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- EMDB-66264: A ternary complex of NUT with BAK1 and SCREW2 -

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Basic information

Entry
Database: EMDB / ID: EMD-66264
TitleA ternary complex of NUT with BAK1 and SCREW2
Map data
Sample
  • Complex: A ternary complex of NUT with BAK1 and SCREW2
    • Protein or peptide: AT5G25930 protein
    • Protein or peptide: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
    • Protein or peptide: Transmembrane protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / PLANT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsBai YF / Yu JF / Xiao Y
Funding support China, 1 items
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 YF / Yu JF / Xiao Y
History
DepositionSep 18, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66264.png

Downloads & links

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Map

FileDownload / File: emd_66264.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.166
Minimum - Maximum-0.7432641 - 1.2479858
Average (Standard dev.)0.00082977547 (±0.029654017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66264_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66264_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A ternary complex of NUT with BAK1 and SCREW2

EntireName: A ternary complex of NUT with BAK1 and SCREW2
Components
  • Complex: A ternary complex of NUT with BAK1 and SCREW2
    • Protein or peptide: AT5G25930 protein
    • Protein or peptide: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
    • Protein or peptide: Transmembrane protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: A ternary complex of NUT with BAK1 and SCREW2

SupramoleculeName: A ternary complex of NUT with BAK1 and SCREW2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: AT5G25930 protein

MacromoleculeName: AT5G25930 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 70.2165 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAFKSIAVLS ACIIVGSALP GSQFNDQSTL LNLKRDLGDP PSLRLWNNTS SPCNWSEITC TAGNVTGINF KNQNFTGTVP TTICDLSNL NFLDLSFNYF AGEFPTVLYN CTKLQYLDLS QNLLNGSLPV DIDRLSPELD YLDLAANGFS GDIPKSLGRI S KLKVLNLY ...String:
MAFKSIAVLS ACIIVGSALP GSQFNDQSTL LNLKRDLGDP PSLRLWNNTS SPCNWSEITC TAGNVTGINF KNQNFTGTVP TTICDLSNL NFLDLSFNYF AGEFPTVLYN CTKLQYLDLS QNLLNGSLPV DIDRLSPELD YLDLAANGFS GDIPKSLGRI S KLKVLNLY QSEYDGTFPS EIGDLSELEE LRLALNDKFT PAKIPIEFGK LKKLKYMWLE EMNLIGEISP VVFENMTDLE HV DLSVNNL TGRIPDVLFG LKNLTEFYLF ANGLTGEIPK SISATNLVFL DLSANNLTGS IPVSIGNLTK LQVLNLFNNK LTG EIPPVI GKLPGLKEFK IFNNKLTGEI PAEIGVHSKL ERFEVSENQL TGKLPENLCK GGKLQGVVVY SNNLTGEIPE SLGD CGTLL TVQLQNNDFS GKFPSRIWNA SSMYSLQVSN NSFTGELPEN VAWNMSRIEI DNNRFSGEIP KKIGTWSSLV EFKAG NNQF SGEFPKELTS LSNLISIFLD ENDLTGELPD EIISWKSLIT LSLSKNKLSG EIPRALGLLP RLLNLDLSEN QFSGGI PPE IGSLKLTTFN VSSNRLTGGI PEQLDNLAYE RSFLNNSNLC ADNPVLSLPD CRKQRRGSRG FPGKILEHHH HHH

UniProtKB: AT5G25930 protein

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Macromolecule #2: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

MacromoleculeName: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 24.873441 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MERRLMIPCF FWLILVLDLV LRVSGNAEGD ALSALKNSLA DPNKVLQSWD ATLVTPCTWF HVTCNSDNSV TRVDLGNANL SGQLVMQLG QLPNLQYLEL YSNNITGTIP EQLGNLTELV SLDLYLNNLS GPIPSTLGRL KKLRFLRLNN NSLSGEIPRS L TAVLTLQV ...String:
MERRLMIPCF FWLILVLDLV LRVSGNAEGD ALSALKNSLA DPNKVLQSWD ATLVTPCTWF HVTCNSDNSV TRVDLGNANL SGQLVMQLG QLPNLQYLEL YSNNITGTIP EQLGNLTELV SLDLYLNNLS GPIPSTLGRL KKLRFLRLNN NSLSGEIPRS L TAVLTLQV LDLSNNPLTG DIPVNGSFSL FTPISFANTK LTPLPASPPP PISPTPPSPA GSLEHHHHHH

UniProtKB: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

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Macromolecule #3: Transmembrane protein

MacromoleculeName: Transmembrane protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 2.357619 KDa
SequenceString:
GPVRGSGRNG CTNIPRGSGR CHN

UniProtKB: Transmembrane protein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 45725
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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