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- PDB-4r26: Crystal structure of human Fab PGT124, a broadly neutralizing and... -

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Basic information

Entry
Database: PDB / ID: 4r26
TitleCrystal structure of human Fab PGT124, a broadly neutralizing and potent HIV-1 neutralizing antibody
Components
  • PGR124-Light Chain
  • PGT124-Heavy Chain
KeywordsIMMUNE SYSTEM / IGG Fold / Antibody / HIV-1 binding
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Immunoglobulin lambda constant 3 / IGH@ protein / IgG L chain
Similarity search - Component
Biological speciesNomascus leucogenys (northern white-cheeked gibbon)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4969 Å
AuthorsGarces, F. / Kong, L. / Wilson, I.A.
CitationJournal: Cell / Year: 2014
Title: Structural evolution of glycan recognition by a family of potent HIV antibodies.
Authors: Fernando Garces / Devin Sok / Leopold Kong / Ryan McBride / Helen J Kim / Karen F Saye-Francisco / Jean-Philippe Julien / Yuanzi Hua / Albert Cupo / John P Moore / James C Paulson / Andrew B ...Authors: Fernando Garces / Devin Sok / Leopold Kong / Ryan McBride / Helen J Kim / Karen F Saye-Francisco / Jean-Philippe Julien / Yuanzi Hua / Albert Cupo / John P Moore / James C Paulson / Andrew B Ward / Dennis R Burton / Ian A Wilson /
Abstract: The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of ...The HIV envelope glycoprotein (Env) is densely covered with self-glycans that should help shield it from recognition by the human immune system. Here, we examine how a particularly potent family of broadly neutralizing antibodies (Abs) has evolved common and distinct structural features to counter the glycan shield and interact with both glycan and protein components of HIV Env. The inferred germline antibody already harbors potential binding pockets for a glycan and a short protein segment. Affinity maturation then leads to divergent evolutionary branches that either focus on a single glycan and protein segment (e.g., Ab PGT124) or engage multiple glycans (e.g., Abs PGT121-123). Furthermore, other surrounding glycans are avoided by selecting an appropriate initial antibody shape that prevents steric hindrance. Such molecular recognition lessons are important for engineering proteins that can recognize or accommodate glycans.
History
DepositionAug 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref.db_code ..._entity.pdbx_description / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PGR124-Light Chain
H: PGT124-Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7935
Polymers48,5172
Non-polymers2763
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-32 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.686, 40.331, 84.457
Angle α, β, γ (deg.)90.00, 91.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody PGR124-Light Chain / Ig lambda chain C region DOT / Ig lambda chain C region NEWM / Ig lambda-3 chain C regions


Mass: 23056.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nomascus leucogenys (northern white-cheeked gibbon), (gene. exp.) Homo sapiens (human)
Gene: IGLC3 / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P0DOY3, UniProt: S6BGD6*PLUS
#2: Antibody PGT124-Heavy Chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 25460.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Cell line (production host): HEK-293F / Production host: Homo sapiens (human) / References: UniProt: P0DOX5, UniProt: Q6GMX6*PLUS
#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.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 4000, 0.2M MgCl2, 0.1M Tris-HCL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.4969→42.211 Å / Num. all: 15032 / Num. obs: 14303 / % possible obs: 95.4 % / Observed criterion σ(F): 2.7

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Processing

Software
NameVersionClassification
PHENIX(molecular replacement)model building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(molecular replacement)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4969→42.211 Å / SU ML: 0.31 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2668 731 5.12 %
Rwork0.2332 --
obs0.235 14284 95.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4969→42.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 18 65 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153420
X-RAY DIFFRACTIONf_angle_d1.5654660
X-RAY DIFFRACTIONf_dihedral_angle_d15.4041206
X-RAY DIFFRACTIONf_chiral_restr0.099526
X-RAY DIFFRACTIONf_plane_restr0.011590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4969-2.68960.35281460.2932559X-RAY DIFFRACTION91
2.6896-2.96020.31981320.28312661X-RAY DIFFRACTION94
2.9602-3.38840.30321510.25192775X-RAY DIFFRACTION97
3.3884-4.26840.23451510.22032720X-RAY DIFFRACTION96
4.2684-42.21660.23951510.20642838X-RAY DIFFRACTION96

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