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- PDB-6vsr: Crystal structure of macaque anti-HIV-1 antibody RM20F -

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Basic information

Entry
Database: PDB / ID: 6vsr
TitleCrystal structure of macaque anti-HIV-1 antibody RM20F
Components
  • RM20F Fab Heavy Chain
  • RM20F Fab Light Chain
KeywordsIMMUNE SYSTEM / HIV / antibody / non-human primates
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.176 Å
AuthorsOyen, D. / Yuan, 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
DepositionFeb 11, 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

Downloads & links

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Assembly

Deposited unit
A: RM20F Fab Heavy Chain
B: RM20F Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7656
Polymers47,3812
Non-polymers3844
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-74 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.459, 75.646, 115.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody RM20F Fab Heavy Chain


Mass: 24138.064 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)
#2: Antibody RM20F Fab Light Chain


Mass: 23242.801 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)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.82 Å3/Da / Density % sol: 56.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: The RM20F Fab was crystallized from a solution containing 10 mg/mL protein in 1X TBS with a well solution containing 0.1M MES, pH 5.0 and 2M ammonium sulfate. The crystals were cryoprotected ...Details: The RM20F Fab was crystallized from a solution containing 10 mg/mL protein in 1X TBS with a well solution containing 0.1M MES, pH 5.0 and 2M ammonium sulfate. The crystals were cryoprotected by soaking in a well solution supplemented with 30% ethylene glycol

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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: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.176→36.73 Å / Num. obs: 28053 / % possible obs: 98.6 % / Redundancy: 4 % / Biso Wilson estimate: 21.34 Å2 / CC1/2: 0.84 / Net I/σ(I): 7.7
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 1364 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CSZ

5csz


Resolution: 2.176→36.721 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.84
RfactorNum. reflection% reflection
Rfree0.2409 1374 4.91 %
Rwork0.1972 --
obs0.1992 27996 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.9 Å2 / Biso mean: 28.0592 Å2 / Biso min: 9.55 Å2
Refinement stepCycle: final / Resolution: 2.176→36.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 20 288 3591
Biso mean--37.48 31.98 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023438
X-RAY DIFFRACTIONf_angle_d0.5514702
X-RAY DIFFRACTIONf_chiral_restr0.044527
X-RAY DIFFRACTIONf_plane_restr0.003602
X-RAY DIFFRACTIONf_dihedral_angle_d12.3462046
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1762-2.2540.26721070.2444225883
2.254-2.34420.27491390.2364267399
2.3442-2.45090.26611440.2382263898
2.4509-2.58010.30031460.23622675100
2.5801-2.74170.28571360.22072712100
2.7417-2.95330.2431330.20972722100
2.9533-3.25030.22831310.198270999
3.2503-3.72020.2591590.174266698
3.7202-4.68560.18291390.1482275999
4.6856-36.7210.22431400.1976281096
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5993-3.2971.73023.9349-1.29592.2552-0.01820.0516-0.3221-0.03720.06220.39560.0667-0.31980.00370.1493-0.0350.00690.206-0.02180.1635-12.97-9.8689-28.2543
22.0757-1.4556-0.36543.5998-0.96433.6076-0.02290.0499-0.058-0.00120.03020.00090.1306-0.01670.01590.1037-0.03520.00620.1177-0.01550.1217-6.329-3.485-27.8439
35.9809-0.4094-2.76951.20720.18693.0698-0.1273-0.1903-0.07280.00230.0608-0.00720.24210.09040.06670.1253-0.0053-0.01120.1040.00860.1469-14.1504-23.7925-3.3247
47.1876-0.3304-7.55630.30480.42518.2127-0.39090.3192-0.5737-0.0088-0.03150.01990.5352-0.14920.39420.1689-0.0210.00710.2318-0.01360.2144-21.3851-28.0572-7.7786
57.06132.5923-5.99872.1281-3.84427.40560.2013-0.1561-0.1110.4081-0.3462-0.2397-0.47650.09850.16350.3208-0.102-0.01230.3102-0.03580.182-4.438.7631-4.5075
61.95550.1616-1.10963.2262-0.15724.48540.1312-0.140.0720.1040.06020.1855-0.2507-0.0419-0.16930.1709-0.00940.01550.1143-0.00130.1373-9.66688.6673-13.1891
71.38592.6098-2.96095.0267-5.8366.91850.128-0.3032-0.0041-0.0389-0.34730.10880.09680.61270.1890.2311-0.06190.00350.2025-0.02630.1363-11.4968-2.06097.0583
81.8963-1.8799-0.81234.76382.11312.1785-0.2714-0.2199-0.20720.33160.28920.03720.2850.213-0.00220.21470.03310.05580.20230.04690.1575-10.0615-24.51568.0176
91.2881-1.0368-0.1594.34570.28282.0153-0.1573-0.2867-0.31750.51330.21520.09780.31620.067-0.04910.19480.04710.0160.28640.05990.2051-7.9584-24.237610.6868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )A1 - 33
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 124 )A34 - 124
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 201 )A125 - 201
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 227 )A202 - 227
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 25 )B1 - 25
6X-RAY DIFFRACTION6chain 'B' and (resid 26 through 101 )B26 - 101
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 113 )B102 - 113
8X-RAY DIFFRACTION8chain 'B' and (resid 114 through 150 )B114 - 150
9X-RAY DIFFRACTION9chain 'B' and (resid 151 through 213 )B151 - 213

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