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- PDB-6ca7: Crystal structure of PCT64_13C, a strain specific anti-HIV antibody -

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Basic information

Entry
Database: PDB / ID: 6ca7
TitleCrystal structure of PCT64_13C, a strain specific anti-HIV antibody
Components
  • PCT64_13C heavy chain
  • PCT64_13C light chain
KeywordsIMMUNE SYSTEM / Antibody / neutralizing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.643 Å
AuthorsMurrell, S. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
International AIDS Vaccine InitiativeOPP1084519 United States
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
History
DepositionJan 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PCT64_13C light chain
H: PCT64_13C heavy chain


Theoretical massNumber of molelcules
Total (without water)48,9822
Polymers48,9822
Non-polymers00
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Fab
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-20 kcal/mol
Surface area21220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.091, 68.848, 78.502
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody PCT64_13C light chain


Mass: 23327.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PCT64_13C heavy chain


Mass: 25654.537 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 10% 2-propanol, 10% glycerol, 0.1 HEPES pH 7.5, and 20% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 55491 / % possible obs: 99.4 % / Redundancy: 5.9 % / Rpim(I) all: 0.04 / Net I/σ(I): 19.6
Reflection shellResolution: 1.64→1.68 Å / Num. unique all: 2478 / Rpim(I) all: 0.24

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FEH

5feh


Resolution: 1.643→42.971 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.02
RfactorNum. reflection% reflection
Rfree0.1896 2634 4.75 %
Rwork0.1693 --
obs0.1703 55470 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.643→42.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 0 515 3926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063687
X-RAY DIFFRACTIONf_angle_d0.8915061
X-RAY DIFFRACTIONf_dihedral_angle_d18.8191341
X-RAY DIFFRACTIONf_chiral_restr0.058565
X-RAY DIFFRACTIONf_plane_restr0.005661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6432-1.6730.26071120.22942554X-RAY DIFFRACTION91
1.673-1.70520.22121370.20462737X-RAY DIFFRACTION99
1.7052-1.740.23411390.19292801X-RAY DIFFRACTION100
1.74-1.77790.2351320.19022781X-RAY DIFFRACTION100
1.7779-1.81920.25221290.19532765X-RAY DIFFRACTION100
1.8192-1.86470.27181150.18752825X-RAY DIFFRACTION100
1.8647-1.91510.20621370.18172765X-RAY DIFFRACTION100
1.9151-1.97150.16581700.17182805X-RAY DIFFRACTION100
1.9715-2.03510.17621540.16752738X-RAY DIFFRACTION100
2.0351-2.10790.20741410.17282759X-RAY DIFFRACTION100
2.1079-2.19220.22791350.17042821X-RAY DIFFRACTION100
2.1922-2.2920.16861370.17782799X-RAY DIFFRACTION100
2.292-2.41280.21931240.17542797X-RAY DIFFRACTION100
2.4128-2.5640.20021520.18482800X-RAY DIFFRACTION100
2.564-2.76190.18881620.17862773X-RAY DIFFRACTION100
2.7619-3.03980.19161690.17382765X-RAY DIFFRACTION100
3.0398-3.47950.19371390.16152820X-RAY DIFFRACTION100
3.4795-4.38310.15521060.14412865X-RAY DIFFRACTION100
4.3831-42.98590.15641440.1562866X-RAY DIFFRACTION100

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