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- PDB-4xc3: Crystal structure of human 4E10 Fab in complex with its peptide e... -

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Basic information

Entry
Database: PDB / ID: 4xc3
TitleCrystal structure of human 4E10 Fab in complex with its peptide epitope on HIV-1 gp41; crystals cryoprotected with rac-glycerol 1-phosphate
Components
  • 4E10 Fab heavy chain
  • 4E10 Fab light chain
  • MODIFIED FRAGMENT OF HIV-1 GLYCOPROTEIN (GP41) INCLUDING THE MPER REGION 671-683
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
SN-GLYCEROL-1-PHOSPHATE / Unknown ligand / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.63 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 17, 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 1.3Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MODIFIED FRAGMENT OF HIV-1 GLYCOPROTEIN (GP41) INCLUDING THE MPER REGION 671-683
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1226
Polymers49,7783
Non-polymers3443
Water13,709761
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-33 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.541, 44.704, 85.942
Angle α, β, γ (deg.)90.00, 113.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11P-678-

TRP

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Components

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide MODIFIED FRAGMENT OF HIV-1 GLYCOPROTEIN (GP41) INCLUDING THE MPER REGION 671-683


Mass: 2201.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P05877*PLUS

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Antibody , 2 types, 2 molecules LH

#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)

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Non-polymers , 3 types, 764 molecules

#4: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O6P
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsONE UNKNOWN LIGANDS (UNL) HAS BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ENVIRONMENTS, ...ONE UNKNOWN LIGANDS (UNL) HAS BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ENVIRONMENTS, THE COMPOUNDS MAY BE A FRAGMENT OF POLYETHYLENE GLYCOL 8000 OR A FEATURE RELATED TO THE RAC-GLYCEROL 1-PHOSPHATE COMPOUND SOAKED INTO THE CRYSTAL. 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: 2.79 Å3/Da / Density % sol: 55.97 %
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: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2011
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: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→32.796 Å / Num. obs: 67194 / % possible obs: 97.3 % / Redundancy: 4 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.045 / Net I/σ(I): 20.47
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.1 / % possible all: 74.2

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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
PHASER2.1.4phasing
RefinementResolution: 1.63→32.796 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1799 3359 5 %Random selection
Rwork0.1369 ---
obs0.139 67185 97.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.63→32.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 30 764 4180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063784
X-RAY DIFFRACTIONf_angle_d1.0625200
X-RAY DIFFRACTIONf_dihedral_angle_d13.1281425
X-RAY DIFFRACTIONf_chiral_restr0.041583
X-RAY DIFFRACTIONf_plane_restr0.005676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.65230.2934980.24791862X-RAY DIFFRACTION68
1.6523-1.6770.28231200.22692284X-RAY DIFFRACTION84
1.677-1.70320.2941320.20232500X-RAY DIFFRACTION91
1.7032-1.73110.24981360.17822592X-RAY DIFFRACTION95
1.7311-1.7610.21531400.16022649X-RAY DIFFRACTION98
1.761-1.7930.24661420.14732700X-RAY DIFFRACTION97
1.793-1.82750.19311420.13272706X-RAY DIFFRACTION100
1.8275-1.86480.20161410.13252683X-RAY DIFFRACTION98
1.8648-1.90530.19221420.12992686X-RAY DIFFRACTION100
1.9053-1.94960.19551430.13422728X-RAY DIFFRACTION99
1.9496-1.99840.16411420.12962686X-RAY DIFFRACTION100
1.9984-2.05240.16691420.12792692X-RAY DIFFRACTION99
2.0524-2.11280.16111430.12012732X-RAY DIFFRACTION100
2.1128-2.18090.16931430.1222709X-RAY DIFFRACTION99
2.1809-2.25890.18381440.11432733X-RAY DIFFRACTION100
2.2589-2.34930.15141450.12072755X-RAY DIFFRACTION100
2.3493-2.45620.14871430.12892724X-RAY DIFFRACTION100
2.4562-2.58560.20011440.1392719X-RAY DIFFRACTION100
2.5856-2.74760.17081440.1442747X-RAY DIFFRACTION100
2.7476-2.95960.20251460.15192763X-RAY DIFFRACTION100
2.9596-3.25720.17521440.14512751X-RAY DIFFRACTION100
3.2572-3.72790.19341460.13432779X-RAY DIFFRACTION100
3.7279-4.69460.15941460.11632776X-RAY DIFFRACTION100
4.6946-32.80230.14721510.14542870X-RAY DIFFRACTION100

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