[English] 日本語
Yorodumi
- EMDB-48601: Structure of the Junin virus glycoprotein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48601
TitleStructure of the Junin virus glycoprotein complex
Map data
Sample
  • Complex: Glycoprotein complex from Junin virus
    • Protein or peptide: JUNV GP1
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: JUNV GP2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION
Keywordsfusogen / glycoprotein / membrane / complex / VIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Arenavirus glycoprotein, zinc binding domain / Arenavirus glycoprotein / Arenavirus glycoprotein
Similarity search - Domain/homology
Pre-glycoprotein polyprotein GP complex
Similarity search - Component
Biological speciesMammarenavirus juninense
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsMann CJ / Abraham J
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP5OD023084 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH grant T32AI700245 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)T32GM144273 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Microbiol / Year: 2025
Title: Molecular organization of the New World arenavirus spike glycoprotein complex.
Authors: Colin J Mann / Pan Yang / Daniel Olal / Xiaoyi Fan / Katherine Nabel Smith / Lars E Clark / Florian Krammer / Yuemin Bian / Jonathan Abraham /
Abstract: Of the multiple arenaviruses that cause haemorrhagic fevers in the Americas, all lack reliable therapeutic options, and only one has a vaccine. The arenavirus glycoprotein complex (GPC) binds ...Of the multiple arenaviruses that cause haemorrhagic fevers in the Americas, all lack reliable therapeutic options, and only one has a vaccine. The arenavirus glycoprotein complex (GPC) binds cellular receptors and mediates pH-dependent fusion of viral and host cell membranes during entry. GPC comprises GP1, GP2 and stable signal peptide (SSP) subunits. SSP remains associated with the mature glycoprotein complex and regulates pH-dependent membrane fusion through an unclear mechanism. We report cryo-EM structures of Junin virus and Machupo virus GPC stabilized in the prefusion conformation using an amino acid substitution in the transmembrane region of SSP at 3.0 Å and 2.9 Å resolution, respectively. Mutational analyses, cell-cell fusion assays and molecular dynamics simulations reveal how contacts in the membrane-proximal and transmembrane regions of GPC regulate pH-dependent membrane fusion. The structures may aid in the design of therapeutic antibody cocktails, small-molecule inhibitors and vaccines against arenaviruses.
History
DepositionJan 10, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48601.png

Downloads & links

-
Map

FileDownload / File: emd_48601.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å		0.83 Å/pix.
x 480 pix.
= 398.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.001710142 - 1.860544
Average (Standard dev.)0.00033752568 (±0.013332623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_48601_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_48601_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Glycoprotein complex from Junin virus

EntireName: Glycoprotein complex from Junin virus
Components
  • Complex: Glycoprotein complex from Junin virus
    • Protein or peptide: JUNV GP1
    • Protein or peptide: Pre-glycoprotein polyprotein GP complex
    • Protein or peptide: JUNV GP2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: ZINC ION

-
Supramolecule #1: Glycoprotein complex from Junin virus

SupramoleculeName: Glycoprotein complex from Junin virus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mammarenavirus juninense / Strain: MC2

-
Macromolecule #1: JUNV GP1

MacromoleculeName: JUNV GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus juninense
Molecular weightTheoretical: 22.311578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EEAFKIGLHT EFQTVSFSMV GLFSNNPHDL PLLCTLNKSH LYIKGGNASF KISFDDIAVL LPEYDVIIQH PADMSWCSKS DDQIWLSQW FMNAVGHDWY LDPPFLCRNR TKTEGFIFQV NTSKTGINEN YAKKFKTGMH HLYREYPDSC LDGKLCLMKA Q PTSWPLQC ...String:
EEAFKIGLHT EFQTVSFSMV GLFSNNPHDL PLLCTLNKSH LYIKGGNASF KISFDDIAVL LPEYDVIIQH PADMSWCSKS DDQIWLSQW FMNAVGHDWY LDPPFLCRNR TKTEGFIFQV NTSKTGINEN YAKKFKTGMH HLYREYPDSC LDGKLCLMKA Q PTSWPLQC PLDHVNTLHF LTRGKNIQLP RRSLK

UniProtKB: Pre-glycoprotein polyprotein GP complex

-
Macromolecule #2: Pre-glycoprotein polyprotein GP complex

MacromoleculeName: Pre-glycoprotein polyprotein GP complex / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus juninense / Strain: MC2
Molecular weightTheoretical: 6.31551 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGQFISFMQE IPTFLQEALN IALVAVSLIA IIAGVVNLYK SGLFQFFVFL ALAGRSCT

UniProtKB: Pre-glycoprotein polyprotein GP complex

-
Macromolecule #3: JUNV GP2

MacromoleculeName: JUNV GP2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mammarenavirus juninense / Strain: MC2
Molecular weightTheoretical: 27.026191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AFFSWSLTDS SGKDTPGGYC LEEWMLVAAK MKCFGNTAVA KCNLNHDSEF CDMLRLFDYN KNAIKTLNDE TKKQVNLMGQ TINALISDN LLMKNKIREL MSVPYCNYTK FWYVNHTLSG QHSLPRCWLI KNNSYLNISD FRNDWILESD FLISEMLSKE Y SDRQGKTP ...String:
AFFSWSLTDS SGKDTPGGYC LEEWMLVAAK MKCFGNTAVA KCNLNHDSEF CDMLRLFDYN KNAIKTLNDE TKKQVNLMGQ TINALISDN LLMKNKIREL MSVPYCNYTK FWYVNHTLSG QHSLPRCWLI KNNSYLNISD FRNDWILESD FLISEMLSKE Y SDRQGKTP LTLVDICFWS TVFFTASLFL HLVGIPTHRH IRGEACPLPH RLNSLGGCRC GKYPNLKKPT VWRRGH

UniProtKB: Pre-glycoprotein polyprotein GP complex

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 7 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
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: FEI FALCON IV (4k x 4k) / Average electron dose: 50.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83055
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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