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- PDB-5i8c: Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue ... -

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Basic information

Entry
Database: PDB / ID: 5i8c
TitleCrystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex with Broadly Neutralizing Antibody VRC34.01 Fab
Components
  • HIV-1 Clade A BG505 Fusion Peptide (residue 512-520)
  • VRC34.01 Fab heavy chain
  • VRC34.01 Fab light chain
KeywordsIMMUNE SYSTEM / HIV-1 / envelope / trimer / fusion peptide / antibody / neutralizing
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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsXu, K. / Zhou, T. / Liu, K. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Science / Year: 2016
Title: Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody.
Authors: Rui Kong / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Thomas Lemmin / Kevin Liu / Gabriel Ozorowski / Cinque Soto / Justin D Taft / Robert T Bailer / Evan M Cale / Lei Chen / Chang W Choi ...Authors: Rui Kong / Kai Xu / Tongqing Zhou / Priyamvada Acharya / Thomas Lemmin / Kevin Liu / Gabriel Ozorowski / Cinque Soto / Justin D Taft / Robert T Bailer / Evan M Cale / Lei Chen / Chang W Choi / Gwo-Yu Chuang / Nicole A Doria-Rose / Aliaksandr Druz / Ivelin S Georgiev / Jason Gorman / Jinghe Huang / M Gordon Joyce / Mark K Louder / Xiaochu Ma / Krisha McKee / Sijy O'Dell / Marie Pancera / Yongping Yang / Scott C Blanchard / Walther Mothes / Dennis R Burton / Wayne C Koff / Mark Connors / Andrew B Ward / Peter D Kwong / John R Mascola /
Abstract: The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the ...The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VRC34.01 Fab heavy chain
B: VRC34.01 Fab light chain
C: HIV-1 Clade A BG505 Fusion Peptide (residue 512-520)


Theoretical massNumber of molelcules
Total (without water)47,7823
Polymers47,7823
Non-polymers00
Water13,673759
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-33 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.471, 74.895, 84.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody VRC34.01 Fab heavy chain


Mass: 23797.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Homo sapiens (human)
#2: Antibody VRC34.01 Fab light chain


Mass: 23138.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV-1 Clade A BG505 Fusion Peptide (residue 512-520)


Mass: 846.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q2N0S7*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Imidazole pH8, 0.2M Calcium Acetate, 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 60235 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.066 / Net I/av σ(I): 39.328 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.57-1.66.60.1331100
1.54-1.575.30.14193.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JPI

4jpi


Resolution: 1.54→36.786 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.54
RfactorNum. reflection% reflection
Rfree0.1815 3032 5.04 %
Rwork0.1595 --
obs0.1606 60165 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 46.18 Å2 / Biso mean: 13.7693 Å2 / Biso min: 2.28 Å2
Refinement stepCycle: final / Resolution: 1.54→36.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 0 759 4112
Biso mean---24.93 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d1.1874667
X-RAY DIFFRACTIONf_chiral_restr0.052530
X-RAY DIFFRACTIONf_plane_restr0.007596
X-RAY DIFFRACTIONf_dihedral_angle_d12.8521215
LS refinement shellResolution: 1.54→1.5631 Å
RfactorNum. reflection% reflection
Rfree0.2205 149 -
Rwork0.1586 2440 -
obs--95 %

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