9WV4 | pdb_00009wv4

Crystal structure of human ZMYND8 MYND domain

PDB DOI: https://doi.org/10.2210/pdb9WV4/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-19 Released: 2025-10-08
Deposition Author(s): Srivastava, D.K., Roy, S.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.274 (Depositor), 0.273 (DCC)
R-Value Work:
0.242 (Depositor), 0.243 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The chromatin reader ZMYND8 recruits the NuRD component GATAD2A through its MYND domain to regulate MAPT213 long noncoding RNA transcription.

Srivastava, D.K., Nandi, S., Karmakar, A., Das, C., Roy, S.

(2026) J Biol Chem 302: 111463-111463

PubMed: 41999894 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2026.111463
Primary Citation Related Structures:
9WV4

PubMed Abstract:
The zinc finger MYND-type containing eight protein (ZMYND8) is a chromatin reader that regulates neuronal gene expression by controlling the microtubule-associated protein tau (MAPT) locus. Here, we investigate how ZMYND8 regulates expression of the long non-coding RNA MAPT213 through its interaction with GATA zinc finger domain containing 2A (GATAD2A), a component of the Nucleosome Remodelling and Deacetylase complex. ZMYND8 exhibits opposite regulatory effects on protein-coding MAPT and non-coding MAPT213 transcripts in a manner dependent on its MYND domain, promoting MAPT expression while suppressing MAPT213 levels. Chromatin immunoprecipitation experiments demonstrated that ZMYND8 specifically recruits GATAD2A to the MAPT213 internal regulatory region, establishing a direct link between protein binding and transcriptional control. We determined the crystal structure of the ZMYND8 coiled-coil MYND domain at high resolution, revealing a homodimeric architecture. The MYND domain specifically recognizes GATAD2A through direct interaction with proline-rich motifs in GATAD2A's central region. Structure-function analysis identified critical binding interface residues, while quantitative measurements revealed moderate-affinity interactions enhanced through multivalent binding mechanisms. These findings establish the molecular basis for ZMYND8-mediated recruitment of chromatin remodeling complexes to specific genomic loci and provide a structural framework for understanding transcriptional regulation of MAPT213.

Organizational Affiliation

Structural Biology and Bio-Informatics Division, Council of Scientific & Industrial Research-Indian Institute of Chemical Biology, Kolkata, India.

Macromolecule Content

Total Structure Weight: 60.69 kDa
Atom Count: 4,107
Modeled Residue Count: 451
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYND-type zinc finger-containing chromatin reader ZMYND8	A [auth B], B [auth C], C [auth A], D	126	Homo sapiens	Mutation(s): 0 Gene Names: ZMYND8, KIAA1125, PRKCBP1, RACK7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULU4 (Homo sapiens) Explore Q9ULU4 Go to UniProtKB: Q9ULU4
GTEx: ENSG00000101040
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ULU4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG (Subject of Investigation/LOI) Query on PEG Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain H [auth B] SDF format, chain G [auth B] MOL2 format, chain N [auth D] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] mmCIF format, chain N [auth D] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B]	G [auth B], H [auth B], N [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain N [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain N [auth D]
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth C] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain J [auth C] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain J [auth C] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] J [auth C] K [auth C] L [auth A] E [auth B], F [auth B], J [auth C], K [auth C], L [auth A], M [auth A], O [auth D], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth D] Focus chain P [auth D]