9V6R | pdb_00009v6r

Hexameric RVFV GnGc-Fab140 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of the Rift Valley fever virus envelope protein in complex with a potent neutralization antibody.

Zhang, L.Meng, K.Xiang, Y.

(2025) Proc Natl Acad Sci U S A 122: e2514862122-e2514862122

  • DOI: https://doi.org/10.1073/pnas.2514862122
  • Primary Citation of Related Structures:  
    9V6N, 9V6R

  • PubMed Abstract: 

    Entry of Rift Valley fever virus (RVFV) into host cells is mediated by the viral glycoproteins Gn and Gc. Structural details and assembly mechanism of Gn and Gc on the surface of RVFV remain unclear. Here, we stabilized the GnGc with the neutralizing monoclonal antibody RVFV-140 and determined a near-atomic resolution structure of the GnGc hexamer in complex with the fragment antigen binding (Fab) domain of RVFV-140 (Fab140). Our structure showed that RVFV-140 recognizes a ternary epitope and crosslinks two adjacent Gn heads within the hexamer, thus preventing the prefusion to postfusion transition of the glycoproteins. The intraglycoprotein and interglycoprotein interactions within the GnGc hexamer involve van der Waals forces and hydrogen bonds, which are mainly located between Gn heads, and Gn domain C and Gc domain III. Assembly of the GnGc hexamer requires dramatic conformational changes in the loops L231-L244, D280-Q286, Q380-D386, and A427-Y429 of Gn and the hinge region between domains I and II of Gc. The construction of viral capsomeres with the hexameric structure of recombinant GnGc shows that the capsomeres interact primarily through residues 693 to 713 in domain I of Gc. These interactions vary depending on the local environment of each capsomere.


  • Organizational Affiliation
    • Beijing Frontier Research Center for Biological Structure, Center for Infection Biology, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, People's Republic of China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelopment polyprotein1,064Rift Valley fever virusMutation(s): 0 
UniProt
Find proteins for A2T069 (Rift valley fever virus)
Explore A2T069 
Go to UniProtKB:  A2T069
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2T069
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab140 light chain224Homo sapiensMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab140 heavy chain248Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
Y [auth U],
AA [auth a],
BA [auth b],
CA [auth c],
DA [auth d],
Y [auth U],
Z
3N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth A]
FA [auth B]
GA [auth C]
HA [auth H]
IA [auth I]
EA [auth A],
FA [auth B],
GA [auth C],
HA [auth H],
IA [auth I],
JA [auth L],
KA [auth M],
LA [auth P],
MA [auth Q],
NA [auth T],
OA [auth V],
PA [auth Y]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31925023
National Natural Science Foundation of China (NSFC)China21827810
National Natural Science Foundation of China (NSFC)China31861143027

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-24
    Type: Initial release