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- PDB-5uko: Structure of unliganded anti-gp120 CD4bs antibody DH522IA Fab -

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Basic information

Entry
Database: PDB / ID: 5uko
TitleStructure of unliganded anti-gp120 CD4bs antibody DH522IA Fab
Components
  • DH522IA Fab fragment heavy chain
  • DH522IA Fab fragment light chain
KeywordsIMMUNE SYSTEM / HIV gp120 immune system
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNicely, N.I.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1-AI100645 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI087202 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI118571 United States
Duke University Center for AIDS ResearchP30-AI-64518 United States
CitationJournal: Nat Commun / Year: 2017
Title: Initiation of HIV neutralizing B cell lineages with sequential envelope immunizations.
Authors: Wilton B Williams / Jinsong Zhang / Chuancang Jiang / Nathan I Nicely / Daniela Fera / Kan Luo / M Anthony Moody / Hua-Xin Liao / S Munir Alam / Thomas B Kepler / Akshaya Ramesh / Kevin ...Authors: Wilton B Williams / Jinsong Zhang / Chuancang Jiang / Nathan I Nicely / Daniela Fera / Kan Luo / M Anthony Moody / Hua-Xin Liao / S Munir Alam / Thomas B Kepler / Akshaya Ramesh / Kevin Wiehe / James A Holland / Todd Bradley / Nathan Vandergrift / Kevin O Saunders / Robert Parks / Andrew Foulger / Shi-Mao Xia / Mattia Bonsignori / David C Montefiori / Mark Louder / Amanda Eaton / Sampa Santra / Richard Scearce / Laura Sutherland / Amanda Newman / Hilary Bouton-Verville / Cindy Bowman / Howard Bomze / Feng Gao / Dawn J Marshall / John F Whitesides / Xiaoyan Nie / Garnett Kelsoe / Steven G Reed / Christopher B Fox / Kim Clary / Marguerite Koutsoukos / David Franco / John R Mascola / Stephen C Harrison / Barton F Haynes / Laurent Verkoczy /
Abstract: A strategy for HIV-1 vaccine development is to define envelope (Env) evolution of broadly neutralizing antibodies (bnAbs) in infection and to recreate those events by vaccination. Here, we report ...A strategy for HIV-1 vaccine development is to define envelope (Env) evolution of broadly neutralizing antibodies (bnAbs) in infection and to recreate those events by vaccination. Here, we report host tolerance mechanisms that limit the development of CD4-binding site (CD4bs), HCDR3-binder bnAbs via sequential HIV-1 Env vaccination. Vaccine-induced macaque CD4bs antibodies neutralize 7% of HIV-1 strains, recognize open Env trimers, and accumulate relatively modest somatic mutations. In naive CD4bs, unmutated common ancestor knock-in mice EnvB cell clones develop anergy and partial deletion at the transitional to mature B cell stage, but become Env upon receptor editing. In comparison with repetitive Env immunizations, sequential Env administration rescue anergic Env (non-edited) precursor B cells. Thus, stepwise immunization initiates CD4bs-bnAb responses, but immune tolerance mechanisms restrict their development, suggesting that sequential immunogen-based vaccine regimens will likely need to incorporate strategies to expand bnAb precursor pools.
History
DepositionJan 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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: DH522IA Fab fragment heavy chain
L: DH522IA Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)47,2732
Polymers47,2732
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-22 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.708, 68.708, 176.184
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody DH522IA Fab fragment heavy chain


Mass: 24526.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody DH522IA Fab fragment light chain


Mass: 22747.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.08 M sodium acetate pH 4.6, 1.6 M ammonium sulfate, 20% glycerol

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20786 / % possible obs: 93.1 % / Redundancy: 4.1 % / Rsym value: 0.117 / Net I/σ(I): 13.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UKP

