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- PDB-6vos: Crystal structure of macaque anti-HIV-1 antibody RM20J -

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Basic information

Entry
Database: PDB / ID: 6vos
TitleCrystal structure of macaque anti-HIV-1 antibody RM20J
Components
  • RM20J Fab heavy chain
  • RM20J Fab light chain
KeywordsIMMUNE SYSTEM / HIV / antibody / non-human primates
Function / homology3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 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

Downloads & links

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Assembly

Deposited unit
H: RM20J Fab heavy chain
L: RM20J Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0809
Polymers46,7382
Non-polymers2,3427
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-38 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.260, 111.260, 141.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11L-409-

HOH

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody RM20J Fab heavy chain


Mass: 23425.123 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 RM20J Fab light chain


Mass: 23312.805 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)

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Non-polymers , 5 types, 231 molecules

#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.67 Å3/Da / Density % sol: 73.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: The RM20J Fab was crystallized from a solution containing 10 mg/mL protein in 1X TBS with a well solution containing 0.1M MES, pH 6.0, 5% PEG3000 and 40% PEG400, with no cryoprotectant supplemented.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03322 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.299→50 Å / Num. obs: 40057 / % possible obs: 100 % / Redundancy: 17.5 % / CC1/2: 0.897 / Net I/σ(I): 28
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 1946 / CC1/2: 0.441

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VOR

6vor


Resolution: 2.299→35.867 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.48
RfactorNum. reflection% reflection
Rfree0.2113 1999 5 %
Rwork0.1811 --
obs0.1827 39954 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.07 Å2 / Biso mean: 62.9402 Å2 / Biso min: 34.62 Å2
Refinement stepCycle: final / Resolution: 2.299→35.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 62 224 3573
Biso mean--96.15 67.61 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073456
X-RAY DIFFRACTIONf_angle_d0.9494693
X-RAY DIFFRACTIONf_chiral_restr0.054529
X-RAY DIFFRACTIONf_plane_restr0.006594
X-RAY DIFFRACTIONf_dihedral_angle_d10.5372769
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2992-2.35670.3931380.3332262099
2.3567-2.42040.38221410.28182673100
2.4204-2.49160.28611400.2472676100
2.4916-2.5720.29371410.22492674100
2.572-2.66390.27551410.22652668100
2.6639-2.77050.28981420.21832690100
2.7705-2.89660.24771410.20362685100
2.8966-3.04920.21631410.20272681100
3.0492-3.24010.19411430.19162702100
3.2401-3.49010.23551420.19112716100
3.4901-3.8410.20041450.17282737100
3.841-4.39590.19471430.15092739100
4.3959-5.53510.16791480.14312776100
5.5351-35.8670.18781530.1777291899
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)
11.4742-1.761.216.6563-3.88712.4110.2001-0.24680.30530.7828-0.1779-0.1613-0.81620.2284-0.02820.5706-0.1306-0.14570.53240.02520.653644.5366-40.33216.7962
22.92550.9745-1.60995.4399-0.16093.3417-0.0131-0.06560.3429-0.0074-0.0841-0.1915-0.14870.24580.11640.4425-0.021-0.12360.40590.07210.499147.0247-50.5613.8452
32.29871.2879-0.96134.0464-1.50212.34150.01790.03820.43040.17790.00950.0037-0.12270.0028-0.00820.4533-0.0235-0.11920.45390.09770.556241.0807-45.44842.5332
46.0109-1.5784-0.49393.4218-0.02191.3504-0.1804-0.36510.18870.354-0.0408-0.1134-0.3005-0.06160.21790.66880.0542-0.12540.522-0.05260.43722.9095-19.8341-5.8069
52.43360.7027-0.16334.1808-5.00046.1631-0.9019-0.16790.36930.6530.03460.0819-1.643-0.91720.94190.81480.1607-0.11180.5816-0.15650.572915.1758-10.2044-15.6963
62.58810.2005-2.28191.4399-0.09952.3370.19230.33140.369-0.16540.04120.37840.0195-0.4123-0.20360.476-0.003-0.09590.5480.10080.596220.5544-55.6842-4.5011
74.9558-1.1242-1.08972.16830.8082.93940.00290.05520.25430.04350.11190.0871-0.0206-0.2013-0.1170.4414-0.0075-0.06190.40730.08960.466825.6793-56.60673.0891
85.09112.3992-2.56925.902-4.21544.73080.1887-0.3392-0.08620.38-0.18430.1231-0.28580.20370.04480.47950.0315-0.13190.468-0.0190.390818.0832-29.5274-14.12
96.2948-1.45172.84857.373-3.04422.10680.2970.0932-0.6903-0.4311-0.15830.0090.72560.2298-0.2220.59060.0878-0.10470.5002-0.05620.645125.7363-32.8801-23.9842
103.14161.8426-2.28583.2356-3.06193.2479-0.0565-0.1745-0.1768-0.0793-0.0023-0.00590.01110.15750.06260.49920.0304-0.09620.4408-0.06730.483518.9074-29.8083-18.3112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 1:17)H1 - 17
2X-RAY DIFFRACTION2(chain H and resid 18:81)H18 - 81
3X-RAY DIFFRACTION3(chain H and resid 82:118)H82 - 118
4X-RAY DIFFRACTION4(chain H and resid 119:213)H119 - 213
5X-RAY DIFFRACTION5(chain H and resid 214:222)H214 - 222
6X-RAY DIFFRACTION6(chain L and resid 1:26)L1 - 26
7X-RAY DIFFRACTION7(chain L and resid 27:106)L27 - 106
8X-RAY DIFFRACTION8(chain L and resid 107:147)L107 - 147
9X-RAY DIFFRACTION9(chain L and resid 148:161)L148 - 161
10X-RAY DIFFRACTION10(chain L and resid 162:214)L162 - 214

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