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

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Basic information

Entry
Database: PDB / ID: 4xaw
TitleCrystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 gp41: Crystals cryoprotected with phosphatidic acid (08:0 PA)
Components
  • 4E10 Fab heavy chain
  • 4E10 Fab light chain
  • FRAGMENT OF HIV GLYCOPROTEIN (GP41) including the MPER region 671-683
KeywordsIMMUNE SYSTEM / HIV-1 gp41 MPER / 4E10 Fab / lipid membrane
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: 1.47 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 15, 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 / Category: pdbx_audit_support / 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 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,7645
Polymers49,7643
Non-polymers02
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-25 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.709, 44.290, 85.064
Angle α, β, γ (deg.)90.00, 113.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-678-

TRP

21H-409-

HOH

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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 FRAGMENT OF HIV GLYCOPROTEIN (GP41) including the MPER region 671-683


Mass: 2187.582 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.: 490 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTWO UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ...TWO UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ENVIRONMENTS, THE COMPOUNDS MAY BE FRAGMENTS OF POLYETHYLENE GLYCOL 8000 OR LIPID TAIL FRAGMENTS OF 1,2-DIOCTANOYL-SN-GLYCERO-3-PHOSPHATE. THE DATA ARE INSUFFICIENT TO DISTINGUISH BETWEEN THE TWO COMPOUNDS AND THE TRUE IDENTITY OF THE LIGAND IS UNKNOWN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: Crystals grew from 1:1 protein complex: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: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 5, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.47→23.684 Å / Num. obs: 86888 / % possible obs: 95.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.068 / Net I/σ(I): 10.7
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.4 / % possible all: 73.8

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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
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FX7

2fx7


Resolution: 1.47→23.684 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 4345 5 %Random selection
Rwork0.1483 ---
obs0.1499 86885 95.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 1.47→23.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 35 490 3903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143806
X-RAY DIFFRACTIONf_angle_d1.4375209
X-RAY DIFFRACTIONf_dihedral_angle_d13.6921428
X-RAY DIFFRACTIONf_chiral_restr0.109576
X-RAY DIFFRACTIONf_plane_restr0.007681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.49020.3012990.21041872X-RAY DIFFRACTION66
1.4902-1.50780.26771140.19282167X-RAY DIFFRACTION76
1.5078-1.52610.22851230.17792353X-RAY DIFFRACTION81
1.5261-1.54550.20731310.17282496X-RAY DIFFRACTION86
1.5455-1.56580.26561330.16512497X-RAY DIFFRACTION89
1.5658-1.58720.19441370.16292608X-RAY DIFFRACTION90
1.5872-1.60990.2061440.16332738X-RAY DIFFRACTION95
1.6099-1.63390.24831460.17012776X-RAY DIFFRACTION96
1.6339-1.65950.21231470.15622795X-RAY DIFFRACTION98
1.6595-1.68670.21481490.15212824X-RAY DIFFRACTION99
1.6867-1.71570.19711530.13972903X-RAY DIFFRACTION100
1.7157-1.74690.18641510.13112880X-RAY DIFFRACTION100
1.7469-1.78050.18691520.1252891X-RAY DIFFRACTION100
1.7805-1.81680.1631500.12612848X-RAY DIFFRACTION100
1.8168-1.85630.17711520.12392887X-RAY DIFFRACTION100
1.8563-1.89950.16651510.12582874X-RAY DIFFRACTION100
1.8995-1.9470.18651520.12512882X-RAY DIFFRACTION100
1.947-1.99960.16991520.12552883X-RAY DIFFRACTION100
1.9996-2.05840.17291510.12812866X-RAY DIFFRACTION100
2.0584-2.12480.1631500.13442869X-RAY DIFFRACTION99
2.1248-2.20070.15481520.13752889X-RAY DIFFRACTION99
2.2007-2.28870.14751520.13632867X-RAY DIFFRACTION99
2.2887-2.39280.20021510.14062884X-RAY DIFFRACTION100
2.3928-2.51880.2061520.15032890X-RAY DIFFRACTION99
2.5188-2.67640.20271520.1632874X-RAY DIFFRACTION99
2.6764-2.88280.17671500.16552873X-RAY DIFFRACTION99
2.8828-3.17230.20391540.16952921X-RAY DIFFRACTION99
3.1723-3.62990.18371520.15272869X-RAY DIFFRACTION99
3.6299-4.56790.1391500.13422855X-RAY DIFFRACTION96
4.5679-23.68680.18111430.16592709X-RAY DIFFRACTION89

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