[English] 日本語
Yorodumi
- EMDB-48275: Native tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48275
TitleNative tagless Lassa virus spike complex bound to ARN-75039 at pH 8.0
Map dataRaw map
Sample
  • Complex: Spike complex of Lassa virus bound by 12.1F and ARN-75039
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: Glycoprotein G1
    • Protein or peptide: 12.1F Heavy chain
    • Protein or peptide: 12.1F Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: UNKNOWN LIGAND
  • Ligand: (4S)-3-(4-tert-butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
  • Ligand: water
KeywordsSpike 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 speciesLassa virus Josiah / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsCohen-Dvashi H / Katz M / Diskin R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The pH-induced Conformational Changes and Inhibition Mechanism of the Lassa Virus Spike Complex
Authors: Cohen-Dvashi H / Katz M / Diskin R
History
DepositionDec 11, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_48275.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw map
Voxel sizeX=Y=Z: 0.8242 Å
Density
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.21260443 - 0.4580315
Average (Standard dev.)0.00009475183 (±0.00767006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 296.712 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Spike complex of Lassa virus bound by 12.1F and ARN-75039

EntireName: Spike complex of Lassa virus bound by 12.1F and ARN-75039
Components
  • Complex: Spike complex of Lassa virus bound by 12.1F and ARN-75039
    • Protein or peptide: Glycoprotein G2
    • Protein or peptide: Glycoprotein G1
    • Protein or peptide: 12.1F Heavy chain
    • Protein or peptide: 12.1F Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: UNKNOWN LIGAND
  • Ligand: (4S)-3-(4-tert-butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
  • Ligand: water

-
Supramolecule #1: Spike complex of Lassa virus bound by 12.1F and ARN-75039

SupramoleculeName: Spike complex of Lassa virus bound by 12.1F and ARN-75039
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lassa virus Josiah

-
Macromolecule #1: Glycoprotein G2

MacromoleculeName: Glycoprotein G2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
Molecular weightTheoretical: 26.828064 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRLKAE AQMSIQLINK AVNALINDQ LIMKNHLRDI MGIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE Y MERQGKTP ...String:
GTFTWTLSDS EGKDTPGGYC LTRWMLIEAE LKCFGNTAVA KCNEKHDEEF CDMLRLFDFN KQAIQRLKAE AQMSIQLINK AVNALINDQ LIMKNHLRDI MGIPYCNYSK YWYLNHTTTG RTSLPKCWLV SNGSYLNETH FSDDIEQQAD NMITEMLQKE Y MERQGKTP LGLVDLFVFS TSFYLISIFL HLVKIPTHRH IVGKSCPKPH RLNHMGICSC GLYKQPGVPV KWKR

UniProtKB: Pre-glycoprotein polyprotein GP complex

-
Macromolecule #2: Glycoprotein G1

MacromoleculeName: Glycoprotein G1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lassa virus Josiah
Molecular weightTheoretical: 29.064402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL ...String:
MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKN NSHHYIMVGN ETGLELTLTN TSIINHKFCN LSDAHKKNLY DHALMSIIST FHLSIPNFNQ YEAMSCDFNG G KISVQYNL SHSYAGDAAN HCGTVANGVL QTFMRMAWGG SYIALDSGRG NWDCIMTSYQ YLIIQNTTWE DHCQFSRPSP IG YLGLLSQ RTRDIYISRR LL

UniProtKB: Pre-glycoprotein polyprotein GP complex

-
Macromolecule #3: 12.1F Heavy chain

MacromoleculeName: 12.1F Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.79373 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGAG LLKPSETLSL SCTVDGESFN GFFWTWIRQP PGKGLEWIGE INHLASTGYN PSLKSRVTIS VDTSKNQFSL KLTSVTAAD TAVYYCARGY SYGFAWPNYH YLDVWGKGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLQESGAG LLKPSETLSL SCTVDGESFN GFFWTWIRQP PGKGLEWIGE INHLASTGYN PSLKSRVTIS VDTSKNQFSL KLTSVTAAD TAVYYCARGY SYGFAWPNYH YLDVWGKGTT VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKRVEPKSCD KTHGGDYKDD DD KGTENLY FQ

-
Macromolecule #4: 12.1F Light chain

MacromoleculeName: 12.1F Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.492086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQHKP GQAPRLLIYG ASKRATGIPS RFSGSGSGTD FSLTISSLEP EDFAVYYCQ HRSDWRTTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQHKP GQAPRLLIYG ASKRATGIPS RFSGSGSGTD FSLTISSLEP EDFAVYYCQ HRSDWRTTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Macromolecule #14: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 14 / Number of copies: 2 / Formula: UNX
Molecular weightTheoretical: 54.938 Da
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

-
Macromolecule #15: (4S)-3-(4-tert-butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phen...

MacromoleculeName: (4S)-3-(4-tert-butoxyphenyl)-7-methyl-6-{4-[(propan-2-yl)oxy]phenyl}imidazo[1,2-a]pyridine
type: ligand / ID: 15 / Number of copies: 1 / Formula: A1BK9
Molecular weightTheoretical: 414.539 Da

-
Macromolecule #16: water

MacromoleculeName: water / type: ligand / ID: 16 / Number of copies: 983 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
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: 38.0 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: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: stochastic gradient descent
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 523003
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