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- PDB-7u04: IOMA class antibody ACS101 -

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Basic information

Entry
Database: PDB / ID: 7u04
TitleIOMA class antibody ACS101
Components
  • IOMA class antibody ACS101 heavy chain
  • IOMA class antibody ACS101 light chain
KeywordsIMMUNE SYSTEM / Antibody / IOMA / HIV / STRUCTURAL PROTEIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsFarokhi, E. / Stanfield, R.L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Consortia for HIV/AIDS Vaccine Development United States
CitationJournal: Nat Commun / Year: 2022
Title: Identification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein.
Authors: Jelle van Schooten / Elinaz Farokhi / Anna Schorcht / Tom L G M van den Kerkhof / Hongmei Gao / Patricia van der Woude / Judith A Burger / Tim G Rijkhold Meesters / Tom Bijl / Riham ...Authors: Jelle van Schooten / Elinaz Farokhi / Anna Schorcht / Tom L G M van den Kerkhof / Hongmei Gao / Patricia van der Woude / Judith A Burger / Tim G Rijkhold Meesters / Tom Bijl / Riham Ghalaiyini / Hannah L Turner / Jessica Dorning / Barbera D C van Schaik / Antoine H C van Kampen / Celia C Labranche / Robyn L Stanfield / Devin Sok / David C Montefiori / Dennis R Burton / Michael S Seaman / Gabriel Ozorowski / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils /
Abstract: A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope ...A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3). Here, we describe three IOMA-class NAbs, ACS101-103, with up to 37% breadth, that share many characteristics with IOMA, including an average-length CDRL3. Cryo-electron microscopy revealed that ACS101 shares interactions with those observed with other VH1-2 and VH1-46-class bNAbs, but exhibits a unique binding mode to residues in loop D. Analysis of longitudinal sequences from the patient suggests that a transmitter/founder-virus lacking the N276 glycan might have initiated the development of these NAbs. Together these data strengthen the rationale for germline-targeting vaccination strategies to induce IOMA-class bNAbs and provide a wealth of sequence and structural information to support such strategies.
History
DepositionFeb 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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
L: IOMA class antibody ACS101 light chain
H: IOMA class antibody ACS101 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0185
Polymers47,7412
Non-polymers2763
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, This is a Fab that has one light and one heavy chain.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-26 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.130, 67.130, 199.293
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Antibody IOMA class antibody ACS101 light chain


Mass: 22900.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody IOMA class antibody ACS101 heavy chain


Mass: 24840.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 10% (v/v) glycerol, 0.1M of HEPES (pH 7.5), 5% (w/v) polyethylene glycol 3000 and 30% (v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.31→43.75 Å / Num. obs: 23788 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 47.22 Å2 / CC1/2: 0.88 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.043 / Rrim(I) all: 0.136 / Net I/σ(I): 19.3
Reflection shellResolution: 2.31→2.34 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1113 / CC1/2: 0.5 / Rpim(I) all: 0.49 / Rrim(I) all: 1.32 / % possible all: 100

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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: 6D2P

6d2p


Resolution: 2.31→43.75 Å / SU ML: 0.2895 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3666
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2562 1134 4.78 %
Rwork0.217 22592 -
obs0.2189 23726 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.43 Å2
Refinement stepCycle: LAST / Resolution: 2.31→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 18 77 3396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213402
X-RAY DIFFRACTIONf_angle_d0.57724637
X-RAY DIFFRACTIONf_chiral_restr0.0446521
X-RAY DIFFRACTIONf_plane_restr0.0037587
X-RAY DIFFRACTIONf_dihedral_angle_d12.06761207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.410.35261240.30562729X-RAY DIFFRACTION98.72
2.41-2.540.33111380.2712773X-RAY DIFFRACTION99.97
2.54-2.70.31281440.27342802X-RAY DIFFRACTION100
2.7-2.910.31191410.25582793X-RAY DIFFRACTION100
2.91-3.20.28771230.25092813X-RAY DIFFRACTION100
3.2-3.660.28061610.22572806X-RAY DIFFRACTION99.97
3.66-4.610.22641460.18672857X-RAY DIFFRACTION100
4.62-43.750.2121570.18513019X-RAY DIFFRACTION99.87

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