[English] 日本語
Yorodumi
- PDB-9q5v: Structure of the Measles virus Fusion glycoprotein ectodomain in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9q5v
TitleStructure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies mAb77 and Y10F
Components
  • Fusion glycoprotein F0
  • Y10F heavy chain
  • Y10F light chain
  • mAb77 heavy chain
  • mAb77 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / glycoprotein / immune system / measles / high-resolution / ectodomain / fusion / antibody / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesMeasles morbillivirus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsZyla, D. / Niemeyer, G. / Porotto, M. / Saphire, E.O.
Funding support Switzerland, United States, 7items
OrganizationGrant numberCountry
Swiss National Science FoundationP2EZP3_195680 Switzerland
Swiss National Science FoundationP500PB_210992 Switzerland
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS105699 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS091263 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI176833 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R56AI183536-01A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI180456-02 United States
CitationJournal: To Be Published
Title: Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies mAb77 and Y10F
Authors: Zyla, D. / Niemeyer, G. / Porotto, M. / Saphire, E.O.
History
DepositionAug 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
D: Fusion glycoprotein F0
E: Fusion glycoprotein F0
F: Fusion glycoprotein F0
G: Y10F light chain
I: Y10F heavy chain
J: mAb77 light chain
K: mAb77 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,47219
Polymers496,05810
Non-polymers3,4139
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Fusion glycoprotein F0


Mass: 57379.539 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles morbillivirus / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q786F3

-
Antibody , 4 types, 4 molecules GIJK

#2: Antibody Y10F light chain


Mass: 25209.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Y10F heavy chain


Mass: 52295.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody mAb77 light chain


Mass: 23543.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody mAb77 heavy chain


Mass: 50732.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

-
Sugars , 2 types, 9 molecules

#6: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: 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.: 2 / 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

Component
IDNameTypeEntity IDParent-IDSource
1Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies mAb77 and Y10FCOMPLEX#1-#50MULTIPLE SOURCES
2Measles virus Fusion glycoprotein ectodomainCOMPLEX#11RECOMBINANT
3Y10F LCCOMPLEX#21RECOMBINANT
4Y10F HCCOMPLEX#3-#41RECOMBINANT
5Variable region of Fab77COMPLEX#4-#51RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.350 MDaNO
25
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Measles morbillivirus645098Ichinose-B95a
23Mus musculus (house mouse)10090
34Mus musculus (house mouse)10090
45Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Drosophila melanogaster (fruit fly)7227S2
33Cricetulus griseus (Chinese hamster)10029ExpiCHO
44Cricetulus griseus (Chinese hamster)10029ExpiCHO
55Cricetulus griseus (Chinese hamster)10029
Buffer solutionpH: 8 / Details: HEPES 50 mM, pH 8.0, NaCl 150 mM
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 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 magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 8700
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2EPUimage acquisition
4cryoSPARC4.5CTF correction
9PHENIX2.0_rc1model refinement
10cryoSPARC4.5initial Euler assignment
11cryoSPARC4.5final Euler assignment
12cryoSPARC4.5classification
13cryoSPARC4.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4600000
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 221000 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
18UUT

8uut

18UUT1PDBexperimental model
21AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 49.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002314299
ELECTRON MICROSCOPYf_angle_d0.44819431
ELECTRON MICROSCOPYf_chiral_restr0.04362325
ELECTRON MICROSCOPYf_plane_restr0.00312457
ELECTRON MICROSCOPYf_dihedral_angle_d5.59062309

+
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