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- PDB-3j5m: Cryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 ... -

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Basic information

Entry
Database: PDB / ID: 3j5m
TitleCryo-EM structure of the BG505 SOSIP.664 HIV-1 Env trimer with 3 PGV04 Fabs
Components
  • BG505 SOSIP gp120
  • BG505 SOSIP gp41
  • PGV04 heavy chain
  • PGV04 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 trimeric spike / gp140 / SOSIP / broadly neutralizing antibody / PGV04 / Env / envelope glycoprotein / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsLyumkis, D. / Julien, J.-P. / Wilson, I.A. / Ward, A.B.
CitationJournal: Science / Year: 2013
Title: Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer.
Authors: Dmitry Lyumkis / Jean-Philippe Julien / Natalia de Val / Albert Cupo / Clinton S Potter / Per-Johan Klasse / Dennis R Burton / Rogier W Sanders / John P Moore / Bridget Carragher / Ian A ...Authors: Dmitry Lyumkis / Jean-Philippe Julien / Natalia de Val / Albert Cupo / Clinton S Potter / Per-Johan Klasse / Dennis R Burton / Rogier W Sanders / John P Moore / Bridget Carragher / Ian A Wilson / Andrew B Ward /
Abstract: The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly ...The HIV-1 envelope glycoprotein (Env) trimer contains the receptor binding sites and membrane fusion machinery that introduce the viral genome into the host cell. As the only target for broadly neutralizing antibodies (bnAbs), Env is a focus for rational vaccine design. We present a cryo-electron microscopy reconstruction and structural model of a cleaved, soluble Env trimer (termed BG505 SOSIP.664 gp140) in complex with a CD4 binding site (CD4bs) bnAb, PGV04, at 5.8 angstrom resolution. The structure reveals the spatial arrangement of Env components, including the V1/V2, V3, HR1, and HR2 domains, as well as shielding glycans. The structure also provides insights into trimer assembly, gp120-gp41 interactions, and the CD4bs epitope cluster for bnAbs, which covers a more extensive area and defines a more complex site of vulnerability than previously described.
History
DepositionOct 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name

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Structure visualization

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Assembly

Deposited unit
A: BG505 SOSIP gp120
B: BG505 SOSIP gp41
C: PGV04 light chain
D: PGV04 heavy chain
E: BG505 SOSIP gp120
F: BG505 SOSIP gp41
G: PGV04 light chain
H: PGV04 heavy chain
I: BG505 SOSIP gp120
J: BG505 SOSIP gp41
K: PGV04 light chain
L: PGV04 heavy chain


Theoretical massNumber of molelcules
Total (without water)318,91312
Polymers318,91312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein BG505 SOSIP gp120


Mass: 53121.105 Da / Num. of mol.: 3 / Fragment: UNP residues 30-504 / Mutation: T332N,A501C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein BG505 SOSIP gp41


Mass: 5464.728 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK / Production host: Homo sapiens (human)
#3: Antibody PGV04 light chain


Mass: 23073.822 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#4: Antibody PGV04 heavy chain


Mass: 24644.771 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
Sequence detailsTHE SEQUENCE OF CHAINS B, F, AND J IS ...THE SEQUENCE OF CHAINS B, F, AND J IS AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD (CONTAINS I559P AND T605C MUTATIONS) BUT ALL RESIDUES ARE MODELED AS ALANINE AND REPORTED AS "UNKNOWN RESIDUE."

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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

Component
IDNameTypeDetailsParent-ID
1Fully glycosylated BG505 SOSIP.664 Envelope trimer with 3 broadly neutralizing PGV04 FabsCOMPLEXthree SOSIP.664 gp140 subunits (trimeric HIV-1 spike) with 3 PGV04 Fabs0
2BG505 SOSIP.664 HIV-1 Envelope glycoprotein gp1401
3Fragment antigen bindingFragment antigen-binding1
Molecular weightValue: 0.6 MDa / Experimental value: NO
Buffer solutionName: TBS / pH: 7.5 / Details: TBS
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh C-Flat CF-22-4C, plasma treated for 5 seconds
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: 3 uL sample applied to grid, adsorbed for 30 seconds, blotted, and plunge-frozen in liquid ethane
Method: Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 ...Method: Specimen was prepared for cryo-EM by applying 3 microliters of sample to a freshly plasma cleaned holey carbon C-flat grid (Protochips, Inc.), allowing the sample to adsorb to the grid for 30 seconds, followed by blotting with a small piece of filter paper and plunge-freezing into liquid ethane using a manual cryo-plunger in an ambient environment (4 C).

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20 / Date: Feb 21, 2013 / Details: electron counting mode
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 29000 X / Calibrated magnification: 29000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Astigmatism: objective lens astigmatism was corrected by observing Thon rings with the Leginon software
Camera length: 0 mm
Specimen holderSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingElectron dose: 32 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 6355
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1FREALIGN3D reconstruction
2Xmipp3D reconstruction
CTF correctionDetails: Frealign
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionMethod: projection matching using a resolution-limited scheme
Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49572 / Nominal pixel size: 1.21 Å / Actual pixel size: 1.21 Å
Details: Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers (Single particle details: reconstructed using a resolution-limited refinement procedure ...Details: Final maps were calculated after sorting for the presence of sub-stoichiometrically labeled trimers (Single particle details: reconstructed using a resolution-limited refinement procedure implemented in Xmipp and Frealign) (Single particle--Applied symmetry: C3)
Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
IDPDB-ID 3D fitting-ID
13SE9

3se9

1
22B4C

2b4c

1
33U2S

3u2s

1
41ENV

1env

1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms20379 0 0 0 20379

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