[English] 日本語
Yorodumi
- EMDB-63395: Cryo-EM structure of the Nipah G head domain in complex with thre... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63395
TitleCryo-EM structure of the Nipah G head domain in complex with three Fabs
Map data
Sample
  • Complex: The quaternary complex of Nipah virus G protein with LN3D3, S2B10, and S1E2 antibody Fab
    • Protein or peptide: Glycoprotein G
    • Protein or peptide: NIV LN3D3 Fab Heavy Chain
    • Protein or peptide: NIV LN3D3 Fab Light Chain
    • Protein or peptide: NiV S2B10 Fab Heavy Chain
    • Protein or peptide: NiV S2B10 Fab Light Chain
    • Protein or peptide: NiV S1E2 Fab Heavy Chain
    • Protein or peptide: NiV S1E2 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNipah G protein / Antibodies / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / exo-alpha-sialidase activity / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / membrane
Similarity search - Function
Haemagglutinin-neuraminidase / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesHenipavirus nipahense / Mesocricetus auratus (golden hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsWang Y / Deng Z / Zhao H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: NPJ Vaccines / Year: 2025
Title: Antigenic landscape of Nipah virus attachment glycoprotein analysis reveals a protective immunodominant epitope across species.
Authors: Dan Zhou / Yong Wang / Yanfeng Yao / Wenhua Kuang / Rao Cheng / Gan Zhang / Hang Liu / Xin Li / Sandra Chiu / Zengqin Deng / Haiyan Zhao /
Abstract: Nipah virus (NiV) and Hendra virus (HeV), two highly pathogenic Henipaviruses (HNVs), pose a significant public health threat. The attachment glycoprotein (G) plays a crucial role in viral attachment ...Nipah virus (NiV) and Hendra virus (HeV), two highly pathogenic Henipaviruses (HNVs), pose a significant public health threat. The attachment glycoprotein (G) plays a crucial role in viral attachment and entry, making it an attractive target for vaccine and therapeutic antibody development. However, the antigenic landscape and neutralization sensitivity of the diverse HNV G proteins remain poorly defined. Here, we systematically characterize 27 monoclonal antibodies (mAbs) elicited by NiV G head (G) nanoparticle-immunized mice. Among these, 25 mAbs exhibit neutralizing activity against two major NiV strains, NiV-Malaysia and NiV-Bangladesh, with five mAbs also cross-inhibiting HeV infection. Notably, mAbs from two distinct groups conferred complete protection to hamsters against lethal NiV-Malaysia challenge. Structural analysis of NiV G in complex with representative Fabs reveals four non-overlapping epitopes, including two novel antigenic sites and one public protective epitope shared across species. MAbs targeting the novel sites bind to the top or side faces of G protein's β-propeller and inhibit viral infection by blocking either receptor engagement or membrane fusion. MAbs recognizing the public epitope block the receptor binding directly. Our study provides a comprehensive antigenic map of the NiV G and offers new insights and opportunities for antibody-based therapies and rational vaccine development.
History
DepositionFeb 8, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_63395.png

Downloads & links

-
Map

FileDownload / File: emd_63395.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.5714711 - 2.2947097
Average (Standard dev.)-0.00013784683 (±0.04203848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_63395_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63395_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The quaternary complex of Nipah virus G protein with LN3D3, S2B10...

EntireName: The quaternary complex of Nipah virus G protein with LN3D3, S2B10, and S1E2 antibody Fab
Components
  • Complex: The quaternary complex of Nipah virus G protein with LN3D3, S2B10, and S1E2 antibody Fab
    • Protein or peptide: Glycoprotein G
    • Protein or peptide: NIV LN3D3 Fab Heavy Chain
    • Protein or peptide: NIV LN3D3 Fab Light Chain
    • Protein or peptide: NiV S2B10 Fab Heavy Chain
    • Protein or peptide: NiV S2B10 Fab Light Chain
    • Protein or peptide: NiV S1E2 Fab Heavy Chain
    • Protein or peptide: NiV S1E2 Fab Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: The quaternary complex of Nipah virus G protein with LN3D3, S2B10...

