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- PDB-5cey: Crystal Structure of Fab 9H+3L, a putative precursor of the PGT12... -

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Basic information

Entry
Database: PDB / ID: 5cey
TitleCrystal Structure of Fab 9H+3L, a putative precursor of the PGT121 family of potent HIV-1 antibodies
Components(Antibody 9H+3L Fab ...) x 2
KeywordsIMMUNE SYSTEM / HIV-1 / antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.387 Å
AuthorsWilson, I.A. / Garces, F.
CitationJournal: Immunity / Year: 2015
Title: Affinity Maturation of a Potent Family of HIV Antibodies Is Primarily Focused on Accommodating or Avoiding Glycans.
Authors: Fernando Garces / Jeong Hyun Lee / Natalia de Val / Alba Torrents de la Pena / Leopold Kong / Cristina Puchades / Yuanzi Hua / Robyn L Stanfield / Dennis R Burton / John P Moore / Rogier W ...Authors: Fernando Garces / Jeong Hyun Lee / Natalia de Val / Alba Torrents de la Pena / Leopold Kong / Cristina Puchades / Yuanzi Hua / Robyn L Stanfield / Dennis R Burton / John P Moore / Rogier W Sanders / Andrew B Ward / Ian A Wilson /
Abstract: The high-mannose patch on the HIV-1 envelope (Env) glycoprotein is the epicenter for binding of the potent broadly neutralizing PGT121 family of antibodies, but strategies for generating such ...The high-mannose patch on the HIV-1 envelope (Env) glycoprotein is the epicenter for binding of the potent broadly neutralizing PGT121 family of antibodies, but strategies for generating such antibodies by vaccination have not been defined. We generated structures of inferred antibody intermediates by X-ray crystallography and electron microscopy to elucidate the molecular events that occurred during evolution of this family. Binding analyses revealed that affinity maturation was primarily focused on avoiding, accommodating, or binding the N137 glycan. The overall antibody approach angle to Env was defined very early in the maturation process, yet some variation evolved in the PGT121 family branches that led to differences in glycan specificities in their respective epitopes. Furthermore, we determined a crystal structure of the recombinant BG505 SOSIP.664 HIV-1 trimer with a PGT121 family member at 3.0 Å that, in concert with these antibody intermediate structures, provides insights to advance design of HIV vaccine candidates.
History
DepositionJul 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody 9H+3L Fab light chain
B: Antibody 9H+3L Fab heavy chain
C: Antibody 9H+3L Fab light chain
D: Antibody 9H+3L Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5028
Polymers97,6934
Non-polymers8094
Water1,838102
1
A: Antibody 9H+3L Fab light chain
B: Antibody 9H+3L Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2214
Polymers48,8472
Non-polymers3742
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-29 kcal/mol
Surface area21030 Å2
MethodPISA
2
C: Antibody 9H+3L Fab light chain
D: Antibody 9H+3L Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2814
Polymers48,8472
Non-polymers4352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-32 kcal/mol
Surface area21280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.736, 338.146, 62.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Antibody 9H+3L Fab light chain


Mass: 23426.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody 9H+3L Fab heavy chain


Mass: 25419.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 4 types, 106 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PE7 / 1-DEOXY-1-THIO-HEPTAETHYLENE GLYCOL


Mass: 342.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 293.14 K / Method: vapor diffusion, sitting drop
Details: 40% (v/v) PEG 600, 0.1M NaCl and 0.1 M Na citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.387→45.747 Å / Num. obs: 33105 / % possible obs: 94.2 % / Redundancy: 4.6 % / Rsym value: 0.13 / Net I/σ(I): 7.87
Reflection shellHighest resolution: 2.4 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.26 / % possible all: 72.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R26

4r26


Resolution: 2.387→45.747 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1645 4.98 %
Rwork0.2241 --
obs0.2265 33008 93.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.387→45.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 53 102 6805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046887
X-RAY DIFFRACTIONf_angle_d0.7479369
X-RAY DIFFRACTIONf_dihedral_angle_d11.2662446
X-RAY DIFFRACTIONf_chiral_restr0.0331053
X-RAY DIFFRACTIONf_plane_restr0.0051183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3869-2.45710.38471060.29291754X-RAY DIFFRACTION66
2.4571-2.53640.35531090.28772097X-RAY DIFFRACTION76
2.5364-2.62710.32931210.30262398X-RAY DIFFRACTION87
2.6271-2.73220.3341510.28452570X-RAY DIFFRACTION93
2.7322-2.85660.39751420.27922764X-RAY DIFFRACTION99
2.8566-3.00720.30591620.25812706X-RAY DIFFRACTION100
3.0072-3.19550.31751350.26042799X-RAY DIFFRACTION100
3.1955-3.44220.26721350.2342817X-RAY DIFFRACTION100
3.4422-3.78840.25691400.21832787X-RAY DIFFRACTION100
3.7884-4.33620.24781490.19512817X-RAY DIFFRACTION100
4.3362-5.46180.21821320.17272868X-RAY DIFFRACTION99
5.4618-45.75570.23371630.20872986X-RAY DIFFRACTION98

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