[English] 日本語
Yorodumi
- EMDB-71259: Andes virus glycoprotein tetramer in complex with ADI-65534 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71259
TitleAndes virus glycoprotein tetramer in complex with ADI-65534 Fab
Map data
Sample
  • Complex: In situ Andes virus glycoprotein tetramer bound to ADI-65534 Fab
    • Protein or peptide: ADI-65534 variable heavy chain
    • Protein or peptide: ADI-65534 variable light chain
    • Protein or peptide: Glycoprotein N
    • Protein or peptide: Glycoprotein C
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGn/Gc / tetramer / hantavirus / prefusion / antibody / neutralizing / quaternary epitope / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMcFadden E / Guo L / McLellan JS
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI181977 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142777 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 14, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71259.png

Downloads & links

-
Map

FileDownload / File: emd_71259.map.gz / Format: CCP4 / Size: 385.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 398 pix.
= 331.136 Å		0.83 Å/pix.
x 504 pix.
= 419.328 Å		0.83 Å/pix.
x 504 pix.
= 419.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.8
Minimum - Maximum-0.07211552 - 17.549617999999999
Average (Standard dev.)0.04709617 (±0.5682209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-59-60-11
Dimensions504504398
Spacing504504398
CellA: 419.328 Å / B: 419.328 Å / C: 331.13602 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : In situ Andes virus glycoprotein tetramer bound to ADI-65534 Fab

EntireName: In situ Andes virus glycoprotein tetramer bound to ADI-65534 Fab
Components
  • Complex: In situ Andes virus glycoprotein tetramer bound to ADI-65534 Fab
    • Protein or peptide: ADI-65534 variable heavy chain
    • Protein or peptide: ADI-65534 variable light chain
    • Protein or peptide: Glycoprotein N
    • Protein or peptide: Glycoprotein C
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: In situ Andes virus glycoprotein tetramer bound to ADI-65534 Fab

SupramoleculeName: In situ Andes virus glycoprotein tetramer bound to ADI-65534 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Orthohantavirus andesense

-
Macromolecule #1: ADI-65534 variable heavy chain

MacromoleculeName: ADI-65534 variable heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.043771 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRL SCAASGFEFS SYAMHWVRQA PGKGLEWVAV TWFDVSKKDY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARN LIRYSVSYFP VHGMDVWGQG TTVTVSS

-
Macromolecule #2: ADI-65534 variable light chain

MacromoleculeName: ADI-65534 variable light chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.028531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL HTYGYNVLDW YLQRPGQSPQ LLISLGSYRA SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALHP FTFGGGTKVE IK

-
Macromolecule #3: Glycoprotein N

MacromoleculeName: Glycoprotein N / type: protein_or_peptide / ID: 3 / 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

-
Macromolecule #4: Glycoprotein C

MacromoleculeName: Glycoprotein C / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Orthohantavirus andesense
Molecular weightTheoretical: 66.793562 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 KTVGSGSALP GNPDHREMGE TLPEEVGEYR QPSGGSVPVS PGPPSGLEPT SSSPYGGGSF NSSINNIHEM EIQLKD ALE KNQQWLVYDQ QREVYVKGLL AKIFELEKKT ETAAGGGSHH HHHHHH

UniProtKB: Envelopment polyprotein

-
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 4 / 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

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: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 12483
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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