[English] 日本語
Yorodumi
- PDB-11lp: Mouse monoclonal antibody A11 in complex with rabies virus glycop... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11lp
TitleMouse monoclonal antibody A11 in complex with rabies virus glycoprotein
Components
  • (Monoclonal Antibody A11 ...) x 2
  • (Monoclonal Antibody RVA122 ...) x 2
  • Glycoprotein
KeywordsVIRAL PROTEIN / Rabies / Rabies virus glycoprotein / antibody
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 speciesHomo sapiens (human)
Mus musculus (house mouse)
Lyssavirus rabies
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.92 Å
AuthorsCallaway, H.M. / Zyla, D. / Hastie, K. / Harkins, S. / Kothalawalage, S. / Samarasinghe, S. / Flynn, A. / Hariharan, C. / Yin, J. / Corti, D. ...Callaway, H.M. / Zyla, D. / Hastie, K. / Harkins, S. / Kothalawalage, S. / Samarasinghe, S. / Flynn, A. / Hariharan, C. / Yin, J. / Corti, D. / Bouhry, H. / Dessain, S. / Saphire, E.O.
Funding support United States, 2items
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, H.M. / Zyla, D. / Hastie, K. / Harkins, S. / Kothalawalage, S. / Samarasinghe, S. / Flynn, A. / Hariharan, C. / Yin, J. / Corti, D. / Bouhry, H. / Dessain, S. / Saphire, E.O.
History
DepositionMar 3, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Monoclonal Antibody RVA122 Light Chain
M: Monoclonal Antibody A11 Heavy Chain
G: Monoclonal Antibody RVA122 Heavy Chain
B: Glycoprotein
D: Monoclonal Antibody RVA122 Light Chain
H: Monoclonal Antibody RVA122 Light Chain
C: Glycoprotein
A: Glycoprotein
I: Monoclonal Antibody RVA122 Heavy Chain
E: Monoclonal Antibody RVA122 Heavy Chain
K: Monoclonal Antibody A11 Heavy Chain
O: Monoclonal Antibody A11 Heavy Chain
L: Monoclonal Antibody A11 Light Chain
J: Monoclonal Antibody A11 Light Chain
N: Monoclonal Antibody A11 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)468,39324
Polymers466,40215
Non-polymers1,9919
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Antibody , 4 types, 12 molecules FDHMKOGIELJN

#1: Antibody Monoclonal Antibody RVA122 Light Chain


Mass: 23449.830 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody Monoclonal Antibody A11 Heavy Chain


Mass: 28052.158 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)
#3: Antibody Monoclonal Antibody RVA122 Heavy Chain


Mass: 28196.096 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#5: Antibody Monoclonal Antibody A11 Light Chain


Mass: 23565.166 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)

-
Protein / Sugars , 2 types, 12 molecules BCA

#4: Protein Glycoprotein


Mass: 52204.164 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lyssavirus rabies / Production host: Homo sapiens (human) / References: UniProt: P08667
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex of RABV-G pre-fusion trimers with RVA122 and A11 Fabs
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Lyssavirus rabies
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMSodium chlorideNaCl1
227 mMPotassium ChlorideKCl1
3100 mMSodium PhosphateNa2HPO41
418 mMPotassium PhosphateKH2PO41
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.19_4092model refinement
3EPUimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 770823 / Symmetry type: POINT
RefinementHighest resolution: 2.92 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00219665
ELECTRON MICROSCOPYf_angle_d0.49526685
ELECTRON MICROSCOPYf_dihedral_angle_d4.8252730
ELECTRON MICROSCOPYf_chiral_restr0.0672946
ELECTRON MICROSCOPYf_plane_restr0.0143363

+
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