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- PDB-9nrx: Venezuelan Equine Encephalitis Virus in complex with the single d... -

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Basic information

Entry
Database: PDB / ID: 9nrx
TitleVenezuelan Equine Encephalitis Virus in complex with the single domain antibody V2B3
Components
  • E1 envelope glycoprotein
  • E2 envelope glycoprotein
  • Single domain antibody (nanobody) V2B3
KeywordsViral protein/Immune System / Venezuelan Equine Encephalitis virus / Virus-Like Particle / VIRUS LIKE PARTICLE / single domain antibody / nanobody / Viral protein-Immune System complex
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity ...T=4 icosahedral viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
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 speciesVenezuelan equine encephalitis virus
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsPletnev, S. / Kwong, P.D. / Zhou, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J Virol / Year: 2025
Title: Demonstration of efficacy, cryo-EM-epitope identification, and breadth of two anti-alphavirus bispecific single domain antibodies.
Authors: Christina L Gardner / Sergei Pletnev / Jinny L Liu / George P Anderson / Lisa C Shriver-Lake / Tatsiana Bylund / Courtney Green / Tyler Stephens / Matthew S Sutton / Yaroslav Tsybovsky / ...Authors: Christina L Gardner / Sergei Pletnev / Jinny L Liu / George P Anderson / Lisa C Shriver-Lake / Tatsiana Bylund / Courtney Green / Tyler Stephens / Matthew S Sutton / Yaroslav Tsybovsky / Mario Roederer / Peter D Kwong / Tongqing Zhou / Ellen R Goldman / Crystal W Burke /
Abstract: Venezuelan equine encephalitis virus (VEEV) is an arbovirus that causes a disease in which 4%-14% of individuals can develop neurological symptoms. Prior to 1970, VEEV was developed as a biological ...Venezuelan equine encephalitis virus (VEEV) is an arbovirus that causes a disease in which 4%-14% of individuals can develop neurological symptoms. Prior to 1970, VEEV was developed as a biological threat agent due to its stability and high morbidity when administered by aerosol. Currently, no FDA-licensed vaccines nor therapeutics for VEEV exist. Single-domain antibodies (sdAbs) may provide a therapeutic option due to their small size and ability to bind recessed epitopes not recognized by conventional antibodies. This study identified two bivalent sdAbs that were able to protect mice from a lethal challenge against both epizootic and enzootic subtypes of VEEV. Cryo-EM structures of sdAb-VEEV complexes revealed the sdAbs that comprised the bivalent sdAbs to recognize a mixture of conserved and non-conserved regions of the VEEV envelope proteins. While all three of the cryo-EM-characterized epitopes were unique in terms of their recognized VEEV residues, two sdAbs, V2B3 and V2C3, overlapped sterically, explaining why only their combinations with the non-sterically overlapping sdAb V3A8f, which composed the bivalent sdAbs described here, were so particularly effective. Binding and neutralization studies found that the bivalent sdAbs have the potential to be broad-spectrum anti-alphavirus therapeutics as they cross-neutralize multiple alphaviruses.IMPORTANCEAlphaviruses are no longer geographically constrained to one region of the world but are expanding to be of global concern. In many regions of the world, multiple alphaviruses co-circulate; therefore, having a therapeutic that is pan-alphavirus is important. A cocktail of multiple pan-alphavirus binding/neutralizing antibodies (Abs) may provide optimal coverage against alphaviruses while decreasing the prevalence of viral escape mutants, which could cause the therapeutic to no longer be efficacious. Structures of these Abs, defining their recognition, could assist in identifying optimal combinations. A bivalent pan-alphavirus single-domain antibody could be used in a cocktail with already identified alphavirus IgG antibodies.
History
DepositionMar 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.1Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: E1 envelope glycoprotein
G: E1 envelope glycoprotein
J: E2 envelope glycoprotein
N: E2 envelope glycoprotein
O: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
X: Single domain antibody (nanobody) V2B3
Y: Single domain antibody (nanobody) V2B3
Z: Single domain antibody (nanobody) V2B3
b: E1 envelope glycoprotein
g: E1 envelope glycoprotein
j: E2 envelope glycoprotein
n: E2 envelope glycoprotein
o: E1 envelope glycoprotein
q: E2 envelope glycoprotein
R: E1 envelope glycoprotein
S: E1 envelope glycoprotein
T: E2 envelope glycoprotein
U: E2 envelope glycoprotein
V: E1 envelope glycoprotein
W: E2 envelope glycoprotein
r: E1 envelope glycoprotein
s: E1 envelope glycoprotein
t: E2 envelope glycoprotein
u: E2 envelope glycoprotein
v: E1 envelope glycoprotein
w: E2 envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)1,179,26227
Polymers1,179,26227
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
E1 envelope glycoprotein / Togavirin


Mass: 47952.066 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A0C4MX98
#2: Protein
E2 envelope glycoprotein / Togavirin


Mass: 47113.746 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A0C4MX98
#3: Antibody Single domain antibody (nanobody) V2B3


Mass: 12824.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: venezuelan equine encephalitis virus in complex with single domain antibody V2B3
Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Venezuelan equine encephalitis virus
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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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 defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12480

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cryoSPARC4.4.3CTF correction
7UCSF Chimera1.14model fitting
9cryoSPARC4.4.3initial Euler assignment
10cryoSPARC4.4.3final Euler assignment
11cryoSPARC4.4.3classification
12cryoSPARC4.4.33D reconstruction
13PHENIXdev-5245model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 41401
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2451747 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00473077
ELECTRON MICROSCOPYf_angle_d0.71899495
ELECTRON MICROSCOPYf_dihedral_angle_d5.5269936
ELECTRON MICROSCOPYf_chiral_restr0.04810970
ELECTRON MICROSCOPYf_plane_restr0.00612886

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