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- PDB-7ra7: Crystal structure of rabbit anti-HIV Fab 11A -

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Basic information

Entry
Database: PDB / ID: 7ra7
TitleCrystal structure of rabbit anti-HIV Fab 11A
Components
  • 11A Fab heavy chain
  • 11A Fab light chain
KeywordsIMMUNE SYSTEM / antibody antigen neutralizing antibody HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOyen, D. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI144462 United States
Bill & Melinda Gates FoundationOPP1196345 United States
Citation
Journal: To Be Published
Title: Limited breadth of anti-HIV Env glycan hole antibodies is further hindered by strain-specific peptide interactions
Authors: Ozorowski, G. / Cottrell, C.A. / Oyen, D. / de Val, N. / Copps, J. / Scaring, N. / Polveroni, T.M. / Wilson, I.A. / Ward, A.B.
#1: Journal: Immunity / Year: 2018
Title: Electron-Microscopy-Based Epitope Mapping Defines Specificities of Polyclonal Antibodies Elicited during HIV-1 BG505 Envelope Trimer Immunization.
Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton ...Authors: Matteo Bianchi / Hannah L Turner / Bartek Nogal / Christopher A Cottrell / David Oyen / Matthias Pauthner / Raiza Bastidas / Rebecca Nedellec / Laura E McCoy / Ian A Wilson / Dennis R Burton / Andrew B Ward / Lars Hangartner /
Abstract: Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a ...Characterizing polyclonal antibody responses via currently available methods is inherently complex and difficult. Mapping epitopes in an immune response is typically incomplete, which creates a barrier to fully understanding the humoral response to antigens and hinders rational vaccine design efforts. Here, we describe a method of characterizing polyclonal responses by using electron microscopy, and we applied this method to the immunization of rabbits with an HIV-1 envelope glycoprotein vaccine candidate, BG505 SOSIP.664. We detected known epitopes within the polyclonal sera and revealed how antibody responses evolved during the prime-boosting strategy to ultimately result in a neutralizing antibody response. We uncovered previously unidentified epitopes, including an epitope proximal to one recognized by human broadly neutralizing antibodies as well as potentially distracting non-neutralizing epitopes. Our method provides an efficient and semiquantitative map of epitopes that are targeted in a polyclonal antibody response and should be of widespread utility in vaccine and infection studies.
#2: Journal: Cell Rep / Year: 2016
Title: Holes in the Glycan Shield of the Native HIV Envelope Are a Target of Trimer-Elicited Neutralizing Antibodies.
Authors: Laura E McCoy / Marit J van Gils / Gabriel Ozorowski / Terrence Messmer / Bryan Briney / James E Voss / Daniel W Kulp / Matthew S Macauley / Devin Sok / Matthias Pauthner / Sergey Menis / ...Authors: Laura E McCoy / Marit J van Gils / Gabriel Ozorowski / Terrence Messmer / Bryan Briney / James E Voss / Daniel W Kulp / Matthew S Macauley / Devin Sok / Matthias Pauthner / Sergey Menis / Christopher A Cottrell / Jonathan L Torres / Jessica Hsueh / William R Schief / Ian A Wilson / Andrew B Ward / Rogier W Sanders / Dennis R Burton /
Abstract: A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently ...A major advance in the search for an HIV vaccine has been the development of a near-native Envelope trimer (BG505 SOSIP.664) that can induce robust autologous Tier 2 neutralization. Here, potently neutralizing monoclonal antibodies (nAbs) from rabbits immunized with BG505 SOSIP.664 are shown to recognize an immunodominant region of gp120 centered on residue 241. Residue 241 occupies a hole in the glycan defenses of the BG505 isolate, with fewer than 3% of global isolates lacking a glycan site at this position. However, at least one conserved glycan site is missing in 89% of viruses, suggesting the presence of glycan holes in most HIV isolates. Serum evidence is consistent with targeting of holes in natural infection. The immunogenic nature of breaches in the glycan shield has been under-appreciated in previous attempts to understand autologous neutralizing antibody responses and has important potential consequences for HIV vaccine design.
History
DepositionJun 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: 11A Fab heavy chain
L: 11A Fab light chain
A: 11A Fab heavy chain
B: 11A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3219
Polymers93,6984
Non-polymers6235
Water6,738374
1
H: 11A Fab heavy chain
L: 11A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9453
Polymers46,8492
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-44 kcal/mol
Surface area18430 Å2
MethodPISA
2
A: 11A Fab heavy chain
B: 11A Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3766
Polymers46,8492
Non-polymers5264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-60 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.359, 73.877, 86.446
Angle α, β, γ (deg.)90.000, 97.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody 11A Fab heavy chain


Mass: 24072.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody 11A Fab light chain


Mass: 22777.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate, 0.2M lithium sulfate, 30% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 2.2→45.9 Å / Num. obs: 44732 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 38.17 Å2 / CC1/2: 0.86 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.078 / Rrim(I) all: 0.201 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1 / Num. unique obs: 2195 / CC1/2: 0.56 / Rpim(I) all: 0.55 / Rrim(I) all: 1.3 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 2.2→45.9 Å / SU ML: 0.323 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2954
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 2241 5.04 %
Rwork0.2149 42193 -
obs0.2168 44434 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6319 0 36 374 6729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216499
X-RAY DIFFRACTIONf_angle_d0.56198910
X-RAY DIFFRACTIONf_chiral_restr0.04361055
X-RAY DIFFRACTIONf_plane_restr0.00331134
X-RAY DIFFRACTIONf_dihedral_angle_d11.92242215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.35711170.37232335X-RAY DIFFRACTION85.7
2.24-2.30.3861300.3342625X-RAY DIFFRACTION97.45
2.3-2.350.32641490.31792600X-RAY DIFFRACTION97.9
2.35-2.420.34321380.29052638X-RAY DIFFRACTION97.71
2.42-2.490.33521220.27352673X-RAY DIFFRACTION97.83
2.49-2.570.3381220.28032645X-RAY DIFFRACTION97.77
2.57-2.660.33061510.29332619X-RAY DIFFRACTION98.12
2.66-2.770.32261520.28382662X-RAY DIFFRACTION98.32
2.77-2.890.30581380.262646X-RAY DIFFRACTION98.37
2.89-3.050.3131400.24742671X-RAY DIFFRACTION98.8
3.05-3.240.3031550.23962657X-RAY DIFFRACTION98.6
3.24-3.490.27661370.22012684X-RAY DIFFRACTION98.91
3.49-3.840.22651380.17762694X-RAY DIFFRACTION98.99
3.84-4.390.17711520.1552687X-RAY DIFFRACTION99.09
4.39-5.530.16351660.13932679X-RAY DIFFRACTION98.65
5.53-45.90.2051340.18122678X-RAY DIFFRACTION95.52

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