[English] 日本語
Yorodumi
- EMDB-48331: Structure of the Respiratory Syncytial Virus Fusion Protein Bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48331
TitleStructure of the Respiratory Syncytial Virus Fusion Protein Bound to Human Antibodies RSV_2245 and RSV_3301
Map dataDeepEMhancer sharpened map. Used for some refinement and model building
Sample
  • Complex: Complex of trimeric fusion protein bound 1:1 to 2245 Fab VH/VL and 3301 Fab VH/VL
    • Protein or peptide: Fusion glycoprotein F2
    • Protein or peptide: Fusion glycoprotein F1
    • Protein or peptide: 2245 Fab Heavy Chain
    • Protein or peptide: 2245 Fab Light Chain
    • Protein or peptide: 3301 Fab Heavy Chain
    • Protein or peptide: 3301 Fab Light Chain
Keywordsfusion protein / trimer / antibody / complex / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHomo sapiens (human) / Respiratory syncytial virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJohnson NV / McLellan JS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Generation of antigen-specific paired heavy-light chain antibody sequences using large language models
Authors: Wasdin PT / Johnson NV / Janke AK / Held S / Marinov TM / Jordaan G / Vandenabeele L / Pantouli F / Gillespie RA / Vukovich MJ / Holt CM / Kim JR / Hansman G / Logue J / Chu HY / Andrews SF ...Authors: Wasdin PT / Johnson NV / Janke AK / Held S / Marinov TM / Jordaan G / Vandenabeele L / Pantouli F / Gillespie RA / Vukovich MJ / Holt CM / Kim JR / Hansman G / Logue J / Chu HY / Andrews SF / Kanekiyo M / Sautto G / Ross T / Sheward DJ / McLellan JS / Abu-Shmais AA / Georgiev IS
History
DepositionDec 17, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48331.png

Downloads & links

-
Map

FileDownload / File: emd_48331.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map. Used for some refinement and model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 358.272 Å		0.93 Å/pix.
x 384 pix.
= 358.272 Å		0.93 Å/pix.
x 384 pix.
= 358.272 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.933 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.0018145235 - 2.1063974
Average (Standard dev.)0.0011516755 (±0.023689535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 358.272 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Sharpened map. Used for some refinement and model building

Fileemd_48331_additional_1.map
AnnotationSharpened map. Used for some refinement and model building
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_48331_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_48331_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of trimeric fusion protein bound 1:1 to 2245 Fab VH/VL an...

EntireName: Complex of trimeric fusion protein bound 1:1 to 2245 Fab VH/VL and 3301 Fab VH/VL
Components
  • Complex: Complex of trimeric fusion protein bound 1:1 to 2245 Fab VH/VL and 3301 Fab VH/VL
    • Protein or peptide: Fusion glycoprotein F2
    • Protein or peptide: Fusion glycoprotein F1
    • Protein or peptide: 2245 Fab Heavy Chain
    • Protein or peptide: 2245 Fab Light Chain
    • Protein or peptide: 3301 Fab Heavy Chain
    • Protein or peptide: 3301 Fab Light Chain

-
Supramolecule #1: Complex of trimeric fusion protein bound 1:1 to 2245 Fab VH/VL an...

SupramoleculeName: Complex of trimeric fusion protein bound 1:1 to 2245 Fab VH/VL and 3301 Fab VH/VL
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Fusion glycoprotein F2

MacromoleculeName: Fusion glycoprotein F2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus
Molecular weightTheoretical: 7.913058 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
NITEEFYQST CSAVSKGYLS ALRTGWYTSV ITIELSNIKE IKCNGTDAKV KLIKQELDKY KNAVTELQLL

UniProtKB: Fusion glycoprotein F0

-
Macromolecule #2: Fusion glycoprotein F1

MacromoleculeName: Fusion glycoprotein F1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus
Molecular weightTheoretical: 40.693469 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FLGFLLGVGS AIASGVAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI VNKQSCSIPN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMSIIKEE V LAYVVQLP ...String:
FLGFLLGVGS AIASGVAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI VNKQSCSIPN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMSIIKEE V LAYVVQLP LYGVIDTPCW KLHTSPLCTT NTKEGSNICL TRTDRGWYCD NAGSVSFFPQ AETCKVQSNR VFCDTMNSLT LP SEVNLCN VDIFNPKYDC KIMTSKTDVS SSVITSLGAI VSCYGKTKCT ASNKNRGIIK TFSNGCDYVS NKGVDTVSVG NTL YYVNKQ EGKSLYVKGE PIINFYDPLV FPSDEFDASI SQVNEKINQS LAFI

UniProtKB: Fusion glycoprotein F0

-
Macromolecule #3: 2245 Fab Heavy Chain

MacromoleculeName: 2245 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.915721 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYSFS SFGVSWVRQA PGQGLEWLGW ISAYNGNTDY AQKVQGRLTM TTDTSTNTAY MELRNLRSD DTAVYYCARD PPASAAAMFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYSFS SFGVSWVRQA PGQGLEWLGW ISAYNGNTDY AQKVQGRLTM TTDTSTNTAY MELRNLRSD DTAVYYCARD PPASAAAMFD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDK

-
Macromolecule #4: 2245 Fab Light Chain

MacromoleculeName: 2245 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.06575 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVVMTQSPLS LPVTLGQPAS ISCRSSQSLV YSDGDTYLSW FQQRPGQSPR RLIYKVSNRD SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQGTHW PPAFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DVVMTQSPLS LPVTLGQPAS ISCRSSQSLV YSDGDTYLSW FQQRPGQSPR RLIYKVSNRD SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQGTHW PPAFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

-
Macromolecule #5: 3301 Fab Heavy Chain

MacromoleculeName: 3301 Fab Heavy Chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.90092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGPT LVKPTQTLTL TCSFSGFSLS TRGVGVGWVR QPPGKALECL GFTYWDGDEY YSPSLRNRVT ISKDTSKNQV VLTLTNMDP VDTATYFCVH SDLYDRGGYY LYYFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLVESGPT LVKPTQTLTL TCSFSGFSLS TRGVGVGWVR QPPGKALECL GFTYWDGDEY YSPSLRNRVT ISKDTSKNQV VLTLTNMDP VDTATYFCVH SDLYDRGGYY LYYFDYWGQG TLVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEPKS CDK

-
Macromolecule #6: 3301 Fab Light Chain

MacromoleculeName: 3301 Fab Light Chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.46098 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIRVTQSPSS LSASVGDRVT ITCRASQTIA SYVNWYQQKP GRAPELLIYA ASILQSGVPS RFSGRGSGTD FTLTINGLQP EDFATYYCQ QSYSSPWTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIRVTQSPSS LSASVGDRVT ITCRASQTIA SYVNWYQQKP GRAPELLIYA ASILQSGVPS RFSGRGSGTD FTLTINGLQP EDFATYYCQ QSYSSPWTFG QGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140634
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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