[English] 日本語
Yorodumi
- PDB-9cqb: Antibody 1G8 bound to the central conserved domain of RSV G -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cqb
TitleAntibody 1G8 bound to the central conserved domain of RSV G
Components
  • Fab 1G8 Heavy Chain
  • Fab 1G8 Light Chain
  • Mature secreted glycoprotein G
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / respiratory syncytial virus / G glycoprotein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Translation of respiratory syncytial virus mRNAs / adhesion receptor-mediated virion attachment to host cell / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / plasma membrane
Similarity search - Function
Major surface glycoprotein G / Pneumovirus attachment glycoprotein G
Similarity search - Domain/homology
Major surface glycoprotein G
Similarity search - Component
Biological speciesHomo sapiens (human)
Respiratory syncytial virus A2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJuarez, M.J. / DuBois, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI166066 United States
CitationJournal: Sci Rep / Year: 2025
Title: Structures of respiratory syncytial virus G bound to broadly reactive antibodies provide insights into vaccine design.
Authors: Maria G Juarez / Sara M O'Rourke / John V Dzimianski / Delia Gagnon / Gabriel Penunuri / Vitor H B Serrão / Russell B Corbett-Detig / Lawrence M Kauvar / Rebecca M DuBois /
Abstract: Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in infants and older adults. The attachment glycoprotein (RSV G) binds to the chemokine receptor CX3CR1 ...Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease in infants and older adults. The attachment glycoprotein (RSV G) binds to the chemokine receptor CX3CR1 to promote viral entry and modulate host immunity. Antibodies against RSV G are a known correlate of protection. Previously, several broadly reactive, high-affinity anti-RSV G human monoclonal antibodies were isolated from RSV-exposed individuals and were shown to be protective in vitro and in vivo. Here, we determined the structures of three of these antibodies in complex with RSV G and defined distinct conformational epitopes comprised of highly conserved RSV G residues. Binding competition and structural studies demonstrated that this highly conserved region displays two non-overlapping antigenic sites. Analyses of anti-RSV G antibody sequences reveal that antigenic site flexibility may promote the elicitation of diverse antibody germlines. Together, these findings provide a foundation for next-generation RSV prophylactics, and they expand concepts in vaccine design for the elicitation of germline lineage-diverse, broadly reactive, high-affinity antibodies.
History
DepositionJul 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab 1G8 Light Chain
B: Fab 1G8 Heavy Chain
D: Mature secreted glycoprotein G


Theoretical massNumber of molelcules
Total (without water)57,2753
Polymers57,2753
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-44 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.394, 67.394, 286.346
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Antibody Fab 1G8 Light Chain


Mass: 23567.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 1G8 Heavy Chain


Mass: 27972.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Mature secreted glycoprotein G / Mature sG


Mass: 5735.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03423
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: .15M Sodium Thiocyanate and 16% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→286.35 Å / Num. obs: 27297 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 51.91 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.7
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 1310 / CC1/2: 0.553

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→58.37 Å / SU ML: 0.4537 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.1111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2632 2007 7.38 %
Rwork0.2258 25188 -
obs0.2286 27195 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 0 16 3594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873666
X-RAY DIFFRACTIONf_angle_d1.09054995
X-RAY DIFFRACTIONf_chiral_restr0.0591567
X-RAY DIFFRACTIONf_plane_restr0.0084636
X-RAY DIFFRACTIONf_dihedral_angle_d16.711312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.41981370.36991734X-RAY DIFFRACTION99.68
2.56-2.630.38241360.35061760X-RAY DIFFRACTION99.58
2.63-2.710.33531430.3241773X-RAY DIFFRACTION99.84
2.71-2.80.35571400.32331769X-RAY DIFFRACTION99.74
2.8-2.90.32551380.29761747X-RAY DIFFRACTION99.95
2.9-3.010.35341420.28911774X-RAY DIFFRACTION99.84
3.01-3.150.30871420.26611770X-RAY DIFFRACTION99.95
3.15-3.320.29881420.25731783X-RAY DIFFRACTION100
3.32-3.520.31141420.23651792X-RAY DIFFRACTION100
3.52-3.80.27711440.22961807X-RAY DIFFRACTION100
3.8-4.180.23421450.20481821X-RAY DIFFRACTION100
4.18-4.780.19871440.16891817X-RAY DIFFRACTION100
4.78-6.020.18821470.17861860X-RAY DIFFRACTION100
6.02-58.370.23051650.18261981X-RAY DIFFRACTION100

+
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