[English] 日本語
Yorodumi
- EMDB-72283: Structure of the Measles Virus Fusion Glycoprotein Ectodomain in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72283
TitleStructure of the Measles Virus Fusion Glycoprotein Ectodomain in Postfusion Conformation Bound to Neutralizing Antibody H8
Map datasharpened map
Sample
  • Complex: Structure of the Measles Virus Fusion Glycoprotein Ectodomain in Postfusion Conformation Bound to Neutralizing Antibody H8
    • Complex: Measles virus Fusion glycoprotein ectodomain
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: H8 LC
      • Protein or peptide: mAb H8 light chain
    • Complex: H8 HC
      • Protein or peptide: mAb H8 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsZyla D / Niemeyer G / Porotto M / Saphire EO
Funding support Switzerland, United States, 7 items
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 Postfusion Conformation Bound to Neutralizing Antibody H8
Authors: Zyla D / Niemeyer G / Porotto M / Saphire EO
History
DepositionAug 22, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72283.png

Downloads & links

-
Map

FileDownload / File: emd_72283.map.gz / Format: CCP4 / Size: 759.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 584 pix.
= 513.92 Å		0.88 Å/pix.
x 584 pix.
= 513.92 Å		0.88 Å/pix.
x 584 pix.
= 513.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0519
Minimum - Maximum-0.45156863 - 0.7018453
Average (Standard dev.)-0.0000046350538 (±0.0084492685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions584584584
Spacing584584584
CellA=B=C: 513.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72283_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened map

Fileemd_72283_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half 2

Fileemd_72283_half_map_1.map
Annotationhalf 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half 1

Fileemd_72283_half_map_2.map
Annotationhalf 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Structure of the Measles Virus Fusion Glycoprotein Ectodomain in ...

EntireName: Structure of the Measles Virus Fusion Glycoprotein Ectodomain in Postfusion Conformation Bound to Neutralizing Antibody H8
Components
  • Complex: Structure of the Measles Virus Fusion Glycoprotein Ectodomain in Postfusion Conformation Bound to Neutralizing Antibody H8
    • Complex: Measles virus Fusion glycoprotein ectodomain
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: H8 LC
      • Protein or peptide: mAb H8 light chain
    • Complex: H8 HC
      • Protein or peptide: mAb H8 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Structure of the Measles Virus Fusion Glycoprotein Ectodomain in ...

SupramoleculeName: Structure of the Measles Virus Fusion Glycoprotein Ectodomain in Postfusion Conformation Bound to Neutralizing Antibody H8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 350 KDa

-
Supramolecule #2: Measles virus Fusion glycoprotein ectodomain

SupramoleculeName: Measles virus Fusion glycoprotein ectodomain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a

-
Supramolecule #3: H8 LC

SupramoleculeName: H8 LC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

-
Supramolecule #4: H8 HC

SupramoleculeName: H8 HC / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Measles morbillivirus
Molecular weightTheoretical: 57.379539 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRR HKRFAGVVLA GAALGVATAA QITAGIALHQ SMLNSQAIDN LRASLETTNQ A IEAIRQAG ...String:
MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRR HKRFAGVVLA GAALGVATAA QITAGIALHQ SMLNSQAIDN LRASLETTNQ A IEAIRQAG QGMILAVQGV QDYINNELIP SMNQLSCDLI GQKLGLKLLR YYTEILSLFG PSLRDPISAE ISIQALSYAL GG DINKVLE KLGYSGGDLL GILESRGIKA RITHVDTESY FIVLSIAYPT LSEIKGVIVH RLEGVSYNIG SQEWYTTVPK YVA TQGYLI SNFDESSCTF MPEGTVCSQN ALYPMSPLLQ ECLRGSTKSC ARTLVSGSFG NRFILSQGNL IANCASILCK CYTT GTIIN QDPDKILTYI AADHCPVVEV NGVTIQVGSR RYPDAVYLHR IDLGPPISLG RLDVGTNLGN AIAKLEDAKE LLESS DQIL RSMKGLSSTS IGVDDDDKAG WSHPQFEKGG GSGGGSGGGS WSHPQFEK

UniProtKB: Fusion glycoprotein F0

-
Macromolecule #2: mAb H8 heavy chain

MacromoleculeName: mAb H8 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 51.896449 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSQ VQLQQSGAEL VRPGTSVKIS CKASGYTFIN YWLGWVKQRP GHGLEWIGDI YPGGGHTKYN EKFKGKATL TADTSSSTAY MQLSSLTSED SAVFFCARSG VGSSYYYWGQ GTTLTVSSAS TKGPSVFPLA PSSKSTSGGT A ALGCLVKD ...String:
MGWSCIILFL VATATGVHSQ VQLQQSGAEL VRPGTSVKIS CKASGYTFIN YWLGWVKQRP GHGLEWIGDI YPGGGHTKYN EKFKGKATL TADTSSSTAY MQLSSLTSED SAVFFCARSG VGSSYYYWGQ GTTLTVSSAS TKGPSVFPLA PSSKSTSGGT A ALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SC DKGLEVL FQGPTHTCPP CPAPELLGGP SVFLFPPKPK DTLMISRTPE VTCVVVDVSH EDPEVKFNWY VDGVEVHNAK TKP REEQYN STYRVVSVLT VLHQDWLNGK EYKCKVSNKA LPAPIEKTIS KAKGQPREPQ VYTLPPSRDE LTKNQVSLTC LVKG FYPSD IAVEWESNGQ PENNYKTTPP VLDSDGSFFL YSKLTVDKSR WQQGNVFSCS VMHEALHNHY TQKSLSLSPG K

-
Macromolecule #3: mAb H8 light chain

MacromoleculeName: mAb H8 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.641641 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSD IVLTQSPASL AVSLGQRATI SCRASKSVSS SGYSFLHWYQ QKPGQPPKLL IYLASNLDSG VPARFSGSG SGTDFTLNIH PVEEEDATTY YCQHSWELPT FGGGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV ...String:
MGWSCIILFL VATATGVHSD IVLTQSPASL AVSLGQRATI SCRASKSVSS SGYSFLHWYQ QKPGQPPKLL IYLASNLDSG VPARFSGSG SGTDFTLNIH PVEEEDATTY YCQHSWELPT FGGGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 8 / Details: HEPES 50 mM, pH 8.0, NaCl 150 mM
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 3 / Number real images: 7700 / Average exposure time: 2.0 sec. / Average electron dose: 70.0 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: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4600000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 312000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

8utf

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9q71:
Structure of the Measles Virus Fusion Glycoprotein Ectodomain in Postfusion Conformation Bound to Neutralizing Antibody H8

+
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