5ukp


Resolution: 2.3→23.181 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.67
RfactorNum. reflection% reflection
Rfree0.2674 1944 9.7 %
Rwork0.1807 --
obs0.1892 20038 89.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→23.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 0 147 3414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083351
X-RAY DIFFRACTIONf_angle_d1.1334566
X-RAY DIFFRACTIONf_dihedral_angle_d13.3091171
X-RAY DIFFRACTIONf_chiral_restr0.04520
X-RAY DIFFRACTIONf_plane_restr0.006578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.34990.32531180.22971096X-RAY DIFFRACTION79
2.3499-2.41340.40141280.24041248X-RAY DIFFRACTION87
2.4134-2.48430.3271360.24481243X-RAY DIFFRACTION88
2.4843-2.56440.38311330.24851301X-RAY DIFFRACTION92
2.5644-2.65590.32781320.24491265X-RAY DIFFRACTION89
2.6559-2.76210.35661440.24961293X-RAY DIFFRACTION90
2.7621-2.88760.32461490.23131335X-RAY DIFFRACTION94
2.8876-3.03950.31671420.21341364X-RAY DIFFRACTION95
3.0395-3.22950.29261460.2081355X-RAY DIFFRACTION95
3.2295-3.47810.31161430.19321315X-RAY DIFFRACTION91
3.4781-3.82670.26191230.18111158X-RAY DIFFRACTION79
3.8267-4.37720.2481340.14951170X-RAY DIFFRACTION81
4.3772-5.50260.19151510.1281400X-RAY DIFFRACTION94
5.5026-23.18180.221650.15171551X-RAY DIFFRACTION98
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)
12.39770.16640.35855.17710.66982.64560.30170.3202-0.0176-0.2269-0.1571-0.1977-0.35440.1007-0.13860.45790.05470.13990.42420.00080.420545.3828-5.4439-12.3252
22.71830.6549-0.11855.08810.94182.85530.26110.0309-0.0158-0.1101-0.0636-0.3389-0.43870.2858-0.18270.41510.03030.09950.2783-0.01630.429848.9748-0.9816-6.0805
30.71820.7628-0.09491.68921.28032.01560.09280.01310.1566-0.07380.0610.1407-0.156-0.1468-0.19390.34490.08630.07030.3220.03120.390338.4072-11.2262-14.5368
44.9872-0.36611.75032.5637-0.82836.326-0.25370.34930.3265-0.16730.25430.0801-0.28760.15270.04070.32540.00050.01410.3451-0.05440.375334.0443-23.3948-30.0935
50.28080.18360.6172.44081.77392.0804-0.90290.7517-0.2358-2.11490.8032-0.5127-0.55010.0406-0.19570.6238-0.18880.19420.6829-0.0980.698633.2917-32.4585-42.3598
63.44942.2431.55664.63672.25862.21940.052-0.71670.290.0821-0.30580.5485-0.0663-0.61220.05270.29920.05410.04570.31130.04090.369223.3725-2.32871.1742
73.01270.87060.40583.32292.01442.80470.06110.10110.1668-0.4028-0.04640.2643-0.2231-0.0070.00550.43890.08230.03750.3780.03660.404525.7317-0.0462-6.4929
85.87056.41276.09576.70586.55726.31540.33780.29190.32580.4886-0.49150.46410.1793-0.0186-0.0680.4438-0.0130.00440.32680.02240.589913.5629-14.973-11.7577
92.8728-0.2432-0.73663.0141.95052.3159-0.0340.27770.0062-0.167-0.0093-0.33760.23660.01270.08830.3648-0.0010.05240.38390.02210.31624.5427-35.187-24.3304
104.48370.10061.26722.80760.95493.2274-0.1542-0.0861-0.03440.07530.1217-0.05690.17410.06340.01420.33130.02660.03940.35370.02460.297722.9881-35.0081-22.7612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 2:43)
2X-RAY DIFFRACTION2(chain H and resid 44:81)
3X-RAY DIFFRACTION3(chain H and resid 82:132)
4X-RAY DIFFRACTION4(chain H and resid 133:209)
5X-RAY DIFFRACTION5(chain H and resid 210:215)
6X-RAY DIFFRACTION6(chain L and resid 2:33)
7X-RAY DIFFRACTION7(chain L and resid 34:102)
8X-RAY DIFFRACTION8(chain L and resid 103:110)
9X-RAY DIFFRACTION9(chain L and resid 111:156)
10X-RAY DIFFRACTION10(chain L and resid 157:208)

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