9WUM | pdb_00009wum

A ternary complex of NUT with BAK1 and SCREW2

PDB DOI: https://doi.org/10.2210/pdb9WUM/pdb
EM Map EMD-66264: EMDB EMDataResource

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-09-18 Released: 2026-06-03
Deposition Author(s): Bai, Y.F., Yu, J.F., Xiao, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

A ternary complex of NUT with BAK1 and SCREW2

Bai, Y.F., Yu, J.F., Xiao, Y.

To be published.

Macromolecule Content

Total Structure Weight: 102.46 kDa
Atom Count: 6,441
Modeled Residue Count: 793
Deposited Residue Count: 887
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AT5G25930 protein	A	636	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At5g25930
UniProt
Find proteins for B9DFY2 (Arabidopsis thaliana) Explore B9DFY2 Go to UniProtKB: B9DFY2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9DFY2
Glycosylation
Glycosylation Sites: 15	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1	B [auth C]	228	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BAK1, ELG, SERK3, At4g33430, F17M5.190 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q94F62 (Arabidopsis thaliana) Explore Q94F62 Go to UniProtKB: Q94F62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q94F62
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain B [auth C]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein	C [auth B]	23	Arabidopsis thaliana	Mutation(s): 0
UniProt
Find proteins for Q8L9Z1 (Arabidopsis thaliana) Explore Q8L9Z1 Go to UniProtKB: Q8L9Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8L9Z1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth C], T [auth C], U [auth C], V [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]