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- EMDB-36741: Langya Henipavirus attachment protein -

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Basic information

Entry
Database: EMDB / ID: EMD-36741
TitleLangya Henipavirus attachment protein
Map dataThe LayV-G protein map file.
Sample
  • Complex: Homotetramer of Langya virus attachment protein G
    • Protein or peptide: langya virus attachment protein G
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION
KeywordsLangya Henipavirus attachment protein / G protein / homotetramer / Viral surface glycoprotein. / VIRAL PROTEIN
Biological speciesHenipavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsYan RH / Guo YY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A special homotetrameric architecture of langya virus glycoprotein
Authors: Yan RH / Guo YY
History
DepositionJul 5, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36741.png

Downloads & links

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Map

FileDownload / File: emd_36741.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe LayV-G protein map file.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 420.48 Å		1.1 Å/pix.
x 384 pix.
= 420.48 Å		1.1 Å/pix.
x 384 pix.
= 420.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.56306565 - 1.7283171
Average (Standard dev.)-0.0018629739 (±0.04579257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 420.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: focused transmembrane map

Fileemd_36741_additional_1.map
Annotationfocused transmembrane map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36741_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_36741_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 : Homotetramer of Langya virus attachment protein G

EntireName: Homotetramer of Langya virus attachment protein G
Components
  • Complex: Homotetramer of Langya virus attachment protein G
    • Protein or peptide: langya virus attachment protein G
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SODIUM ION

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Supramolecule #1: Homotetramer of Langya virus attachment protein G

SupramoleculeName: Homotetramer of Langya virus attachment protein G / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Henipavirus
Molecular weightTheoretical: 270 kDa/nm

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Macromolecule #1: langya virus attachment protein G

MacromoleculeName: langya virus attachment protein G / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus
Molecular weightTheoretical: 69.064383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATNKRDVIK TTESTREDKV KKFYGVETAE KVADSISSNK VFILMNTLLI LTGAIITITL NVTNLTTIKN QQAMLKIIQD EVNSKLEMF VSLDQLVKGE IKPKVSLINT AVSVSIPGQI SNLQTKFLQK YVYLEESITK QCTCNPLSGI FPTTKPPPPP T DKPDDDTT ...String:
MATNKRDVIK TTESTREDKV KKFYGVETAE KVADSISSNK VFILMNTLLI LTGAIITITL NVTNLTTIKN QQAMLKIIQD EVNSKLEMF VSLDQLVKGE IKPKVSLINT AVSVSIPGQI SNLQTKFLQK YVYLEESITK QCTCNPLSGI FPTTKPPPPP T DKPDDDTT DDDKVDTTIK PVEYYKPDGC NKTNDHFTMQ PGVNFYTVPN LGPSSSSADE CYTNPSFSIG SSIYMFSQEI RK TDCTTGE ILSIQIVLGR IVDKGQQGPQ ASPLLVWSVP NPKIINSCAV AAGDETGWVL CSVTLTAASG EPIPHMFDGF WLY KFEPDT EVVAYRITGF AYLLDKVYDS VFIGKGGGIQ RGNDLYFQMF GLSRNRQSIK ALCEHGSCLG TGGGGYQVLC DRAV MSFGS EESLISNAYL KVNDVASGKP TIISQTFPPS DSYKGSNGRI YTIGERYGIY LAPSSWNRYL RFGLTPDISV RSTTW LKEK DPIMKVLTTC TNTDKDMCPE ICNTRGYQDI FPLSEDSSFY TYIGITPSNE GTKSFVAVKD DAGHVASITI LPNYYS ITS ATISCFMYKE EIWCIAVTEG RKQKENPQRI YAHSYRVQKM CFNIKPASVV TSLPSNVTIR S

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 6
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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