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- PDB-3dro: Crystal structure of the HIV-1 Cross Neutralizing Antibody 2F5 in... -

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Basic information

Entry
Database: PDB / ID: 3dro
TitleCrystal structure of the HIV-1 Cross Neutralizing Antibody 2F5 in complex with gp41 Peptide ELLELDKWASLWN grown in ammonium sulfate
Components
  • 2F5 Fab heavy chain
  • 2F5 Fab light chain
  • ELLELDKWASLWN gp41 peptide
KeywordsIMMUNE SYSTEM / HIV-1 / gp41 / 2F5 / nmAb
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering ...membrane fusion involved in viral entry into host cell / Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / complement activation, classical pathway / host cell endosome membrane / actin filament organization / antigen binding / Assembly Of The HIV Virion / Budding and maturation of HIV virion / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / blood microparticle / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular exosome / membrane / plasma 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160 / Hepatitis B virus receptor binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsJulien, J.-P. / Bryson, S. / Pai, E.F.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural details of HIV-1 recognition by the broadly neutralizing monoclonal antibody 2F5: epitope conformation, antigen-recognition loop mobility, and anion-binding site.
Authors: Julien, J.P. / Bryson, S. / Nieva, J.L. / Pai, E.F.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 8, 2017Group: Other
Revision 1.3Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2F5 Fab light chain
B: 2F5 Fab heavy chain
P: ELLELDKWASLWN gp41 peptide


Theoretical massNumber of molelcules
Total (without water)49,9673
Polymers49,9673
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-28 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.900, 76.500, 93.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 2F5 Fab light chain


Mass: 23363.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): hybridoma cells
#2: Antibody 2F5 Fab heavy chain


Mass: 24985.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): hybridoma cells / References: UniProt: Q6PYX1*PLUS
#3: Protein/peptide ELLELDKWASLWN gp41 peptide


Mass: 1617.820 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized by Fmoc chemistry. The sequence naturally occurs in Human immunodeficiency virus.
References: UniProt: Q5S532, UniProt: P04578*PLUS

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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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Fab fragment and peptide are incubated in a solution containing 0.01% Tween-20. Crystals are obatined from reservoir solution containing 0.1 M Nacitrate pH 5.6, 1.6 M ammonium sulfate, VAPOR ...Details: Fab fragment and peptide are incubated in a solution containing 0.01% Tween-20. Crystals are obatined from reservoir solution containing 0.1 M Nacitrate pH 5.6, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.9→17 Å / Num. all: 4436 / Num. obs: 4156 / % possible obs: 93.7 % / Redundancy: 6.01 % / Rmerge(I) obs: 0.282
Reflection shellResolution: 3.9→4.14 Å / Redundancy: 5.69 % / Rmerge(I) obs: 0.514 / % possible all: 90.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P8M

2p8m


Resolution: 3.9→16.96 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 1409305.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 209 5 %RANDOM
Rwork0.222 ---
obs0.222 4156 93.6 %-
all-4436 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.0139 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.69 Å20 Å20 Å2
2--6.06 Å20 Å2
3----1.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.35 Å
Refinement stepCycle: LAST / Resolution: 3.9→16.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 0 0 3321
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d29.5
X-RAY DIFFRACTIONc_improper_angle_d1.45
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.762
X-RAY DIFFRACTIONc_scbond_it2.412
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 3.9→4.14 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.223 32 4.9 %
Rwork0.224 620 -
obs--90.9 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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