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- EMDB-38504: Nipah virus fusion glycoprotein in complex with a broadly neutral... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38504
TitleNipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
Map data
Sample
  • Complex: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
    • Complex: Nipah virus fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 5C8 Fab
      • Protein or peptide: 5C8-VL
    • Protein or peptide: 5C8-VH
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHenipavirus / Fusion glycoprotein / Antibody / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHenipavirus nipahense / Macaca (macaques)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsFan PF / Ren Y / Yu CM / Chen W
Funding support China, 1 items
OrganizationGrant numberCountry
Other governmentJCKY2020802B001 China
CitationJournal: To Be Published
Title: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 1D6
Authors: Fan PF / Yu CM / Chen W / Ren Y
History
DepositionDec 30, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_38504.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.032
Minimum - Maximum-0.7906655 - 1.4821433
Average (Standard dev.)-0.00015041539 (±0.025731362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Nipah virus fusion glycoprotein in complex with a broadly neutral...

EntireName: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
Components
  • Complex: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
    • Complex: Nipah virus fusion glycoprotein
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: 5C8 Fab
      • Protein or peptide: 5C8-VL
    • Protein or peptide: 5C8-VH
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Nipah virus fusion glycoprotein in complex with a broadly neutral...

SupramoleculeName: Nipah virus fusion glycoprotein in complex with a broadly neutralizing antibody 5C8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Nipah virus fusion glycoprotein

SupramoleculeName: Nipah virus fusion glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Henipavirus nipahense

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Supramolecule #3: 5C8 Fab

SupramoleculeName: 5C8 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Macaca (macaques)

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 55.073988 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ ...String:
ILHYEKLSKI GLVKGVTRKY KIKSNPLTKD IVIKMIPNVS NMSQCTGSVM ENYKTRLNGI LTPIKGALEI YKNNTHDLVG DVRLAGVIM AGVAIGIATA AQITAGVALY EAMKNADNIN KLKSSIESTN EAVVKLQETA EKTVYVLTAL QDYINTNLVP T IDKISCKQ TELSLDLALS KYLSDLLFVF GPNLQDPVSN SMTIQAISQA FGGNYETLLR TLGYATEDFD DLLESDSITG QI IYVDLSS YYIIVRVYFP ILTEIQQAYI QELLPVSFNN DNSEWISIVP NFILVRNTLI SNIEIGFCLI TKRSVICNQD YAT PMTNNM RECLTGSTEK CPRELVVSSH VPRFALSNGV LFANCISVTC QCQTTGRAIS QSGEQTLLMI DNTTCPTAVL GNVI ISLGK YLGSVNYNSE GIAIGPPVFT DKVDISSQIS SMNQSLQQSK DYIKEAQRLL DGTMKQIEDK IEEILSKIYH IENEI ARIK KLIGEGGSHH HHHH

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: 5C8-VL

MacromoleculeName: 5C8-VL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 14.00351 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQLTQSPSS LSASVGDTVT ITCQASQGIG NNLHWYQQKP GKAPKLLIYR ASSLQSGIPS RFSGSGSGTD YTLTISSLQP EDFAYYCQQ GYSYPFTFGP GTKVDIKRTV AAPSVFIFPP SDEQLKSGTA SV

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Macromolecule #3: 5C8-VH

MacromoleculeName: 5C8-VH / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca (macaques)
Molecular weightTheoretical: 14.331 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG VVKPSETLSL TCAVSGGSIS DSYRWSWIRQ PPGKGLEWIG YIYGSSTSTN YNPSLKSRVT ISKDTSKNQF SLNLSSLTA ADTAVYYCVR VVQYLEWFVD LIEVNWFDVW GPGVLVTVSS A

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / 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

Concentration0.015 mg/mL
BufferpH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 51.91 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 462582
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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