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- PDB-6xcj: Crystal Structure of DH650 Fab from a Rhesus Macaque in Complex w... -

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Basic information

Entry
Database: PDB / ID: 6xcj
TitleCrystal Structure of DH650 Fab from a Rhesus Macaque in Complex with HIV-1 gp120 Core
Components
  • DH650 Fab Heavy Chain
  • DH650 Fab Light Chain
  • Envelope Glycoprotein gp120
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / Fab / antibody / neutralizing / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRaymond, D.D. / Chug, H. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144371 United States
CitationJournal: Science / Year: 2021
Title: Recapitulation of HIV-1 Env-antibody coevolution in macaques leading to neutralization breadth.
Authors: Ryan S Roark / Hui Li / Wilton B Williams / Hema Chug / Rosemarie D Mason / Jason Gorman / Shuyi Wang / Fang-Hua Lee / Juliette Rando / Mattia Bonsignori / Kwan-Ki Hwang / Kevin O Saunders / ...Authors: Ryan S Roark / Hui Li / Wilton B Williams / Hema Chug / Rosemarie D Mason / Jason Gorman / Shuyi Wang / Fang-Hua Lee / Juliette Rando / Mattia Bonsignori / Kwan-Ki Hwang / Kevin O Saunders / Kevin Wiehe / M Anthony Moody / Peter T Hraber / Kshitij Wagh / Elena E Giorgi / Ronnie M Russell / Frederic Bibollet-Ruche / Weimin Liu / Jesse Connell / Andrew G Smith / Julia DeVoto / Alexander I Murphy / Jessica Smith / Wenge Ding / Chengyan Zhao / Neha Chohan / Maho Okumura / Christina Rosario / Yu Ding / Emily Lindemuth / Anya M Bauer / Katharine J Bar / David Ambrozak / Cara W Chao / Gwo-Yu Chuang / Hui Geng / Bob C Lin / Mark K Louder / Richard Nguyen / Baoshan Zhang / Mark G Lewis / Donald D Raymond / Nicole A Doria-Rose / Chaim A Schramm / Daniel C Douek / Mario Roederer / Thomas B Kepler / Garnett Kelsoe / John R Mascola / Peter D Kwong / Bette T Korber / Stephen C Harrison / Barton F Haynes / Beatrice H Hahn / George M Shaw /
Abstract: Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope ...Neutralizing antibodies elicited by HIV-1 coevolve with viral envelope proteins (Env) in distinctive patterns, in some cases acquiring substantial breadth. We report that primary HIV-1 envelope proteins-when expressed by simian-human immunodeficiency viruses in rhesus macaques-elicited patterns of Env-antibody coevolution very similar to those in humans, including conserved immunogenetic, structural, and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions, and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2 apex mode of recognition like that of human broadly neutralizing antibodies (bNAbs) PGT145 and PCT64-35S. Another rhesus antibody bound the CD4 binding site by CD4 mimicry, mirroring human bNAbs 8ANC131, CH235, and VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design.
History
DepositionJun 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
G: Envelope Glycoprotein gp120
H: DH650 Fab Heavy Chain
L: DH650 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,13412
Polymers88,1433
Non-polymers1,9919
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint10 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.52, 122.1, 53.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Envelope Glycoprotein gp120 /


Mass: 39710.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) / References: UniProt: A0A0A7I3C6*PLUS
#2: Antibody DH650 Fab Heavy Chain


Mass: 24290.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Antibody DH650 Fab Light Chain


Mass: 24142.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG 8K, 100mM Tris pH 8, 500mM NaCl

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.999919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999919 Å / Relative weight: 1
ReflectionResolution: 2.8→49.9 Å / Num. obs: 23016 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.998 / Net I/σ(I): 13.99
Reflection shellResolution: 2.8→2.97 Å / Num. unique obs: 3659 / CC1/2: 0.644

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LST

4lst


Resolution: 2.8→48.93 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.844 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.437
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1009 -RANDOM
Rwork0.2267 ---
obs0.2296 20060 87 %-
Displacement parametersBiso mean: 58.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.8219 Å20 Å20 Å2
2--0.8741 Å20 Å2
3----1.696 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 126 21 5712
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811408HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0220583HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3451SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1785HARMONIC5
X-RAY DIFFRACTIONt_it5824HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion805SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7793SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion17.57
LS refinement shellResolution: 2.8→2.87 Å
RfactorNum. reflection% reflection
Rfree0.4196 14 -
Rwork0.3292 --
obs0.3321 402 26.38 %

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