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- PDB-6vor: Crystal structure of macaque anti-HIV-1 antibody RM20E1 -

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Basic information

Entry
Database: PDB / ID: 6vor
TitleCrystal structure of macaque anti-HIV-1 antibody RM20E1
Components
  • RM20E1 Fab heavy chain
  • RM20E1 Fab light chain
KeywordsIMMUNE SYSTEM / HIV / antibody / non-human primates
Function / homologyGLYCINE
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsYuan, M. / 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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
CitationJournal: PLoS Pathog / Year: 2020
Title: Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates.
Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / ...Authors: Christopher A Cottrell / Jelle van Schooten / Charles A Bowman / Meng Yuan / David Oyen / Mia Shin / Robert Morpurgo / Patricia van der Woude / Mariëlle van Breemen / Jonathan L Torres / Raj Patel / Justin Gross / Leigh M Sewall / Jeffrey Copps / Gabriel Ozorowski / Bartek Nogal / Devin Sok / Eva G Rakasz / Celia Labranche / Vladimir Vigdorovich / Scott Christley / Diane G Carnathan / D Noah Sather / David Montefiori / Guido Silvestri / Dennis R Burton / John P Moore / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils /
Abstract: The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown ...The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.
History
DepositionJan 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
A: RM20E1 Fab heavy chain
B: RM20E1 Fab light chain
C: RM20E1 Fab heavy chain
D: RM20E1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5916
Polymers97,4414
Non-polymers1502
Water5,765320
1
A: RM20E1 Fab heavy chain
B: RM20E1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,7202
Polymers48,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-21 kcal/mol
Surface area20580 Å2
MethodPISA
2
C: RM20E1 Fab heavy chain
D: RM20E1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8714
Polymers48,7202
Non-polymers1502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.369, 57.741, 92.745
Angle α, β, γ (deg.)98.740, 94.050, 97.830
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody RM20E1 Fab heavy chain


Mass: 24589.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody RM20E1 Fab light chain


Mass: 24130.783 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: The RM20E1 Fab was crystallized from a solution containing 6.3 mg/mL protein in 1X TBS with a well solution containing 0.1M glycine, pH 10.5, 1.2M NaH2PO4, 0.8M Na2HPO4, and 0.2M Li2SO4, ...Details: The RM20E1 Fab was crystallized from a solution containing 6.3 mg/mL protein in 1X TBS with a well solution containing 0.1M glycine, pH 10.5, 1.2M NaH2PO4, 0.8M Na2HPO4, and 0.2M Li2SO4, with 15% ethylene glycol supplemented as cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 142088 / % possible obs: 85.4 % / Redundancy: 2.7 % / CC1/2: 0.916 / Net I/σ(I): 18.8
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 2413 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IT2

5it2


Resolution: 1.85→32.628 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 36.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 1982 2.61 %
Rwork0.224 73983 -
obs0.2247 75965 76.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.35 Å2 / Biso mean: 39.2758 Å2 / Biso min: 14.5 Å2
Refinement stepCycle: final / Resolution: 1.85→32.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6710 0 10 320 7040
Biso mean--40.93 39.96 -
Num. residues----871
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.89630.4168540.4397217632
1.8963-1.94750.3715740.3528271740
1.9475-2.00480.3507790.3402323247
2.0048-2.06950.3694990.3202383455
2.0695-2.14350.31951250.3098427162
2.1435-2.22930.28941250.3005491371
2.2293-2.33070.35851520.3133575884
2.3307-2.45360.32471740.2769647594
2.4536-2.60720.28041830.2816679698
2.6072-2.80840.30411780.2688667997
2.8084-3.09090.30721890.2524683099
3.0909-3.53770.25891830.2196682099
3.5377-4.45530.20641870.1743669897
4.4553-32.6280.18481800.1649678499

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