7YBF

Crystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B

PDB DOI: https://doi.org/10.2210/pdb7YBF/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Schizosaccharomyces pombe
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-06-29 Released: 2024-01-03
Deposition Author(s): Sun, W., Hu, C., Chen, Y.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.248
R-Value Work: 0.198
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of inner membrane protein Sad1 in complex with histone H2A-H2B

Sun, W., Hu, C., Ye, X., Li, X., Chen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 43.44 kDa
Atom Count: 2,951
Modelled Residue Count: 368
Deposited Residue Count: 395
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B-alpha,Histone H2A-beta	A, B	189	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: htb1, SPCC622.09, hta2, SPAC19G12.06c
UniProt
Find proteins for P04910 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P04910 Go to UniProtKB: P04910
Find proteins for P04913 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P04913 Go to UniProtKB: P04913
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P04913P04910
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spindle pole body-associated protein sad1	C	17	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: sad1, SPBC12D12.01, SPBC16H5.01c
UniProt
Find proteins for Q09825 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q09825 Go to UniProtKB: Q09825
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q09825
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.248
R-Value Work: 0.198
R-Value Observed: 0.203
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.804	α = 90
b = 61.981	β = 101.89
c = 76.016	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-01-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB37010303

Revision History (Full details and data files)

Version 1.0: 2024-01-03
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.