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- PDB-5ukp: Structure of unliganded anti-gp120 CD4bs antibody DH522.1 Fab -

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Basic information

Entry
Database: PDB / ID: 5ukp
TitleStructure of unliganded anti-gp120 CD4bs antibody DH522.1 Fab
Components
  • DH522.1 Fab fragment heavy chain
  • DH522.1 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: DH522.1 Fab fragment heavy chain
L: DH522.1 Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)47,2312
Polymers47,2312
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-24 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.682, 70.682, 169.835
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 DH522.1 Fab fragment heavy chain


Mass: 24484.305 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 DH522.1 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.: 161 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 30% 1,2-propanediol, 20% PEG 400

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 33888 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rsym value: 0.077 / Net I/σ(I): 18.4

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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: The starting model was a hybrid of the heavy chain from CH103UCA Fab (PDB 4QHK) with the light chain from A32 (PDB 3TNM).

4qhk

3tnm


Resolution: 2→41.562 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.97
RfactorNum. reflection% reflection
Rfree0.2361 1929 5.89 %
Rwork0.1916 --
obs0.1942 32746 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→41.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 0 161 3377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073299
X-RAY DIFFRACTIONf_angle_d1.1824496
X-RAY DIFFRACTIONf_dihedral_angle_d12.951149
X-RAY DIFFRACTIONf_chiral_restr0.045512
X-RAY DIFFRACTIONf_plane_restr0.006569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05220.28211240.2132017X-RAY DIFFRACTION90
2.0522-2.10770.23121300.20442068X-RAY DIFFRACTION93
2.1077-2.16970.29051300.19482089X-RAY DIFFRACTION94
2.1697-2.23980.23961350.19562119X-RAY DIFFRACTION94
2.2398-2.31980.24111340.19572130X-RAY DIFFRACTION94
2.3198-2.41270.28751360.19812149X-RAY DIFFRACTION95
2.4127-2.52250.25971400.21712213X-RAY DIFFRACTION97
2.5225-2.65540.29181310.23312189X-RAY DIFFRACTION98
2.6554-2.82180.25941370.22312228X-RAY DIFFRACTION98
2.8218-3.03960.28511440.22222250X-RAY DIFFRACTION99
3.0396-3.34540.27811440.21082281X-RAY DIFFRACTION99
3.3454-3.82910.2471430.19392297X-RAY DIFFRACTION99
3.8291-4.82320.16341430.1432321X-RAY DIFFRACTION100
4.8232-41.57090.17751580.15982466X-RAY DIFFRACTION100
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)
11.08610.28280.50043.721-0.3320.73610.11090.2561-0.195-0.3288-0.00390.50580.0083-0.1865-0.16270.25020.0367-0.06250.2239-0.01180.252319.65668.849571.7007
21.9177-0.40440.48922.0539-0.40951.5-0.020.0803-0.1601-0.17220.02890.23990.1724-0.15450.02760.2351-0.0434-0.03280.20180.02430.241822.003-0.682778.389
31.3087-0.67290.47762.205-0.79391.43340.1320.0966-0.22170.1409-0.130.20610.2309-0.0242-0.00090.2263-0.0274-0.01690.169-0.00240.193626.1754.496676.3153
42.5560.0317-0.60270.9042-0.23261.77370.05480.2407-0.0622-0.07290.04910.0277-0.0496-0.0236-0.11920.1225-0.0021-0.01230.13860.00270.152532.082526.431455.1829
50.56580.250.38674.2270.3663.31920.22890.38720.8467-0.0867-0.3893-0.1275-0.33360.51750.13090.1752-0.0052-0.0520.25160.11220.256746.98696.887185.1843
61.4665-0.23680.24161.338-0.43981.66780.04580.25230.1319-0.2014-0.2427-0.33560.18350.23370.16620.21950.06620.02540.2170.06510.194244.9763-1.336577.7694
73.52720.074-0.68470.9634-0.23752.183-0.12980.26980.3644-0.08510.21780.07440.1756-0.0394-0.11150.19470.0205-0.05750.16170.06130.196938.28211.841683.2907
82.057-0.28420.34230.9113-0.39771.0496-0.05750.00790.2268-0.0249-0.0034-0.0059-0.09750.09080.04310.1257-0.0149-0.01820.14950.0070.162843.675234.759763.3564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 2:26)
2X-RAY DIFFRACTION2(chain H and resid 27:77)
3X-RAY DIFFRACTION3(chain H and resid 78:117)
4X-RAY DIFFRACTION4(chain H and resid 118:215)
5X-RAY DIFFRACTION5(chain L and resid 3:13)
6X-RAY DIFFRACTION6(chain L and resid 14:89)
7X-RAY DIFFRACTION7(chain L and resid 90:106A)
8X-RAY DIFFRACTION8(chain L and resid 107:208)

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