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- PDB-7kkz: Crystal structure of mouse anti-HIV potent neutralizing antibody ... -

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Basic information

Entry
Database: PDB / ID: 7kkz
TitleCrystal structure of mouse anti-HIV potent neutralizing antibody M4H2K1
Components
  • Heavy chain of Fab fragment of mouse monoclonal antibody M4H2K1
  • Light chain of Fab fragment of mouse monoclonal antibody M4H2K1
KeywordsANTIVIRAL PROTEIN / HIV-1 / ENV / MONOCLONAL ANTIBODY / IMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKumar, S. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: mBio / Year: 2021
Title: Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles.
Authors: Sonu Kumar / Xiaohe Lin / Timothy Ngo / Benjamin Shapero / Cindy Sou / Joel D Allen / Jeffrey Copps / Lei Zhang / Gabriel Ozorowski / Linling He / Max Crispin / Andrew B Ward / Ian A Wilson / Jiang Zhu /
Abstract: The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and ...The immunogenicity of gp41-stabilized HIV-1 BG505 envelope (Env) trimers and nanoparticles (NPs) was recently assessed in mice and rabbits. Here, we combined Env-specific B-cell sorting and repertoire sequencing to identify neutralizing antibodies (NAbs) from immunized animals. A panel of mouse NAbs was isolated from mice immunized with a 60-meric I3-01 NP presenting 20 stabilized trimers. Three mouse NAbs potently neutralized BG505.T332N by recognizing a glycan epitope centered in the C3/V4 region on BG505 Env, as revealed by electron microscopy (EM), X-ray crystallography, and epitope mapping. A set of rabbit NAbs was isolated from rabbits immunized with a soluble trimer and a 24-meric ferritin NP presenting 8 trimers. Neutralization assays against BG505.T332N variants confirmed that potent rabbit NAbs targeted previously described glycan holes on BG505 Env and accounted for a significant portion of the autologous NAb response in both the trimer and ferritin NP groups. Last, we examined NAb responses that were induced by non-BG505 Env immunogens. We determined a 3.4-Å-resolution crystal structure for the clade C transmitted/founder (T/F) Du172.17 Env with a redesigned heptad repeat 1 (HR1) bend in gp41. This clade C Env, in a soluble trimer form and in a multivalent form with 8 trimers attached to ferritin NP, and the gp41-stabilized clade A Q482-d12 Env trimer elicited distinct NAb responses in rabbits, with notable differences in neutralization breadth. Although eliciting a broad NAb response remains a major challenge, our study provides valuable information on an HIV-1 vaccine design strategy that combines gp41 stabilization and NP display. Self-assembling protein nanoparticles (NPs) presenting BG505 envelope (Env) trimers can elicit tier 2 HIV-1-neutralizing antibody (NAb) responses more effectively than soluble trimers. In the present study, monoclonal NAbs were isolated from previously immunized mice and rabbits for structural and functional analyses, which revealed that potent mouse NAbs recognize the C3/V4 region and small NP-elicited rabbit NAbs primarily target known glycan holes on BG505 Env. This study validates the gp41 stabilization strategy for HIV-1 Env vaccine design and highlights the challenge in eliciting a broad NAb response.
History
DepositionOct 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 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
Revision 1.3Nov 13, 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
L: Light chain of Fab fragment of mouse monoclonal antibody M4H2K1
H: Heavy chain of Fab fragment of mouse monoclonal antibody M4H2K1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2914
Polymers48,0222
Non-polymers2692
Water11,241624
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-22 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.398, 68.398, 184.723
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11H-484-

HOH

21H-660-

HOH

31H-693-

HOH

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Components

#1: Antibody Light chain of Fab fragment of mouse monoclonal antibody M4H2K1


Mass: 23805.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of Fab fragment of mouse monoclonal antibody M4H2K1


Mass: 24216.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M CHES (pH=9.5), 36% PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 81206 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 18.56 Å2 / CC1/2: 0.94 / Net I/σ(I): 34.9
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3998 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GS1

5gs1


Resolution: 1.5→49.86 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.1798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2161 4071 5.02 %
Rwork0.1833 77079 -
obs0.1849 81150 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.84 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 17 624 3982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893443
X-RAY DIFFRACTIONf_angle_d1.16194677
X-RAY DIFFRACTIONf_chiral_restr0.1068519
X-RAY DIFFRACTIONf_plane_restr0.0073600
X-RAY DIFFRACTIONf_dihedral_angle_d18.75451262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.36791440.28852601X-RAY DIFFRACTION98.11
1.52-1.540.30711060.27142626X-RAY DIFFRACTION99.71
1.54-1.560.27941430.25222634X-RAY DIFFRACTION99.53
1.56-1.580.3011160.24172621X-RAY DIFFRACTION99.78
1.58-1.60.28561510.2362602X-RAY DIFFRACTION99.64
1.6-1.620.2881620.23372603X-RAY DIFFRACTION99.71
1.62-1.640.24381340.22572614X-RAY DIFFRACTION99.82
1.64-1.670.27461420.21732655X-RAY DIFFRACTION99.79
1.67-1.70.26461120.21962592X-RAY DIFFRACTION99.89
1.7-1.730.25361410.21332644X-RAY DIFFRACTION99.86
1.73-1.760.24861560.20672660X-RAY DIFFRACTION99.96
1.76-1.790.23011600.20692596X-RAY DIFFRACTION99.96
1.79-1.830.25231370.20622627X-RAY DIFFRACTION99.96
1.83-1.870.23661640.20472605X-RAY DIFFRACTION99.96
1.87-1.910.21691300.1892664X-RAY DIFFRACTION100
1.91-1.960.25591360.19392658X-RAY DIFFRACTION100
1.96-2.010.23841330.19632671X-RAY DIFFRACTION99.93
2.01-2.070.21361330.19382649X-RAY DIFFRACTION100
2.07-2.140.24531570.18112632X-RAY DIFFRACTION100
2.14-2.210.19661500.18212637X-RAY DIFFRACTION100
2.21-2.30.2241310.1882655X-RAY DIFFRACTION100
2.3-2.410.24131450.18092665X-RAY DIFFRACTION100
2.41-2.540.21171450.18142680X-RAY DIFFRACTION100
2.54-2.690.20871440.18582684X-RAY DIFFRACTION100
2.69-2.90.19081180.18322707X-RAY DIFFRACTION100
2.9-3.190.22641470.18382697X-RAY DIFFRACTION99.93
3.19-3.660.211430.16622718X-RAY DIFFRACTION99.9
3.66-4.610.1621440.1492781X-RAY DIFFRACTION99.9
4.61-49.860.18541470.1612901X-RAY DIFFRACTION99.77

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