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- PDB-4cc8: Pre-fusion structure of trimeric HIV-1 envelope glycoprotein dete... -

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Basic information

Entry
Database: PDB / ID: 4cc8
TitlePre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy
Components
  • GP120Envelope glycoprotein GP120
  • GP41
  • MONOCLONAL ANTIBODY VRC03 FAB HEAVY CHAIN
  • MONOCLONAL ANTIBODY VRC03 FAB LIGHT CHAIN
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / PRE-FUSION STATE
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
HOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsBartesaghi, A. / Merk, A. / Borgnia, M.J. / Milne, J.L.S. / Subramaniam, S.
CitationJournal: Nat Struct Mol Biol / Year: 2013
Title: Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy.
Authors: Alberto Bartesaghi / Alan Merk / Mario J Borgnia / Jacqueline L S Milne / Sriram Subramaniam /
Abstract: The activation of trimeric HIV-1 envelope glycoprotein (Env) by its binding to the cell-surface receptor CD4 and co-receptors (CCR5 or CXCR4) represents the first of a series of events that lead to ...The activation of trimeric HIV-1 envelope glycoprotein (Env) by its binding to the cell-surface receptor CD4 and co-receptors (CCR5 or CXCR4) represents the first of a series of events that lead to fusion between viral and target-cell membranes. Here, we present the cryo-EM structure, at subnanometer resolution (~6 Å at 0.143 FSC), of the 'closed', prefusion state of trimeric HIV-1 Env complexed to the broadly neutralizing antibody VRC03. We show that three gp41 helices at the core of the trimer serve as an anchor around which the rest of Env is reorganized upon activation to the 'open' quaternary conformation. The architecture of trimeric HIV-1 Env in the prefusion state and in the activated intermediate state resembles the corresponding states of influenza hemagglutinin trimers, thus providing direct evidence for the similarity in entry mechanisms used by HIV-1, influenza and related enveloped viruses.
History
DepositionOct 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references / Other / Source and taxonomy
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 2.0Jan 10, 2018Group: Atomic model / Derived calculations
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-2484
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: GP41
B: GP41
C: GP41
D: GP120
E: GP120
F: MONOCLONAL ANTIBODY VRC03 FAB HEAVY CHAIN
G: GP120
H: MONOCLONAL ANTIBODY VRC03 FAB HEAVY CHAIN
I: MONOCLONAL ANTIBODY VRC03 FAB HEAVY CHAIN
J: MONOCLONAL ANTIBODY VRC03 FAB LIGHT CHAIN
K: MONOCLONAL ANTIBODY VRC03 FAB LIGHT CHAIN
L: MONOCLONAL ANTIBODY VRC03 FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)241,17512
Polymers241,17512
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody GP41 /


Mass: 2656.265 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: COMPLETE ECTODOMAIN OF HIV-1 ENV FROM THE CLADE A STRAIN KNH1144 INLCUDING RESIDUES IN THE MEMBRANE PROXIMAL EXTERNAL REGION WITH THE FOLLOWING RESIDUE SUBSTITUTIONS A662E, S668N, AND S676T
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Variant: HIV-1 ISOLATE 00KE_KNH1144 / Plasmid: SOSIP-PPI4, FURIN-PCDNA3.1 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human)
#2: Antibody GP120 / Envelope glycoprotein GP120


Mass: 29293.975 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Variant: HIV-1 ISOLATE 00KE_KNH1144 / Plasmid: SOSIP-PPI4, FURIN-PCDNA3.1 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human)
#3: Antibody MONOCLONAL ANTIBODY VRC03 FAB HEAVY CHAIN


Mass: 25294.525 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human)
#4: Antibody MONOCLONAL ANTIBODY VRC03 FAB LIGHT CHAIN


Mass: 23146.795 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human)
Sequence detailsTHE GP41 COMPONENT (CHAINS A, B, C) INCLUDES UNIPROT Q3ZLH6 RESIDUES 512-681 WITH THE FOLLOWING ...THE GP41 COMPONENT (CHAINS A, B, C) INCLUDES UNIPROT Q3ZLH6 RESIDUES 512-681 WITH THE FOLLOWING SUBSTITUTIONS: I559P, A662E, S668N, AND S676T. THE GP120 COMPONENT (CHAINS D, E, G) INCLUDES UNIPROT Q3ZLH6 RSIDUES 1-511. EXACT SEQUENCE-COORDINATE MAPPING COULD NOT BE MODELED.

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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: COMPLEX OF KNH1144 SOSIP GP140 TRIMER WITH VRC03 FAB. / Type: COMPLEX
Buffer solutionName: TNE BUFFER (10 MM TRIS, 150 MM NACL, 1 MM EDTA) / pH: 7.5 / Details: TNE BUFFER (10 MM TRIS, 150 MM NACL, 1 MM EDTA)
SpecimenConc.: 0.65 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: BLOT FOR 6 SECONDS, BLOT OFFSET OF -2, PLUNGE INTO AN ETHANE SLURRY COOLED BY LIQUID NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Aug 9, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 80 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderTemperature: 80 K
Image recordingElectron dose: 10 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 2000
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2EMAN3D reconstruction
3FREALIGN3D reconstruction
4IMAGIC3D reconstruction
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 6 Å / Num. of particles: 88125 / Nominal pixel size: 1.08 Å
Details: 3SE8, CHAIN G AND CHAINS H, L FITTED AS TWO SEPARATE RIGID BODIES INTO MAP. ONLY HELIX RESIDUES 92-122 OF CHAIN B FITTED BY HAND INTO MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD- ...Details: 3SE8, CHAIN G AND CHAINS H, L FITTED AS TWO SEPARATE RIGID BODIES INTO MAP. ONLY HELIX RESIDUES 92-122 OF CHAIN B FITTED BY HAND INTO MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2484. (DEPOSITION ID: 12023).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--RIGID BODY
Atomic model building
IDPDB-ID 3D fitting-ID
13SE8

3se8

1
23HMG

3hmg

1
RefinementHighest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18528 0 0 0 18528

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