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- PDB-9lue: Cryo-EM structure of the Nipah G head domain in complex with thre... -

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Basic information

Entry
Database: PDB / ID: 9lue
TitleCryo-EM structure of the Nipah G head domain in complex with three Fabs
Components
  • (NIV LN3D3 Fab ...) x 2
  • (NiV S1E2 Fab ...) x 2
  • (NiV S2B10 Fab ...) x 2
  • Glycoprotein G
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Nipah G protein / Antibodies / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsWang, Y. / Deng, Z. / Zhao, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the Nipah G head domain in complex with three Fabs
Authors: Wang, Y. / Deng, Z. / Zhao, H.
History
DepositionFeb 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Glycoprotein G
L: NIV LN3D3 Fab Light Chain
A: NiV S2B10 Fab Heavy Chain
B: NiV S2B10 Fab Light Chain
C: NiV S1E2 Fab Heavy Chain
D: NiV S1E2 Fab Light Chain
H: NIV LN3D3 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,87012
Polymers123,7637
Non-polymers1,1065
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Antibody , 6 types, 6 molecules LABCDH

#2: Antibody NIV LN3D3 Fab Light Chain


Mass: 11781.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Production host: Homo sapiens (human)
#3: Antibody NiV S2B10 Fab Heavy Chain


Mass: 13474.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Production host: Homo sapiens (human)
#4: Antibody NiV S2B10 Fab Light Chain


Mass: 12196.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Production host: Homo sapiens (human)
#5: Antibody NiV S1E2 Fab Heavy Chain


Mass: 13737.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Production host: Homo sapiens (human)
#6: Antibody NiV S1E2 Fab Light Chain


Mass: 11425.794 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Production host: Homo sapiens (human)
#7: Antibody NIV LN3D3 Fab Heavy Chain


Mass: 13380.813 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesocricetus auratus (golden hamster) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 6 molecules G

#1: Protein Glycoprotein G


Mass: 47766.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Henipavirus nipahense / Production host: Homo sapiens (human) / References: UniProt: Q9IH62
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The quaternary complex of Nipah virus G protein with LN3D3, S2B10, and S1E2 antibody Fab
Type: COMPLEX / Entity ID: #1, #7, #2-#6 / Source: NATURAL
Source (natural)Organism: Henipavirus nipahense
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 145635 / Symmetry type: POINT
RefinementHighest resolution: 3.03 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058916
ELECTRON MICROSCOPYf_angle_d0.7812115
ELECTRON MICROSCOPYf_dihedral_angle_d5.6311222
ELECTRON MICROSCOPYf_chiral_restr0.0511327
ELECTRON MICROSCOPYf_plane_restr0.0081542

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