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- EMDB-71241: High-resolution in situ ANDV single tetramer structure -

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Basic information

Entry
Database: EMDB / ID: EMD-71241
TitleHigh-resolution in situ ANDV single tetramer structure
Map data
Sample
  • Complex: ANDV Gn-Gc heterotetramer in a membrane enviroment
    • Complex: Gn
      • Protein or peptide: Glycoprotein N
    • Complex: Gc
      • Protein or peptide: Glycoprotein C
  • Ligand: water
Keywordshantavirus / ANDV / viral glycoprotein / tetramer / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell surface / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell surface / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / signal transduction / zinc ion binding / membrane
Similarity search - Function
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesOrthohantavirus andesense
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsLuqiang G / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: bioRxiv / Year: 2025
Title: High-resolution in situ structures of hantavirus glycoprotein tetramers.
Authors: Luqiang Guo / Elizabeth McFadden / Megan M Slough / E Taylor Stone / Jacob Berrigan / Eva Mittler / Kiara Hatzakis / Troy Hinkley / Heather S Kain / Zunlong Ke / Nikole L Warner / Jesse H ...Authors: Luqiang Guo / Elizabeth McFadden / Megan M Slough / E Taylor Stone / Jacob Berrigan / Eva Mittler / Kiara Hatzakis / Troy Hinkley / Heather S Kain / Zunlong Ke / Nikole L Warner / Jesse H Erasmus / Kartik Chandran / Jason S McLellan /
Abstract: New World hantaviruses cause severe infections in humans, with case fatality rates approaching 40%. Previous structural studies have advanced our understanding of hantavirus glycoprotein architecture ...New World hantaviruses cause severe infections in humans, with case fatality rates approaching 40%. Previous structural studies have advanced our understanding of hantavirus glycoprotein architecture and function, however, the lack of high-resolution in situ structures of the glycoprotein tetramer and its lattice organization has limited mechanistic insights into viral assembly, entry, and antigenicity. Here, we leveraged a virus-like particle (VLP) system to establish a cryo-electron microscopy workflow for lattice-forming viral glycoproteins. This enabled the determination of a 2.35 Å resolution structure of the membrane-embedded Andes virus (ANDV) glycoprotein tetramer, as well as structures of dimers of tetramers and a complex with antibody ADI-65534. These structures reveal previously uncharacterized features of glycoprotein organization, stability, and pH-sensing. Immunization of mice with self-amplifying replicon RNA (repRNA) encoding ANDV-VLPs elicited high levels of glycoprotein-binding antibodies but equivalent titers of neutralizing antibodies compared to repRNA-encoded native ANDV glycoprotein complex. Collectively, these findings advance our understanding of hantavirus glycoprotein assemblies and their function, laying a foundation for structure-based vaccine design efforts.
History
DepositionJun 13, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71241.png

Downloads & links

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Map

FileDownload / File: emd_71241.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å		0.83 Å/pix.
x 448 pix.
= 372.736 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.06366452 - 0.18976977
Average (Standard dev.)0.0006003547 (±0.0071433163)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 372.73602 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_71241_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_71241_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ANDV Gn-Gc heterotetramer in a membrane enviroment

EntireName: ANDV Gn-Gc heterotetramer in a membrane enviroment
Components
  • Complex: ANDV Gn-Gc heterotetramer in a membrane enviroment
    • Complex: Gn
      • Protein or peptide: Glycoprotein N
    • Complex: Gc
      • Protein or peptide: Glycoprotein C
  • Ligand: water

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Supramolecule #1: ANDV Gn-Gc heterotetramer in a membrane enviroment

SupramoleculeName: ANDV Gn-Gc heterotetramer in a membrane enviroment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Orthohantavirus andesense

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Supramolecule #2: Gn

SupramoleculeName: Gn / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Gn ectodomain and two Gn transmembrane domains
Source (natural)Organism: Orthohantavirus andesense

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Supramolecule #3: Gc

SupramoleculeName: Gc / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 / Details: Gc ectodomain and transmembrane domain
Source (natural)Organism: Orthohantavirus andesense

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Macromolecule #1: Glycoprotein N

