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- EMDB-64805: Hexameric RVFV GnGc-Fab140 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-64805
TitleHexameric RVFV GnGc-Fab140 complex
Map data
Sample
  • Complex: Hexameric RVFV GnGc-Fab140 complex
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Fab140 light chain
    • Protein or peptide: Fab140 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsRVFV / complex / hexamer / antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell Golgi membrane / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Phlebovirus nonstructural NS-M / M polyprotein precursor, phlebovirus / Phlebovirus nonstructural protein NS-M / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesRift Valley fever virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang L / Meng K / Xiang Y
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925023 China
National Natural Science Foundation of China (NSFC)21827810 China
National Natural Science Foundation of China (NSFC)31861143027 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Cryo-EM structure of the Rift Valley fever virus envelope protein in complex with a potent neutralization antibody.
Authors: Linjing Zhang / Kaiwen Meng / Ye Xiang /
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. ...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.
History
DepositionMay 27, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64805.png

Downloads & links

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Map

FileDownload / File: emd_64805.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 280 pix.
= 307.412 Å		1.1 Å/pix.
x 280 pix.
= 307.412 Å		1.1 Å/pix.
x 280 pix.
= 307.412 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0156
Minimum - Maximum-0.049029354 - 0.10267196
Average (Standard dev.)0.00053494354 (±0.0035139418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 307.41202 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64805_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_64805_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexameric RVFV GnGc-Fab140 complex

EntireName: Hexameric RVFV GnGc-Fab140 complex
Components
  • Complex: Hexameric RVFV GnGc-Fab140 complex
    • Protein or peptide: Envelopment polyprotein
    • Protein or peptide: Fab140 light chain
    • Protein or peptide: Fab140 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Hexameric RVFV GnGc-Fab140 complex

SupramoleculeName: Hexameric RVFV GnGc-Fab140 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Rift Valley fever virus

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Macromolecule #1: Envelopment polyprotein

MacromoleculeName: Envelopment polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Rift Valley fever virus
Molecular weightTheoretical: 116.711328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PHLRNRPGKG HNYIDGMTQE DATCKPVTYA GACSSFDVLL EKGKFPLFQS YAHHRTLLEA VHDTIIAKAD PPSCDLQSAH GNPCMKEKL VMKTHCPNDY QSAHYLNNDG KMASVKCPPK YELTEDCNFC RQMTGASLKK GSYPLQDLFC QSSEDDGSKL K TKMKGVCE ...String:
PHLRNRPGKG HNYIDGMTQE DATCKPVTYA GACSSFDVLL EKGKFPLFQS YAHHRTLLEA VHDTIIAKAD PPSCDLQSAH GNPCMKEKL VMKTHCPNDY QSAHYLNNDG KMASVKCPPK YELTEDCNFC RQMTGASLKK GSYPLQDLFC QSSEDDGSKL K TKMKGVCE VGVQALKKCD GQLSTAHEVV PFAVFKNSKK VYLDKLDLKT EENLLPDSFV CFEHKGQYKG TMDSGQTKRE LK SFDISQC PKIGGHGSKK CTGDAAFCSA YECTAQYANA YCSHANGSGI VQIQVSGVWK KPLCVGYERV VVKRELSAKP IQR VEPCTT CITKCEPHGL VVRSTGFKIS SAVACASGVC VTGSQSPSTE ITLKYPGISQ SSGGDIGVHM AHDDQSVSSK IVAH CPPQD PCLVHGCIVC AHGLINYQCH TALSAFVVVF VFSSIAIICL AVLYRVLKCL KIAPRKVLNP LMWITAFIRW IYKKM VARV ADNINQVNRE IGWMEGGQLV LGNPAPIPRH APIPRYSTYL MLLLIVSYAS ACSELIQASS RITTCSTEGV NTKCRL SGT ALIRAGSVGA EACLMLKGVK EDQTKFLKIK TVSSELSCRE GQSYWTGSFS PKCLSSRRCH LVGECHVNRC LSWRDNE TS AEFSFVGEST TMRENKCFEQ CGGWGCGCFN VNPSCLFVHT YLQSVRKEAL RVFNCIDWVH KLTLEITDFD GSVSTIDL G ASSSRFTNWG SVSLSLDAEG ISGSNSFSFI ESPGKGYAIV DEPFSEIPRQ GFLGEIRCNS ESSVLSAHES CLRAPNLIS YKPMIDQLEC TTNLIDPFVV FERGSLPQTR NDKTFAASKG NRGVQAFSKG SVQADLTLMF DNFEVDFVGA AVSCDAAFLN LTGCYSCNA GARVCLSITS TGTGSLSAHN KDGSLHIVLP SENGTKDQCQ ILHFTVPEVE EEFMYSCDGD ERPLLVKGTL I AIDPFDDR REAGGESTVV NPKSGSWNFF DWFSGLMSWF GGPLKTILLI CLYVALSIGL FFLLIYLGRT GLSKMWLAAT KK ASDYKDH DGDYKDHDID YKDDDDK

UniProtKB: Envelopment polyprotein

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Macromolecule #2: Fab140 light chain

MacromoleculeName: Fab140 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.581969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SGSPGQSITI SCTGTSSDIG AYNFVSWYQQ HPGTAPKLLI YDVTNRPSGV SNRFSGSKSG NTASLTISGL QAEDEANYY CNSYTSSSHV VFGGGTKLTV LLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSALTQPASV SGSPGQSITI SCTGTSSDIG AYNFVSWYQQ HPGTAPKLLI YDVTNRPSGV SNRFSGSKSG NTASLTISGL QAEDEANYY CNSYTSSSHV VFGGGTKLTV LLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECSQ PRFAAA

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Macromolecule #3: Fab140 heavy chain

MacromoleculeName: Fab140 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.554426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STQSTWAGPG LVKPSQTLSL TCTVSGGSVS SGDYYWSWIR QPPGRGLEWI GYISYSGSTY YNPSLESRIT MSGDTSKQQF SLKLSSVTV ADTAVYYCAT NYFHLHDFGD LYWYFDLWGR GTLVTVSSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS ...String:
STQSTWAGPG LVKPSQTLSL TCTVSGGSVS SGDYYWSWIR QPPGRGLEWI GYISYSGSTY YNPSLESRIT MSGDTSKQQF SLKLSSVTV ADTAVYYCAT NYFHLHDFGD LYWYFDLWGR GTLVTVSSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD Y FPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KSCDKGGGGS SA WSHPQFE K

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 12 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 640793
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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