[English] 日本語
Yorodumi
- EMDB-75729: Mouse monoclonal antibody A2 in complex with rabies virus glycoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75729
TitleMouse monoclonal antibody A2 in complex with rabies virus glycoprotein
Map dataMouse monoclonal antibody A2 in complex with rabies virus glycoprotein
Sample
  • Complex: Complex of RABV-G pre-fusion trimers with RVA122 and A2 Fabs
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Antibody RVA122 Light Chain
    • Protein or peptide: Antibody A2 Light Chain
    • Protein or peptide: Antibody RVA122 Heavy Chain
    • Protein or peptide: Antibody A2 Heavy Chain
KeywordsRabies / Rabies virus glycoprotein / antibody / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


viral membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane
Similarity search - Function
: / Rhabdovirus glycoprotein G PH domain / : / Rhabdovirus spike glycoprotein G central domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain
Similarity search - Domain/homology
Biological speciesLyssavirus rabies / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsCallaway HM / Zyla D / Hastie K / Harkins S / Kothalawalage S / Samarasinghe S / Flynn A / Hariharan C / Yin J / Corti D ...Callaway HM / Zyla D / Hastie K / Harkins S / Kothalawalage S / Samarasinghe S / Flynn A / Hariharan C / Yin J / Corti D / Bouhry H / Dessain S / Saphire EO
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private United States
Other private United States
CitationJournal: To Be Published
Title: Antigenic landscape of rabies and related lyssaviruses revealed by cryo-EM
Authors: Callaway HM / Zyla D / Hastie K / Harkins S / Kothalawalage S / Samarasinghe S / Flynn A / Hariharan C / Yin J / Corti D / Bouhry H / Dessain S / Saphire EO
History
DepositionFeb 26, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_75729.png

Downloads & links

-
Map

FileDownload / File: emd_75729.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMouse monoclonal antibody A2 in complex with rabies virus glycoprotein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.26099858 - 0.7667023
Average (Standard dev.)0.0010013554 (±0.01873096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map A

Fileemd_75729_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_75729_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of RABV-G pre-fusion trimers with RVA122 and A2 Fabs

EntireName: Complex of RABV-G pre-fusion trimers with RVA122 and A2 Fabs
Components
  • Complex: Complex of RABV-G pre-fusion trimers with RVA122 and A2 Fabs
    • Protein or peptide: Glycoprotein
    • Protein or peptide: Antibody RVA122 Light Chain
    • Protein or peptide: Antibody A2 Light Chain
    • Protein or peptide: Antibody RVA122 Heavy Chain
    • Protein or peptide: Antibody A2 Heavy Chain

-
Supramolecule #1: Complex of RABV-G pre-fusion trimers with RVA122 and A2 Fabs

SupramoleculeName: Complex of RABV-G pre-fusion trimers with RVA122 and A2 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Lyssavirus rabies

-
Macromolecule #1: Glycoprotein

MacromoleculeName: Glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lyssavirus rabies
Molecular weightTheoretical: 52.204164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KFPIYTIPDK LGPWSPIDIH HLSCPNNLVV EDEGCTNLSG FSYMELKVGY ISAIKMNGFT CTGVVTEAET YTNFVGYVTT TFKRKHFRP TPDACRAAYN WKMAGDPRYE ESLHNPYPDY HWLRTVKTTK ESLVIISPSV ADLDPYDRSL HSRVFPGGNC S GVAVSSTY ...String:
KFPIYTIPDK LGPWSPIDIH HLSCPNNLVV EDEGCTNLSG FSYMELKVGY ISAIKMNGFT CTGVVTEAET YTNFVGYVTT TFKRKHFRP TPDACRAAYN WKMAGDPRYE ESLHNPYPDY HWLRTVKTTK ESLVIISPSV ADLDPYDRSL HSRVFPGGNC S GVAVSSTY CSTNHDYTIW MPENPRLGMS CDIFTNSRGK RASKGSETCG FVDERGLYKS LKGACKLKLC GVLGLRLMDG TW VAMQTSN ETKWCPPGQL VNLHDFRSDE IEHLVVEELV KKREECLDAL ESIMTTKSVS FRRLSHLRKL VPGFGKAYTI FNK TLMEAD AHYKSVRTWN EIIPSKGCLR VGGRCHPHVN GVFFNGIILG PDGNVLIPEM QSSLLQQHME LLVSSVIPLM HPLA DPSTV FKNGDEAEDF VEVHLGWSHP QFEKGGGSGG GSGGGSWSHP QFEKGSGSGL NDIFEAQKIE WHE