MacromoleculeName: Glycoprotein N / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Orthohantavirus andesense
Molecular weightTheoretical: 72.192648 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGWYLVVLG VCYTLTLAMP KTIYELKMEC PHTVGLGQGY IIGSTELGLI SIEAASDIKL ESSCNFDLHT TSMAQKSFTQ VEWRKKSDT TDTTNAASTT FEAQTKTVNL RGTCILAPEL YDTLKKVKKT VLCYDLTCNQ THCQPTVYLI APVLTCMSIR S CMASVFTS ...String:
MEGWYLVVLG VCYTLTLAMP KTIYELKMEC PHTVGLGQGY IIGSTELGLI SIEAASDIKL ESSCNFDLHT TSMAQKSFTQ VEWRKKSDT TDTTNAASTT FEAQTKTVNL RGTCILAPEL YDTLKKVKKT VLCYDLTCNQ THCQPTVYLI APVLTCMSIR S CMASVFTS RIQVIYEKTH CVTGQLIEGQ CFNPAHTLTL SQPAHTYDTV TLPISCFFTP KKSEQLKVIK TFEGILTKTG CT ENALQGY YVCFLGSHSE PLIVPSLEDI RSAEVVSRML VHPRGEDHDA IQNSQSHLRI VGPITAKVPS TSSTDTLKGT AFA GVPMYS SLSTLVRNAD PEFVFSPGIV PESNHSTCDK KTVPITWTGY LPISGEMEKV TGCTVFCTLA GPGASCEAYS ENGI FNISS PTCLVNKVQR FRGSEQKINF ICQRVDQDVV VYCNGQKKVI LTKTLVIGQC IYTFTSLFSL MPDVAHSLAV ELCVP GLHG WATVMLLSTF CFGWVLIPAV TLIILKCLRV LTFSCSHYTN ESKFKFILEK KKIEYQKTMG SMVCDVCHHE CETAKE LES HRQSCINGQC PYCMTITEAT ESALQAHYSI CKLTGRFQEA LKKSLKKPEV KKGCYRTLGV FRYKSRCYVG LVWCLLL TC EIVIWAASA

UniProtKB: Envelopment polyprotein

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Macromolecule #2: Glycoprotein C

MacromoleculeName: Glycoprotein C / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Orthohantavirus andesense
Molecular weightTheoretical: 58.843688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETPLMESGWS DTAHGVGEIP MKTDLELDFS LPSSSSYSYR RKLTNPANKE ESIPFHFQME KQVIHAEIQP LGHWMDATFN IKTAFHCYG ACQKYSYPWQ TSKCFFEKDY QYETGWGCNP GDCPGVGTGC TACGVYLDKL KSVGKAYKII SLKYTRKVCI Q LGTEQTCK ...String:
ETPLMESGWS DTAHGVGEIP MKTDLELDFS LPSSSSYSYR RKLTNPANKE ESIPFHFQME KQVIHAEIQP LGHWMDATFN IKTAFHCYG ACQKYSYPWQ TSKCFFEKDY QYETGWGCNP GDCPGVGTGC TACGVYLDKL KSVGKAYKII SLKYTRKVCI Q LGTEQTCK HIDANDCLVT PSVKVCIVGT VSKLQPSDTL LFLGPLEQGG IILKQWCTTS CAFGDPGDIM STPSGMRCPE HT GSFRKIC GFATTPVCEY QGNTISGYKR MMATKDSFQS FNLTEPHITT NKLEWIDPDG NTRDHVNLVL NRDVSFQDLS DNP CKVDLH TQAIEGAWGS GVGFTLTCTV GLTECPSFMT SIKACDLAMC YGSTVTNLAR GSNTVKVVGK GGHSGSSFKC CHDT DCSSE GLLASAPHLE RVTGFNQIDS DKVYDDGAPP CTFKCWFTKL GEWLLGILNG NWIVVVVLVV ILILSIIMFS VLCPR RGHK KTVGSLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK

UniProtKB: Envelopment polyprotein

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 452 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (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: 2.2 µm / Nominal defocus min: 0.9 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: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 253514
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9p3i:
High-resolution in situ ANDV single tetramer structure

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