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- PDB-4p9m: Crystal structure of 8ANC195 Fab -

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Basic information

Entry
Database: PDB / ID: 4p9m
TitleCrystal structure of 8ANC195 Fab
Components
  • 8ANC195 Fab heavy chain
  • 8ANC195 light chain
KeywordsIMMUNE SYSTEM / IG FOLD / ANTI HIV / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.13 Å
AuthorsScharf, L. / Bjorkman, P.J.
CitationJournal: Cell Rep / Year: 2014
Title: Antibody 8ANC195 reveals a site of broad vulnerability on the HIV-1 envelope spike.
Authors: Louise Scharf / Johannes F Scheid / Jeong Hyun Lee / Anthony P West / Courtney Chen / Han Gao / Priyanthi N P Gnanapragasam / René Mares / Michael S Seaman / Andrew B Ward / Michel C ...Authors: Louise Scharf / Johannes F Scheid / Jeong Hyun Lee / Anthony P West / Courtney Chen / Han Gao / Priyanthi N P Gnanapragasam / René Mares / Michael S Seaman / Andrew B Ward / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: Broadly neutralizing antibodies (bNAbs) to HIV-1 envelope glycoprotein (Env) can prevent infection in animal models. Characterized bNAb targets, although key to vaccine and therapeutic strategies, ...Broadly neutralizing antibodies (bNAbs) to HIV-1 envelope glycoprotein (Env) can prevent infection in animal models. Characterized bNAb targets, although key to vaccine and therapeutic strategies, are currently limited. We defined a new site of vulnerability by solving structures of bNAb 8ANC195 complexed with monomeric gp120 by X-ray crystallography and trimeric Env by electron microscopy. The site includes portions of gp41 and N-linked glycans adjacent to the CD4-binding site on gp120, making 8ANC195 the first donor-derived anti-HIV-1 bNAb with an epitope spanning both Env subunits. Rather than penetrating the glycan shield by using a single variable-region CDR loop, 8ANC195 inserted its entire heavy-chain variable domain into a gap to form a large interface with gp120 glycans and regions of the gp120 inner domain not contacted by other bNAbs. By isolating additional 8ANC195 clonal variants, we identified a more potent variant, which may be valuable for therapeutic approaches using bNAb combinations with nonoverlapping epitopes.
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Data collection
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description ...Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_struct_oper_list / software
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
L: 8ANC195 light chain
H: 8ANC195 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7483
Polymers49,5272
Non-polymers2211
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-23 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.482, 66.482, 219.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsbiological unit is the same as asym.

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Components

#1: Antibody 8ANC195 light chain


Mass: 23401.984 Da / Num. of mol.: 1 / Fragment: 8ANC195 LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Antibody 8ANC195 Fab heavy chain


Mass: 26125.270 Da / Num. of mol.: 1 / Fragment: 8ANC195 HEAVY CHAIN, IG GAMMA-1 CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: PEG 6000, HEPES, zinc chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2012
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→29.534 Å / Num. all: 34458 / Num. obs: 28097 / % possible obs: 98.92 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.049 / Rrim(I) all: 0.142 / Rsym value: 0.133 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym value% possible all
2.13-2.218.90.583.160.60296
2.090.602100
2.220.444100
2.370.332100
2.560.224100
2.80.155100
3.140.112100
3.620.093100
4.430.074100
6.270.05699.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.23 Å29.73 Å
Translation2.23 Å29.73 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7W

3u7w


Resolution: 2.13→29.53 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.239 1405 5 %
Rwork0.211 --
obs0.212 28096 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.08 Å2
Refinement stepCycle: final / Resolution: 2.13→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 14 178 3440
Biso mean--64.85 40.17 -
Num. residues----438
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013425
X-RAY DIFFRACTIONf_angle_d1.2964662
X-RAY DIFFRACTIONf_dihedral_angle_d15.421204
X-RAY DIFFRACTIONf_chiral_restr0.095533
X-RAY DIFFRACTIONf_plane_restr0.006593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.133-2.20920.29511260.25192411X-RAY DIFFRACTION91
2.2092-2.29760.28251390.24632628X-RAY DIFFRACTION100
2.2976-2.40210.28771390.23772627X-RAY DIFFRACTION100
2.4021-2.52870.30451380.24252643X-RAY DIFFRACTION100
2.5287-2.6870.2641400.24422663X-RAY DIFFRACTION100
2.687-2.89440.2841410.23362667X-RAY DIFFRACTION100
2.8944-3.18530.27231420.23442692X-RAY DIFFRACTION100
3.1853-3.64550.22481420.20912696X-RAY DIFFRACTION100
3.6455-4.59030.20831440.17992739X-RAY DIFFRACTION100
4.5903-29.73450.19451540.1852925X-RAY DIFFRACTION100

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