7W5M

Crystal structure of AtNASP in complex of H3 alpha3 helix peptide

PDB DOI: https://doi.org/10.2210/pdb7W5M/pdb

Classification: CHAPERONE
Organism(s): Arabidopsis thaliana, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-30 Released: 2022-05-18
Deposition Author(s): Liu, Y., Bao, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.227
R-Value Work: 0.184
R-Value Observed: 0.186

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis for histone H3 recognition by NASP in Arabidopsis.

Liu, Y., Chen, L., Wang, N., Wu, B., Bao, H., Huang, H.

(2022) J Integr Plant Biol 64: 2309-2313

PubMed: 35587028 Search on PubMed
DOI: https://doi.org/10.1111/jipb.13277
Primary Citation of Related Structures:
7W5M

PubMed Abstract:
The structural basis for histone recognition by the histone chaperone nuclear autoantigenic sperm protein (NASP) remains largely unclear. Here, we showed that Arabidopsis thaliana AtNASP is a monomer and displays robust nucleosome assembly activity in vitro. Examining the structure of AtNASP complexed with a histone H3 α3 peptide revealed a binding mode that is conserved in human NASP. AtNASP recognizes the H3 N-terminal region distinct from human NASP. Moreover, AtNASP forms a co-chaperone complex with ANTI-SILENCING FUNCTION 1 (ASF1) by binding to the H3 N-terminal region. Therefore, we deciphered the structure of AtNASP and the basis of the AtNASP-H3 interaction.

Organizational Affiliation

Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.

Macromolecule Content

Total Structure Weight: 32.72 kDa
Atom Count: 2,006
Modelled Residue Count: 242
Deposited Residue Count: 288
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tetratricopeptide repeat (TPR)-like superfamily protein	A	268	Arabidopsis thaliana	Mutation(s): 0 Gene Names: AP22.13, AP22_13, At4g37210
UniProt
Find proteins for Q94K88 (Arabidopsis thaliana) Explore Q94K88 Go to UniProtKB: Q94K88
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q94K88
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3 alpha3 helix peptide	B	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243 Go to UniProtKB: P84243
PHAROS: P84243 GTEx: ENSG00000132475 ENSG00000163041
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P84243
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B]	F [auth A], G [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]