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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: To Be Published
Title: Demonstration of in vivo efficacy, epitope identification, and breadth of two anti-alphavirus bispecific single domain antibodies
Authors: Gardner, C.L. / Pletnev, S. / Liu, J.L. / Anderson, G.P. / Shriver-Lake, L.C. / Bylund, T. / Green, C. / Stephens, T. / Sutton, M. / Tsybovsky, Y. / Roederer, M. / Kwong, P.D. / Zhou, T. / ...Authors: Gardner, C.L. / Pletnev, S. / Liu, J.L. / Anderson, G.P. / Shriver-Lake, L.C. / Bylund, T. / Green, C. / Stephens, T. / Sutton, M. / Tsybovsky, Y. / Roederer, M. / Kwong, P.D. / Zhou, T. / Goldman, E.R. / Burke, C.W.
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

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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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