8JG4 | pdb_00008jg4

Crystal Structure of YAF9A YEATS bound to H3K27cr peptide

PDB DOI: https://doi.org/10.2210/pdb8JG4/pdb

Classification: TRANSCRIPTION
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-05-19 Released: 2024-05-22
Deposition Author(s): Li, H.T., Liu, W.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.212 (Depositor), 0.215 (DCC)
R-Value Work:
0.172 (Depositor), 0.175 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8JG4

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

Literature

Crystal Structure of YAF9A YEATS bound to H3K27cr peptide

Li, H.T., Liu, W.Q.

To be published.

Macromolecule Content

Total Structure Weight: 44.23 kDa
Atom Count: 2,739
Modeled Residue Count: 319
Deposited Residue Count: 394
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 14b	A, B	189	Arabidopsis thaliana	Mutation(s): 0 Gene Names: TAF14B, GAS41, YAF9A, At5g45600, K2N11.8
UniProt
Find proteins for Q9FH40 (Arabidopsis thaliana) Explore Q9FH40 Go to UniProtKB: Q9FH40
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9FH40
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	C, D	8	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for P59226 (Arabidopsis thaliana) Explore P59226 Go to UniProtKB: P59226
Entity Groups
UniProt Group	P59226
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCR Query on KCR	C, D	L-PEPTIDE LINKING	C₁₀ H₁₈ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.212 (Depositor), 0.215 (DCC)
R-Value Work: 0.172 (Depositor), 0.175 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.331	α = 90
b = 117.7	β = 90
c = 59.053	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History (Full details and data files)

Version 1.0: 2024-05-22
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.