UniProtKB: Glycoprotein

-
Macromolecule #2: Antibody RVA122 Light Chain

MacromoleculeName: Antibody RVA122 Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.44983 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: QSVLTQSPSA SDTPGQRVTI SCSGSSSNIG SNYVYWYQQF PGTAPKLLIY KSDKRPSGVP DRFSGSTSGT SASLAISGLR SEDEADYYC AAWDNRLSGW LFGGGTKLTV LGTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
QSVLTQSPSA SDTPGQRVTI SCSGSSSNIG SNYVYWYQQF PGTAPKLLIY KSDKRPSGVP DRFSGSTSGT SASLAISGLR SEDEADYYC AAWDNRLSGW LFGGGTKLTV LGTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLRSPV TKSFNRGEC

-
Macromolecule #3: Antibody A2 Light Chain

MacromoleculeName: Antibody A2 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.378893 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: DIVMTQSHKF MSTSVGDRVS ITCKASQDVS TAVAWYQQNP GQSPKLLIYS ASYRYTGVPD RFTGSGSGTD FTFTISSVQT EDLAVYYCQ QHYNTPTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
DIVMTQSHKF MSTSVGDRVS ITCKASQDVS TAVAWYQQNP GQSPKLLIYS ASYRYTGVPD RFTGSGSGTD FTFTISSVQT EDLAVYYCQ QHYNTPTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTH(UNK) GLSSPVTKSF NRGEC

-
Macromolecule #4: Antibody RVA122 Heavy Chain

MacromoleculeName: Antibody RVA122 Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.196096 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: QVHLQESGPG LVKPSETLSL TCTVSGDSMN NFYWGWIRQP AGKGLEWIGY IYYSGTTNYN PSLKSRVTIS IDTSKNQFSL KVNSVTAAD TAVYYCARDS GDYVSYYYYG MDVWGPGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVHLQESGPG LVKPSETLSL TCTVSGDSMN NFYWGWIRQP AGKGLEWIGY IYYSGTTNYN PSLKSRVTIS IDTSKNQFSL KVNSVTAAD TAVYYCARDS GDYVSYYYYG MDVWGPGTTV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDL EVDDDDKAGW SH PQFEKGG GSGGGSGGGS WSHPQFEK

-
Macromolecule #5: Antibody A2 Heavy Chain

MacromoleculeName: Antibody A2 Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 28.263268 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: EVQLQQSGPE LKKPGETVIS CKASGYTFTN YGMNWMKQTP GKGLKWMGWI NTYTGEPTYA DDFKGRFAFS LETSANTAYL QINNLKNED MATYFCTRGD YFGTKYYFDY WGQGTTLTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
EVQLQQSGPE LKKPGETVIS CKASGYTFTN YGMNWMKQTP GKGLKWMGWI NTYTGEPTYA DDFKGRFAFS LETSANTAYL QINNLKNED MATYFCTRGD YFGTKYYFDY WGQGTTLTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDLEVD DDDKAGWSHP QF EKGGGSG GGSGGGSWSH PQFEK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chloride
27.0 mMKClPotassium Chloride
100.0 mMNa2HPO4Sodium Phosphate
18.0 mMKH2PO4Potassium Phosphate
GridModel: C-flat-2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
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: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 484050
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

+
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