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- PDB-3jcb: Structure of Simian Immunodeficiency Virus Envelope Spikes bound ... -

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Database: PDB / ID: 3jcb
TitleStructure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5
DescriptorEnvelope glycoprotein gp120
T-cell surface glycoprotein CD4
(Antibody 36D5 ...) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Cryoelectron tomography / immunology / AIDS / HIV / VIRAL PROTEIN-IMMUNE SYSTEM complex
Specimen sourceSimian immunodeficiency virus / virus / SIV / サル免疫不全ウイルス
Homo sapiens / human
MethodElectron microscopy (Cell / Tomography)
AuthorsHu, G. / Liu, J. / Roux, K. / Taylor, K.A.
CitationJ. Virol., 2017, 91

J. Virol., 2017, 91 Yorodumi Papers
Structure of Simian Immunodeficiency Virus Envelope Spikes Bound with CD4 and Monoclonal Antibody 36D5.
Guiqing Hu / Jun Liu / Kenneth H Roux / Kenneth A Taylor

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 25, 2015 / Release: May 10, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 10, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Database referencescitation / em_image_scans_citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
1.2Aug 30, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.title

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Deposited unit
A: Envelope glycoprotein gp120
B: Antibody 36D5 light chain
C: Antibody 36D5 heavy chain
D: T-cell surface glycoprotein CD4
E: Envelope glycoprotein gp120
I: Envelope glycoprotein gp120

Theoretical massNumber of molelcules
Total (without water)217,2416

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: Polypeptide(L)Envelope glycoprotein gp120

Mass: 50130.594 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999
Source: (natural) Simian immunodeficiency virus / virus / サル免疫不全ウイルス
#2: Polypeptide(L)Antibody 36D5 light chain

Mass: 22291.643 Da / Num. of mol.: 1 / Fragment: Fab / Source: (natural) Homo sapiens / human
#3: Polypeptide(L)Antibody 36D5 heavy chain

Mass: 25115.289 Da / Num. of mol.: 1 / Fragment: Fab / Source: (natural) Homo sapiens / human
#4: Polypeptide(L)T-cell surface glycoprotein CD4

Mass: 19442.045 Da / Num. of mol.: 1 / Fragment: UNP residues 26-200 / Source: (natural) Homo sapiens / human / References: UniProt: P01730

Cellular component

Molecular function

Biological process


Experimental details


EM experimentAggregation state: CELL / Reconstruction method: TOMOGRAPHY

Sample preparation

IDNameTypeParent ID
2Simian immunodeficiency virusVIRUS1
1SIV envelope bound to CD4 and monoclonal antibody 36D5COMPLEX0
3T-cell surface glycoprotein CD4PROTEIN1
4monoclonal antibody 36D5PROTEIN1
Details of virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Plunged into liquid ethane.

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300 / Date: Aug 16, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 31000 / Nominal defocus max: 5000 nm / Nominal defocus min: 4000 nm
Specimen holderSpecimen holder model: OTHER / Specimen holder type: unidentified / Tilt angle max: 65 deg. / Tilt angle min: -65 deg.
Image recordingElectron dose: 100 e/Å2 / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)


EM software
SymmetryPoint symmetry: C1
3D reconstructionNumber of particles: 1181 / Nominal pixel size: 5.7 / Actual pixel size: 5.7 / Details: (Subtomogram Averaging--Applied Symmetry: C1) / Symmetry type: POINT
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4NCO
Number of atoms included #LASTProtein: 13909 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 13909

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