SupramoleculeName: The quaternary complex of Nipah virus G protein with LN3D3, S2B10, and S1E2 antibody Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #7, #2-#6
Source (natural)Organism: Henipavirus nipahense

-
Macromolecule #1: Glycoprotein G

MacromoleculeName: Glycoprotein G / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Henipavirus nipahense
Molecular weightTheoretical: 47.766324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVSNLVGLPN NICLQKTSNQ ILKPKLISYT LPVVGQSGTC ITDPLLAMDE GYFAYSHLER IGSCSRGVSK QRIIGVGEVL DRGDEVPSL FMTNVWTPPN PNTVYHCSAV YNNEFYYVLC AVSTVGDPIL NSTYWSGSLM MTRLAVKPKS NGGGYNQHQL A LRSIEKGR ...String:
GVSNLVGLPN NICLQKTSNQ ILKPKLISYT LPVVGQSGTC ITDPLLAMDE GYFAYSHLER IGSCSRGVSK QRIIGVGEVL DRGDEVPSL FMTNVWTPPN PNTVYHCSAV YNNEFYYVLC AVSTVGDPIL NSTYWSGSLM MTRLAVKPKS NGGGYNQHQL A LRSIEKGR YDKVMPYGPS GIKQGDTLYF PAVGFLVRTE FKYNDSNCPI TKCQYSKPEN CRLSMGIRPN SHYILRSGLL KY NLSDGEN PKVVFIEISD QRLSIGSPSK IYDSLGQPVF YQASFSWDTM IKFGDVLTVN PLVVNWRNNT VISRPGQSQC PRF NTCPEI CWEGVYNDAF LIDRINWISA GVFLDSNQTA ENPVFTVFKD NEILYRAQLA SEDTNAQKTI TNCFLLKNKI WCIS LVEIY DTGDNVIRPK LFAVKIPEQC T

UniProtKB: Glycoprotein G

-
Macromolecule #2: NIV LN3D3 Fab Light Chain

MacromoleculeName: NIV LN3D3 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 11.781964 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIQMTQSPAT LSVTPGDSVS LSCRASQSIS NNLHWYQQKS HESPRLLIKY ASQSISGIPS RFSGSGSGTD FTLSINNLET EDFGMYFCQ HSDSWPFTFG SGTKLEIK

-
Macromolecule #3: NiV S2B10 Fab Heavy Chain

MacromoleculeName: NiV S2B10 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 13.474939 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QMQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYAWNWIRQ FPRNKLEWMG FITYSGSTSY NPSLKSRISL TRDTSKNQFF LQLSSVTTE DTATYYCARS GANWDWFAYW GQGTLVTVSA

-
Macromolecule #4: NiV S2B10 Fab Light Chain

MacromoleculeName: NiV S2B10 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 12.196509 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPAS LAVSLGQRAT ISCRASESVD NYGNSFMHWY QQKPGQPPKL LIYRASKLES GIPARFSGSG SRTDFTLTIN PVEADDVAT YHCQQSNEDP WTFGGGTKLE IK

-
Macromolecule #5: NiV S1E2 Fab Heavy Chain

MacromoleculeName: NiV S1E2 Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 13.737145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QMQLQESGPG LVKPSQSLSL TCSVTGYSIT SGYYWNWIRQ FSGNKLEWMG YINHDGSKNY NPSLKNRISI TRDTSKNQFF LKLNSVTTE DTATYYCARD YGSYYYPMDY WGQGTSVTVS S

-
Macromolecule #6: NiV S1E2 Fab Light Chain

MacromoleculeName: NiV S1E2 Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 11.425794 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPPI MSASPGEKVT ITCSASSSVT FMHWFQQKPG TSPKLWIFST SNLASGVPAR FSGSGSGTSY SLTISRMEAE DAATYYCQQ RSSYPFTFGS GTKLEIK

-
Macromolecule #7: NIV LN3D3 Fab Heavy Chain

MacromoleculeName: NIV LN3D3 Fab Heavy Chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 13.380813 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVKLEESGPE LVKPGASVKM SCKASGYTFT NYVMHWVKQK PGQGLEWIGY VNPYNDGTQY NEKFRDKATL TSDKSSSTVY MELNSLTSE DSAVYYCTRG DYPYWVFEVW GAGTTVTVSS

-
Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 145635
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more