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- PDB-4jy5: Crystal structure of human Fab PGT122, a broadly reactive and pot... -

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Basic information

Entry
Database: PDB / ID: 4jy5
TitleCrystal structure of human Fab PGT122, a broadly reactive and potent HIV-1 neutralizing antibody
Components
  • PGT122 heavy chain
  • PGT122 light chain
KeywordsIMMUNE SYSTEM / Broadly neutralizing antibody against HIV-1 / HIV-1 Env gp120 subunit
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJulien, J.-P. / Diwanji, D.C. / Burton, D.R. / Wilson, I.A.
CitationJournal: PLoS Pathog / Year: 2013
Title: Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans.
Authors: Jean-Philippe Julien / Devin Sok / Reza Khayat / Jeong Hyun Lee / Katie J Doores / Laura M Walker / Alejandra Ramos / Devan C Diwanji / Robert Pejchal / Albert Cupo / Umesh Katpally / Rafael ...Authors: Jean-Philippe Julien / Devin Sok / Reza Khayat / Jeong Hyun Lee / Katie J Doores / Laura M Walker / Alejandra Ramos / Devan C Diwanji / Robert Pejchal / Albert Cupo / Umesh Katpally / Rafael S Depetris / Robyn L Stanfield / Ryan McBride / Andre J Marozsan / James C Paulson / Rogier W Sanders / John P Moore / Dennis R Burton / Pascal Poignard / Andrew B Ward / Ian A Wilson /
Abstract: New broad and potent neutralizing HIV-1 antibodies have recently been described that are largely dependent on the gp120 N332 glycan for Env recognition. Members of the PGT121 family of antibodies, ...New broad and potent neutralizing HIV-1 antibodies have recently been described that are largely dependent on the gp120 N332 glycan for Env recognition. Members of the PGT121 family of antibodies, isolated from an African donor, neutralize ∼70% of circulating isolates with a median IC50 less than 0.05 µg ml(-1). Here, we show that three family members, PGT121, PGT122 and PGT123, have very similar crystal structures. A long 24-residue HCDR3 divides the antibody binding site into two functional surfaces, consisting of an open face, formed by the heavy chain CDRs, and an elongated face, formed by LCDR1, LCDR3 and the tip of the HCDR3. Alanine scanning mutagenesis of the antibody paratope reveals a crucial role in neutralization for residues on the elongated face, whereas the open face, which accommodates a complex biantennary glycan in the PGT121 structure, appears to play a more secondary role. Negative-stain EM reconstructions of an engineered recombinant Env gp140 trimer (SOSIP.664) reveal that PGT122 interacts with the gp120 outer domain at a more vertical angle with respect to the top surface of the spike than the previously characterized antibody PGT128, which is also dependent on the N332 glycan. We then used ITC and FACS to demonstrate that the PGT121 antibodies inhibit CD4 binding to gp120 despite the epitope being distal from the CD4 binding site. Together, these structural, functional and biophysical results suggest that the PGT121 antibodies may interfere with Env receptor engagement by an allosteric mechanism in which key structural elements, such as the V3 base, the N332 oligomannose glycan and surrounding glycans, including a putative V1/V2 complex biantennary glycan, are conformationally constrained.
History
DepositionMar 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: PGT122 light chain
H: PGT122 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4235
Polymers48,1472
Non-polymers2763
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-28 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.340, 42.040, 45.050
Angle α, β, γ (deg.)90.00, 100.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PGT122 light chain


Mass: 22712.082 Da / Num. of mol.: 1 / Fragment: Fab
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)
#2: Antibody PGT122 heavy chain


Mass: 25434.691 Da / Num. of mol.: 1 / Fragment: Fab
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)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1 M CAPS, pH 10.5, 0.2 M sodium chloride, 20% w/v PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 5, 2012
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. all: 39317 / Num. obs: 38560 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.064 / Net I/σ(I): 11.4
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5963 / Rsym value: 0.43 / % possible all: 97.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JY6

4jy6


Resolution: 1.75→38.332 Å / SU ML: 0.51 / σ(F): 1.34 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1893 5.01 %RANDOM
Rwork0.1982 ---
obs0.2004 38556 95.43 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.86 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7889 Å2-0 Å2-2.1184 Å2
2---2.7181 Å20 Å2
3---0.9292 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 18 248 3508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073348
X-RAY DIFFRACTIONf_angle_d1.1714565
X-RAY DIFFRACTIONf_dihedral_angle_d14.7961174
X-RAY DIFFRACTIONf_chiral_restr0.079519
X-RAY DIFFRACTIONf_plane_restr0.005576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77310.39331260.35832625X-RAY DIFFRACTION95
1.7731-1.79740.37821570.32842623X-RAY DIFFRACTION93
1.7974-1.82310.34891170.29842520X-RAY DIFFRACTION89
1.8231-1.85030.28531480.27992690X-RAY DIFFRACTION96
1.8503-1.87920.30211580.25112713X-RAY DIFFRACTION97
1.8792-1.910.30321150.24782691X-RAY DIFFRACTION94
1.91-1.94290.29431510.24172665X-RAY DIFFRACTION97
1.9429-1.97830.25861410.23492674X-RAY DIFFRACTION95
1.9783-2.01630.26921510.22052596X-RAY DIFFRACTION94
2.0163-2.05750.25021500.21322716X-RAY DIFFRACTION97
2.0575-2.10220.26771320.19622663X-RAY DIFFRACTION94
2.1022-2.15110.24751390.19732616X-RAY DIFFRACTION95
2.1511-2.20490.22621420.19842536X-RAY DIFFRACTION89
2.2049-2.26450.24681390.19812667X-RAY DIFFRACTION97
2.2645-2.33110.28981530.21072712X-RAY DIFFRACTION97
2.3311-2.40630.2581330.20252689X-RAY DIFFRACTION97
2.4063-2.49230.21611650.19742742X-RAY DIFFRACTION97
2.4923-2.59210.27921360.19472663X-RAY DIFFRACTION97
2.5921-2.710.29251270.19492743X-RAY DIFFRACTION97
2.71-2.85290.21411300.18382567X-RAY DIFFRACTION92
2.8529-3.03160.22451220.18262769X-RAY DIFFRACTION97
3.0316-3.26550.21371640.1822719X-RAY DIFFRACTION98
3.2655-3.59390.21151390.17352699X-RAY DIFFRACTION98
3.5939-4.11340.23061340.16132682X-RAY DIFFRACTION94
4.1134-5.18050.1711530.16462716X-RAY DIFFRACTION98
5.1805-38.3410.2671390.2122708X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -27.6247 Å / Origin y: 11.2911 Å / Origin z: -5.0793 Å
111213212223313233
T0.1588 Å20.0141 Å2-0.01 Å2-0.0975 Å2-0.0012 Å2--0.1168 Å2
L0.7032 °20.3887 °2-0.2142 °2-0.5903 °2-0.4882 °2--0.7119 °2
S0.0276 Å °-0.1139 Å °-0.0227 Å °0.0907 Å °-0.0969 Å °-0.1055 Å °-0.0467 Å °0.1338 Å °0.0723 Å °
Refinement TLS groupSelection details: all

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