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- EMDB-65053: Cryo-EM structure of AtNUTECD-SCREW2-AtBAK1ECD complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65053
TitleCryo-EM structure of AtNUTECD-SCREW2-AtBAK1ECD complex
Map data
Sample
  • Complex: AtNUTECD-SCREW2-AtBAK1ECD complex
    • Protein or peptide: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
    • Protein or peptide: AT5G25930 protein
    • Protein or peptide: Transmembrane protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAtNUTECD / AtBAK1ECD / SCREW2 / HORMONE
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 / receptor serine/threonine kinase binding / pattern recognition receptor signaling pathway / defense response to fungus / transmembrane receptor protein tyrosine kinase activity / hormone activity ...regulation of pattern recognition receptor signaling pathway / defense response to oomycetes / plant-type hypersensitive response / brassinosteroid mediated signaling pathway / apoplast / 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 / defense response to bacterium / protein kinase activity / non-specific serine/threonine protein kinase / endosome / endosome membrane / protein heterodimerization activity / receptor ligand activity / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex / extracellular region / 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 / Uncharacterized protein / BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsXu Y / Wei X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of AtNUTECD-SCREW2-AtBAK1ECD complex
Authors: Xu Y / Wei X
History
DepositionJun 16, 2025-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65053.png

Downloads & links

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Map

FileDownload / File: emd_65053.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 240 pix.
= 197.76 Å		0.82 Å/pix.
x 240 pix.
= 197.76 Å		0.82 Å/pix.
x 240 pix.
= 197.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.06456 - 3.5968027
Average (Standard dev.)-0.0010786173 (±0.07959748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 197.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65053_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_65053_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 : AtNUTECD-SCREW2-AtBAK1ECD complex

EntireName: AtNUTECD-SCREW2-AtBAK1ECD complex
Components
  • Complex: AtNUTECD-SCREW2-AtBAK1ECD complex
    • Protein or peptide: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
    • Protein or peptide: AT5G25930 protein
    • Protein or peptide: Transmembrane protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: AtNUTECD-SCREW2-AtBAK1ECD complex

SupramoleculeName: AtNUTECD-SCREW2-AtBAK1ECD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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

MacromoleculeName: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 24.63117 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 GSHHHHHH

UniProtKB: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

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Macromolecule #2: AT5G25930 protein

MacromoleculeName: AT5G25930 protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 93.232539 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTRLPLPFLF FFLTSIPLSV FSQFNDQSTL LNLKRDLGDP PSLRLWNNTS SPCNWSEITC TAGNVTGINF KNQNFTGTVP TTICDLSNL NFLDLSFNYF AGEFPTVLYN CTKLQYLDLS QNLLNGSLPV DIDRLSPELD YLDLAANGFS GDIPKSLGRI S KLKVLNLY ...String:
MTRLPLPFLF FFLTSIPLSV FSQFNDQSTL 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 FPGKILAMIL VIAVLLL TI TLFVTFFVVR DYTRKQRRRG LETWKLTSFH RVDFAESDIV SNLMKHYVIG SGGSGKVYKI FVESSGQCVA VKRIWDSK K LDQKLEKEFI AEVEILGTIR HSNIVKLLCC ISREDSKLLV YEYLEKRSLD QWLHGKKKGG TVEANNLTWS QRLNIAVGA AQGLCYMHHD CTPAIIHRDV KSSNILLDSE FNAKI

UniProtKB: AT5G25930 protein

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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: 7.837335 KDa
SequenceString:
MMKKQLVVVV MLVVMFVVFL DATQVEAMRP FPDPVDEIRL LFQALQRGPV RGSGRNGCTN IPRGSGRCHN

UniProtKB: Uncharacterized protein

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / 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 (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: 1.0 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: AlphaFold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 426131
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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