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- PDB-9wum: A ternary complex of NUT with BAK1 and SCREW2 -

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Basic information

Entry
Database: PDB / ID: 9wum
TitleA ternary complex of NUT with BAK1 and SCREW2
Components
  • AT5G25930 protein
  • BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
  • Transmembrane protein
KeywordsPLANT PROTEIN / Complex
Function / homology
Function and homology information


regulation of pattern recognition receptor signaling pathway / defense response to oomycetes / plant-type hypersensitive response / brassinosteroid mediated signaling pathway / apoplast / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / pattern recognition receptor signaling pathway / defense response to fungus / transmembrane receptor protein tyrosine kinase activity ...regulation of pattern recognition receptor signaling pathway / defense response to oomycetes / plant-type hypersensitive response / brassinosteroid mediated signaling pathway / apoplast / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / pattern recognition receptor signaling pathway / defense response to fungus / transmembrane receptor protein tyrosine kinase activity / hormone activity / receptor protein-tyrosine kinase / protein kinase activity / non-specific serine/threonine protein kinase / defense response to bacterium / endosome / endosome membrane / protein heterodimerization activity / receptor ligand activity / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
AT5G25930 protein / Transmembrane protein / BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsBai, Y.F. / Yu, J.F. / Xiao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A ternary complex of NUT with BAK1 and SCREW2
Authors: Bai, Y.F. / Yu, J.F. / Xiao, Y.
History
DepositionSep 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AT5G25930 protein
C: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
B: Transmembrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,46322
Polymers97,4483
Non-polymers5,01619
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein AT5G25930 protein


Mass: 70216.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g25930 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B9DFY2
#2: Protein BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 / AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor ...AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor kinase 3 / AtSERK3 / Somatic embryogenesis receptor-like kinase 3


Mass: 24873.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BAK1, ELG, SERK3, At4g33430, F17M5.190 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q94F62, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#3: Protein/peptide Transmembrane protein


Mass: 2357.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q8L9Z1
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A ternary complex of NUT with BAK1 and SCREW2 / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45725 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036556
ELECTRON MICROSCOPYf_angle_d0.6268914
ELECTRON MICROSCOPYf_dihedral_angle_d7.456965
ELECTRON MICROSCOPYf_chiral_restr0.0511103
ELECTRON MICROSCOPYf_plane_restr0.0061131

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