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- PDB-2fx7: Crystal structure of hiv-1 neutralizing human fab 4e10 in complex... -

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Basic information

Entry
Database: PDB / ID: 2fx7
TitleCrystal structure of hiv-1 neutralizing human fab 4e10 in complex with a 16-residue peptide encompassing the 4e10 epitope on gp41
Components
  • (Fab 4E10) x 2
  • Fragment of HIV glycoprotein (GP41)
KeywordsIMMUNE SYSTEM / immunoglobulin fold / beta-sandwich / antibody-epitope complex
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 / 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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsCardoso, R.M.F. / Brunel, F.M. / Ferguson, S. / Burton, D.R. / Dawson, P.E. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural basis of enhanced binding of extended and helically constrained peptide epitopes of the broadly neutralizing HIV-1 antibody 4E10.
Authors: Cardoso, R.M. / Brunel, F.M. / Ferguson, S. / Zwick, M. / Burton, D.R. / Dawson, P.E. / Wilson, I.A.
#1: Journal: Immunity / Year: 2005
Title: Broadly neutralizing anti-HIV antibody 4E10 recognizes a helical conformation of a highly conserved fusion-associated motif in gp41
Authors: Cardoso, R.M.F. / Zwick, M.B. / Stanfield, R.L. / Kunert, R. / Binley, J.M. / Katinger, H. / Burton, D.R. / Wilson, I.A.
History
DepositionFeb 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999No database reference is currently available for the light and heavy chains (Chain L and H).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 4E10
H: Fab 4E10
P: Fragment of HIV glycoprotein (GP41)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5624
Polymers49,4703
Non-polymers921
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-34 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.940, 44.658, 85.264
Angle α, β, γ (deg.)90.00, 113.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Fab 4E10


Mass: 23292.705 Da / Num. of mol.: 1 / Fragment: Light Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 4E10


Mass: 23990.027 Da / Num. of mol.: 1 / Fragment: Heavy Chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein/peptide Fragment of HIV glycoprotein (GP41)


Mass: 2187.582 Da / Num. of mol.: 1 / Fragment: Peptide Epitope of 4E10 / Mutation: I684K, F685K, I686K / Source method: obtained synthetically
Details: This sequence includes a fragment of the HIV envelope protein gp41
References: UniProt: P05880
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 26% PEG 8000, 0.2 M sodium acetate, 0.2 M sodium thiocyanate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2005
RadiationMonochromator: Curved Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 54368 / Num. obs: 53993 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.065 / Net I/σ(I): 14.8
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 5390 / Rsym value: 0.302 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TZG

1tzg


Resolution: 1.76→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2689 -Random
Rwork0.202 ---
all0.21 54719 --
obs0.21 53993 98.7 %-
Solvent computationBsol: 47.0027 Å2 / ksol: 0.398008 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.231 Å20 Å2-0.921 Å2
2---0.364 Å20 Å2
3----1.867 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: LAST / Resolution: 1.76→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 6 337 3829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcangle_it2.206
X-RAY DIFFRACTIONc_mcbond_it1.363
X-RAY DIFFRACTIONc_scangle_it3.019
X-RAY DIFFRACTIONc_scbond_it2.033
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.76-1.770.362320.277X-RAY DIFFRACTION736
1.77-1.780.362660.277X-RAY DIFFRACTION1115

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