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- PDB-4xbe: Crystal structure of human 4E10 Fab in complex with its peptide e... -

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Basic information

Entry
Database: PDB / ID: 4xbe
TitleCrystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 gp41: crystals cryoprotected with sphingomyelin (02:0 SM (d18:1/2:0)).
Components
  • 4E10 FAB LIGHT CHAIN
  • 4E10 Fab heavy chain
  • PEPTIDE FRAGMENT OF HIV GLYCOPROTEIN (GP41) including the region 671-683 of the MPER
KeywordsIMMUNE SYSTEM / HIV-1 gp41 MPER / 4E10 Fab / membrane lipid
Function / homology
Function and homology information


Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.756 Å
AuthorsIrimia, A. / Stanfield, R.L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI084817 United States
CitationJournal: Immunity / Year: 2016
Title: Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10.
Authors: Irimia, A. / Sarkar, A. / Stanfield, R.L. / Wilson, I.A.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: 4E10 FAB LIGHT CHAIN
H: 4E10 Fab heavy chain
P: PEPTIDE FRAGMENT OF HIV GLYCOPROTEIN (GP41) including the region 671-683 of the MPER


Theoretical massNumber of molelcules
Total (without water)49,6355
Polymers49,6353
Non-polymers02
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-29 kcal/mol
Surface area20380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.657, 44.515, 85.344
Angle α, β, γ (deg.)90.00, 113.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-678-

TRP

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Components

#1: Antibody 4E10 FAB LIGHT CHAIN


Mass: 23395.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#2: Antibody 4E10 Fab heavy chain


Mass: 24180.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pDR12 / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human)
#3: Protein/peptide PEPTIDE FRAGMENT OF HIV GLYCOPROTEIN (GP41) including the region 671-683 of the MPER


Mass: 2058.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P05877*PLUS
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: The complex grew from 1:1 protein:reservoir solution sitting drops equilibrated against 20% PEG 8000, 0.2 M sodium acetate, pH 5.5, 0.2 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2012
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111), non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.756→35.668 Å / Num. obs: 50302 / % possible obs: 92.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 15.2 Å2 / Rsym value: 0.076 / Net I/σ(I): 10
Reflection shellResolution: 1.756→1.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.3 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-20000.98.701data reduction
HKL-20000.98.701data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FX7

2fx7


Resolution: 1.756→35.668 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1965 2515 5 %
Rwork0.1504 --
obs0.1527 50283 91.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.7 Å2
Refinement stepCycle: LAST / Resolution: 1.756→35.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 35 465 3867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053831
X-RAY DIFFRACTIONf_angle_d0.9545251
X-RAY DIFFRACTIONf_dihedral_angle_d13.0241404
X-RAY DIFFRACTIONf_chiral_restr0.036579
X-RAY DIFFRACTIONf_plane_restr0.004695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.756-1.790.28531360.19112589X-RAY DIFFRACTION90
1.79-1.82650.26331430.1742711X-RAY DIFFRACTION95
1.8265-1.86630.23751460.16552775X-RAY DIFFRACTION96
1.8663-1.90970.21681430.16262707X-RAY DIFFRACTION95
1.9097-1.95740.23821440.16112744X-RAY DIFFRACTION95
1.9574-2.01030.21941440.15162730X-RAY DIFFRACTION95
2.0103-2.06950.21331390.15432644X-RAY DIFFRACTION93
2.0695-2.13630.19371290.14442455X-RAY DIFFRACTION85
2.1363-2.21260.21261390.14662653X-RAY DIFFRACTION92
2.2126-2.30120.20371440.14052716X-RAY DIFFRACTION95
2.3012-2.40590.20221440.15022744X-RAY DIFFRACTION95
2.4059-2.53270.22481420.15592702X-RAY DIFFRACTION94
2.5327-2.69140.20481420.16132686X-RAY DIFFRACTION93
2.6914-2.89910.20541390.16482639X-RAY DIFFRACTION91
2.8991-3.19070.21221270.16412415X-RAY DIFFRACTION83
3.1907-3.6520.17681410.14542675X-RAY DIFFRACTION92
3.652-4.59950.1551400.12342670X-RAY DIFFRACTION91
4.5995-35.67530.14441330.14552513X-RAY DIFFRACTION83

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