[English] 日本語
Yorodumi
- PDB-6w09: Human mAbs broadly protect against infection of arthritiogenic al... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w09
TitleHuman mAbs broadly protect against infection of arthritiogenic alphaviruses by recognizing conserved elements of the MXR8 receptor binding domain
Components
  • E1 glycoprotein
  • E2 glycoprotein
  • E3
  • Fab CHK-265 heavy chain
  • Fab CHK-265 light chain
KeywordsVIRUS/IMMUNE SYSTEM / virus / monoclonal antibody / complex / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis ...T=4 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å
AuthorsMiller, A.S. / Kuhn, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: Human mAbs Broadly Protect against Arthritogenic Alphaviruses by Recognizing Conserved Elements of the Mxra8 Receptor-Binding Site.
Authors: Laura A Powell / Andrew Miller / Julie M Fox / Nurgun Kose / Thomas Klose / Arthur S Kim / Robin Bombardi / Rashika N Tennekoon / A Dharshan de Silva / Robert H Carnahan / Michael S Diamond ...Authors: Laura A Powell / Andrew Miller / Julie M Fox / Nurgun Kose / Thomas Klose / Arthur S Kim / Robin Bombardi / Rashika N Tennekoon / A Dharshan de Silva / Robert H Carnahan / Michael S Diamond / Michael G Rossmann / Richard J Kuhn / James E Crowe /
Abstract: Mosquito inoculation of humans with arthritogenic alphaviruses results in a febrile syndrome characterized by debilitating musculoskeletal pain and arthritis. Despite an expanding global disease ...Mosquito inoculation of humans with arthritogenic alphaviruses results in a febrile syndrome characterized by debilitating musculoskeletal pain and arthritis. Despite an expanding global disease burden, no approved therapies or licensed vaccines exist. Here, we describe human monoclonal antibodies (mAbs) that bind to and neutralize multiple distantly related alphaviruses. These mAbs compete for an antigenic site and prevent attachment to the recently discovered Mxra8 alphavirus receptor. Three cryoelectron microscopy structures of Fab in complex with Ross River (RRV), Mayaro, or chikungunya viruses reveal a conserved footprint of the broadly neutralizing mAb RRV-12 in a region of the E2 glycoprotein B domain. This mAb neutralizes virus in vitro by preventing virus entry and spread and is protective in vivo in mouse models. Thus, the RRV-12 mAb and its defined epitope have potential as a therapeutic agent or target of vaccine design against multiple emerging arthritogenic alphavirus infections.
History
DepositionFeb 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-21496
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-21496
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E1 glycoprotein
B: E1 glycoprotein
C: E1 glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein
G: E2 glycoprotein
H: E2 glycoprotein
I: Fab CHK-265 heavy chain
M: Fab CHK-265 light chain
J: Fab CHK-265 heavy chain
N: Fab CHK-265 light chain
K: Fab CHK-265 heavy chain
O: Fab CHK-265 light chain
L: Fab CHK-265 heavy chain
P: Fab CHK-265 light chain
Q: E3
R: E3
S: E3
T: E3


Theoretical massNumber of molelcules
Total (without water)538,09520
Polymers538,09520
Non-polymers00
Water0
1
A: E1 glycoprotein
B: E1 glycoprotein
C: E1 glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein
G: E2 glycoprotein
H: E2 glycoprotein
I: Fab CHK-265 heavy chain
M: Fab CHK-265 light chain
J: Fab CHK-265 heavy chain
N: Fab CHK-265 light chain
K: Fab CHK-265 heavy chain
O: Fab CHK-265 light chain
L: Fab CHK-265 heavy chain
P: Fab CHK-265 light chain
Q: E3
R: E3
S: E3
T: E3
x 60


Theoretical massNumber of molelcules
Total (without water)32,285,6821200
Polymers32,285,6821200
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: E1 glycoprotein
B: E1 glycoprotein
C: E1 glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein
G: E2 glycoprotein
H: E2 glycoprotein
I: Fab CHK-265 heavy chain
M: Fab CHK-265 light chain
J: Fab CHK-265 heavy chain
N: Fab CHK-265 light chain
K: Fab CHK-265 heavy chain
O: Fab CHK-265 light chain
L: Fab CHK-265 heavy chain
P: Fab CHK-265 light chain
Q: E3
R: E3
S: E3
T: E3
x 5


  • icosahedral pentamer
  • 2.69 MDa, 100 polymers
Theoretical massNumber of molelcules
Total (without water)2,690,473100
Polymers2,690,473100
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: E1 glycoprotein
B: E1 glycoprotein
C: E1 glycoprotein
D: E1 glycoprotein
E: E2 glycoprotein
F: E2 glycoprotein
G: E2 glycoprotein
H: E2 glycoprotein
I: Fab CHK-265 heavy chain
M: Fab CHK-265 light chain
J: Fab CHK-265 heavy chain
N: Fab CHK-265 light chain
K: Fab CHK-265 heavy chain
O: Fab CHK-265 light chain
L: Fab CHK-265 heavy chain
P: Fab CHK-265 light chain
Q: E3
R: E3
S: E3
T: E3
x 6


  • icosahedral 23 hexamer
  • 3.23 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)3,228,568120
Polymers3,228,568120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
E1 glycoprotein


Mass: 42721.230 Da / Num. of mol.: 4 / Fragment: UNP residues 810-1202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 181/25 / Gene: SP, CHIKVgp2 / Cell line (production host): BHK-21 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q88628
#2: Protein
E2 glycoprotein


Mass: 38266.254 Da / Num. of mol.: 4 / Fragment: UNP residues 330-667
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 181/25 / Gene: SP, CHIKVgp2 / Cell line (production host): BHK-21 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q88628
#3: Antibody
Fab CHK-265 heavy chain


Mass: 23743.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody
Fab CHK-265 light chain


Mass: 22888.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Protein
E3


Mass: 6904.067 Da / Num. of mol.: 4 / Fragment: UNP residues 266-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Strain: 181/25 / Gene: SP, CHIKVgp2 / Cell line (production host): BHK-21 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q88628

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Chikungunya virus-Fab complexCOMPLEXall0MULTIPLE SOURCES
2Chikungunya virusChikungunyaVIRUS#1-#2, #51RECOMBINANT
3Fab CHK-265COMPLEX#3-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Chikungunya virus37124181/25
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
12Mesocricetus auratus (golden hamster)10036BHK-21
23Homo sapiens (human)9606
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 85 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 18000 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1Appion2.2particle selection
2Leginonimage acquisition
4CTFFINDCTF correction
7EMfitmodel fitting
9PHENIXmodel refinement
11jsprfinal Euler assignment
13jspr3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10395 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

+
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