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- PDB-4jm4: Crystal Structure of PGT 135 Fab -

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Basic information

Entry
Database: PDB / ID: 4jm4
TitleCrystal Structure of PGT 135 Fab
Components
  • PGT 135 Heavy Chain
  • PGT 135 Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin fold
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsKong, L. / Wilson, I.A.
CitationJournal: Nat Struct Mol Biol / Year: 2013
Title: Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120.
Authors: Leopold Kong / Jeong Hyun Lee / Katie J Doores / Charles D Murin / Jean-Philippe Julien / Ryan McBride / Yan Liu / Andre Marozsan / Albert Cupo / Per-Johan Klasse / Simon Hoffenberg / ...Authors: Leopold Kong / Jeong Hyun Lee / Katie J Doores / Charles D Murin / Jean-Philippe Julien / Ryan McBride / Yan Liu / Andre Marozsan / Albert Cupo / Per-Johan Klasse / Simon Hoffenberg / Michael Caulfield / C Richter King / Yuanzi Hua / Khoa M Le / Reza Khayat / Marc C Deller / Thomas Clayton / Henry Tien / Ten Feizi / Rogier W Sanders / James C Paulson / John P Moore / Robyn L Stanfield / Dennis R Burton / Andrew B Ward / Ian A Wilson /
Abstract: A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb ...A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb PGT 135 binds its Asn332 glycan-dependent epitope from its 3.1-Å crystal structure with gp120, CD4 and Fab 17b. PGT 135 interacts with glycans at Asn332, Asn392 and Asn386, using long CDR loops H1 and H3 to penetrate the glycan shield and access the gp120 protein surface. EM reveals that PGT 135 can accommodate the conformational and chemical diversity of gp120 glycans by altering its angle of engagement. Combined structural studies of PGT 135, PGT 128 and 2G12 show that this Asn332-dependent antigenic region is highly accessible and much more extensive than initially appreciated, which allows for multiple binding modes and varied angles of approach; thereby it represents a supersite of vulnerability for antibody neutralization.
History
DepositionMar 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: PGT 135 Heavy Chain
L: PGT 135 Light Chain


Theoretical massNumber of molelcules
Total (without water)49,3712
Polymers49,3712
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-29 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.888, 138.150, 42.337
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody PGT 135 Heavy Chain


Mass: 25575.814 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody PGT 135 Light Chain


Mass: 23795.467 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20% w/v PEG8000, 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.75→31.407 Å / Num. all: 49550 / Num. obs: 49550 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 26.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 27.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 1871 / Rsym value: 0.47 / % possible all: 73.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.751→31.407 Å / SU ML: 0.51 / σ(F): 0 / Phase error: 31.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 2518 5.09 %RANDOM
Rwork0.2072 ---
all0.2091 49464 --
obs0.2091 49464 95.77 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.619 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.8747 Å2-0 Å20 Å2
2---17.2587 Å20 Å2
3---28.1334 Å2
Refinement stepCycle: LAST / Resolution: 1.751→31.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 0 273 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063575
X-RAY DIFFRACTIONf_angle_d1.1124869
X-RAY DIFFRACTIONf_dihedral_angle_d13.2031275
X-RAY DIFFRACTIONf_chiral_restr0.076538
X-RAY DIFFRACTIONf_plane_restr0.004625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.751-1.78510.5111920.41931874X-RAY DIFFRACTION70
1.7851-1.82150.47791140.3882205X-RAY DIFFRACTION82
1.8215-1.86110.41131400.33332394X-RAY DIFFRACTION90
1.8611-1.90440.36951420.28722495X-RAY DIFFRACTION93
1.9044-1.9520.30681350.26272583X-RAY DIFFRACTION95
1.952-2.00480.27281510.24472635X-RAY DIFFRACTION98
2.0048-2.06380.27441570.23162632X-RAY DIFFRACTION99
2.0638-2.13040.26751410.21452708X-RAY DIFFRACTION100
2.1304-2.20650.29161350.21862677X-RAY DIFFRACTION99
2.2065-2.29480.27551260.22292711X-RAY DIFFRACTION100
2.2948-2.39920.28411650.22222686X-RAY DIFFRACTION100
2.3992-2.52560.2821370.22012731X-RAY DIFFRACTION100
2.5256-2.68380.31771470.22432727X-RAY DIFFRACTION100
2.6838-2.89090.22371500.21272727X-RAY DIFFRACTION100
2.8909-3.18160.25091550.20812745X-RAY DIFFRACTION100
3.1816-3.64130.23221330.20142753X-RAY DIFFRACTION100
3.6413-4.58540.20181310.16432810X-RAY DIFFRACTION99
4.5854-31.41170.17751670.17522853X-RAY DIFFRACTION97

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