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- PDB-2f5b: CRYSTAL STRUCTURE OF FAB' FROM THE HIV-1 NEUTRALIZING ANTIBODY 2F... -

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Basic information

Entry
Database: PDB / ID: 2f5b
TitleCRYSTAL STRUCTURE OF FAB' FROM THE HIV-1 NEUTRALIZING ANTIBODY 2F5 IN COMPLEX WITH ITS GP41 EPITOPE
Components
  • PROTEIN (ANTIBODY 2F5 (HEAVY CHAIN))
  • PROTEIN (ANTIBODY 2F5 (LIGHT CHAIN))
  • PROTEIN (GP41 EPITOPE)
KeywordsIMMUNOGLOBULIN / FAB COMPLEX / HIV-1 NEUTRALIZATION / GP41
Function / homology
Function and homology information


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 ...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
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBryson, S. / Julien, J.P. / Hynes, R.C. / Pai, E.F.
CitationJournal: J.Virol. / Year: 2009
Title: Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications.
Authors: Bryson, S. / Julien, J.P. / Hynes, R.C. / Pai, E.F.
History
DepositionApr 9, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 1.4Oct 16, 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: PROTEIN (ANTIBODY 2F5 (LIGHT CHAIN))
H: PROTEIN (ANTIBODY 2F5 (HEAVY CHAIN))
P: PROTEIN (GP41 EPITOPE)


Theoretical massNumber of molelcules
Total (without water)49,1683
Polymers49,1683
Non-polymers00
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-23 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.000, 65.000, 175.600
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 PROTEIN (ANTIBODY 2F5 (LIGHT CHAIN))


Mass: 23363.844 Da / Num. of mol.: 1 / Fragment: FAB' / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody PROTEIN (ANTIBODY 2F5 (HEAVY CHAIN))


Mass: 24955.410 Da / Num. of mol.: 1 / Fragment: FAB' / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Protein/peptide PROTEIN (GP41 EPITOPE)


Mass: 848.920 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q75760*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.5
Details: 1.6M AMMONIUM SULFATE, 0.1 M CITRATE PH 5.0, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.979
DetectorType: SIEMENS / Detector: CCD / Date: Mar 1, 1998 / Details: QUARTZ MIRROR
RadiationMonochromator: SI (1,1,1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→12 Å / Num. all: 45917 / Num. obs: 39621 / % possible obs: 90 % / Redundancy: 2.8 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.035 / Net I/σ(I): 17
Reflection shellResolution: 2→2.1 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.313 / % possible all: 93

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1CLZ

1clz


Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 882815.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1973 5 %RANDOM
Rwork0.232 ---
all-45917 --
obs-39621 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76 Å2 / ksol: 0.4113 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å20 Å20 Å2
2--1.65 Å20 Å2
3---0.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 0 357 3788
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.471.5
X-RAY DIFFRACTIONc_mcangle_it0.872
X-RAY DIFFRACTIONc_scbond_it0.492
X-RAY DIFFRACTIONc_scangle_it0.782.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 298 4.6 %
Rwork0.242 6208 -
obs--86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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