BJ, H2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899 Go to UniProtKB: P06899
PHAROS: P06899 GTEx: ENSG00000124635
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06899
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
DNA (146-MER)	I, J	146	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.33 Å
R-Value Free: 0.263 (Depositor), 0.264 (DCC)
R-Value Work: 0.201 (Depositor), 0.208 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.419	α = 90
b = 100.419	β = 90
c = 186.025	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
MEXT KAKENHI	Japan	25116002
JSPS KAKENHI	Japan	25250023
JSPS KAKENHI	Japan	26890023

Revision History (Full details and data files)

Version 1.0: 2016-06-22
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description