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- PDB-4nuj: Crystal structure of HIV-1 broadly neutralizing antibody PGT152 -

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Basic information

Entry
Database: PDB / ID: 4nuj
TitleCrystal structure of HIV-1 broadly neutralizing antibody PGT152
Components
  • PGT152 heavy chain
  • PGT152 light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / Fab fragment / HIV Envelope
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / Ig-like domain-containing protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.827 Å
AuthorsBlattner, C. / Wilson, I.A.
CitationJournal: Immunity / Year: 2014
Title: Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers.
Authors: Claudia Blattner / Jeong Hyun Lee / Kwinten Sliepen / Ronald Derking / Emilia Falkowska / Alba Torrents de la Peña / Albert Cupo / Jean-Philippe Julien / Marit van Gils / Peter S Lee / ...Authors: Claudia Blattner / Jeong Hyun Lee / Kwinten Sliepen / Ronald Derking / Emilia Falkowska / Alba Torrents de la Peña / Albert Cupo / Jean-Philippe Julien / Marit van Gils / Peter S Lee / Wenjie Peng / James C Paulson / Pascal Poignard / Dennis R Burton / John P Moore / Rogier W Sanders / Ian A Wilson / Andrew B Ward /
Abstract: All previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a ...All previously characterized broadly neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) target one of four major sites of vulnerability. Here, we define and structurally characterize a unique epitope on Env that is recognized by a recently discovered family of human monoclonal antibodies (PGT151-PGT158). The PGT151 epitope is comprised of residues and glycans at the interface of gp41 and gp120 within a single protomer and glycans from both subunits of a second protomer and represents a neutralizing epitope that is dependent on both gp120 and gp41. Because PGT151 binds only to properly formed, cleaved trimers, this distinctive property, and its ability to stabilize Env trimers, has enabled the successful purification of mature, cleaved Env trimers from the cell surface as a complex with PGT151. Here we compare the structural and functional properties of membrane-extracted Env trimers from several clades with those of the soluble, cleaved SOSIP gp140 trimer.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: PGT152 light chain
B: PGT152 heavy chain


Theoretical massNumber of molelcules
Total (without water)50,0782
Polymers50,0782
Non-polymers00
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-25 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.990, 66.300, 84.878
Angle α, β, γ (deg.)90.00, 134.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

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Components

#1: Antibody PGT152 light chain


Mass: 24055.770 Da / Num. of mol.: 1 / Mutation: N107K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#2: Antibody PGT152 heavy chain


Mass: 26022.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686P15220 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: Q6N089, UniProt: S6BAM6*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 4.2
Details: 40% PEG 600, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 17, 2012
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→33 Å / Num. all: 42250 / Num. obs: 42208 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.08 / Net I/σ(I): 28.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NUG

4nug


Resolution: 1.827→32.859 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 2112 5 %
Rwork0.1676 --
obs0.1697 42203 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.827→32.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 0 512 3925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073534
X-RAY DIFFRACTIONf_angle_d1.1734800
X-RAY DIFFRACTIONf_dihedral_angle_d12.0581278
X-RAY DIFFRACTIONf_chiral_restr0.081534
X-RAY DIFFRACTIONf_plane_restr0.005619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.827-1.86950.24051250.20752441X-RAY DIFFRACTION92
1.8695-1.91630.25941350.21382683X-RAY DIFFRACTION100
1.9163-1.96810.27251360.20122688X-RAY DIFFRACTION100
1.9681-2.0260.25381410.19852676X-RAY DIFFRACTION100
2.026-2.09130.25991410.19372665X-RAY DIFFRACTION100
2.0913-2.16610.25551480.1882669X-RAY DIFFRACTION100
2.1661-2.25280.24141470.18892672X-RAY DIFFRACTION100
2.2528-2.35530.25851390.18352701X-RAY DIFFRACTION100
2.3553-2.47940.23281410.1872672X-RAY DIFFRACTION100
2.4794-2.63470.25721370.18412696X-RAY DIFFRACTION100
2.6347-2.8380.23211440.18392689X-RAY DIFFRACTION100
2.838-3.12340.22381360.17282691X-RAY DIFFRACTION100
3.1234-3.57490.18761460.1582699X-RAY DIFFRACTION100
3.5749-4.50220.16721430.13342719X-RAY DIFFRACTION100
4.5022-32.86410.15681530.1412730X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 18.0616 Å / Origin y: -22.719 Å / Origin z: 15.5145 Å
111213212223313233
T0.1098 Å20.0046 Å2-0.0262 Å2-0.0301 Å20.0087 Å2--0.0633 Å2
L0.2912 °2-0.0107 °2-0.0951 °2-0.3196 °20.0388 °2--0.7267 °2
S0.0418 Å °0.03 Å °-0.044 Å °-0.0243 Å °-0.0093 Å °-0.1162 Å °-0.0205 Å °0.0051 Å °0.0154 Å °
Refinement TLS groupSelection details: all

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