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

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Basic information

Entry
Database: PDB / ID: 3jcc
TitleStructure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5
DescriptorEnvelope glycoprotein gp120
Antibody 36D5 light chain
Antibody 36D5 heavy chain
T-cell surface glycoprotein CD4
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 / human / Human
MethodElectron microscopy (Tomography / Vitreous ice (cryo EM))
AuthorsHu, G. / Liu, J. / Roux, K. / Taylor, K.A.
CitationTo be Published

To be Published Search PubMed
Structure of Simian Immunodeficiency Virus Envelope Spikes bound with CD4 and Monoclonal Antibody 36D5
Hu, G. / Liu, J. / Roux, K.H. / Taylor, K.A.

DateDeposition: Nov 25, 2015 / Release: May 10, 2017

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Assembly

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
Polyers217,2416
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)8460
ΔGint (kcal/M)-46
Surface area (A2)97120

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Components

#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 / T-cell surface antigen T4/Leu-3


Mass: 19442.045 Da / Num. of mol.: 1 / Fragment: UNP residues 26-200 / Source: (natural) Homo sapiens / human / References: UniProt: P01730
Sequence detailsENVELOPE GLYCOPROTEIN WAS FROM SIMIAN IMMUNODEFICIENCY VIRUS, BUT THE MODELED SEQUENCE IS FROM HIV-1.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: TOMOGRAPHY / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: SIV envelope spike bound to CD4 and monoclonal antibody 36d5 in the open state
Aggregation state: PARTICLE
Composition: gp120 trimer bound to CD4 and 36D5 in the open state
Number of components: 3
Component
IDNameTypeAssembly id
2Simian immunodeficiency virusVIRUS1
1SIV envelope spike bound to CD4 and monoclonal antibody 36d5 in the open stateCOMPLEX1
3T-cell surface glycoprotein CD4PROTEIN1
4monoclonal antibody 36D5PROTEIN1
Details of the virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus host species: Cercopithecidae / Virus isolate: STRAIN / Virus type: VIRION
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: Plunged into liquid ethane.

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Electron microscopy imaging

MicroscopyMicroscope model: FEI POLARA 300 / Date: Aug 16, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 e/A2 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 31000 X / 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.
CameraType: TVIPS TEMCAM-F415 (4k x 4k)

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Processing

Image selectionNumber of particles: 1796
EM single particle entitySymmetry type: ASYMMETRIC
3D reconstructionNumber of particles: 1796 / Nominal pixel size: 5.7 A/pix / Actual pixel size: 5.7 A/pix / Details: (Subtomogram Averaging--Applied Symmetry: C1)
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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