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- PDB-2fx8: Crystal structure of hiv-1 neutralizing human fab 4e10 in complex... -

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Basic information

Entry
Database: PDB / ID: 2fx8
TitleCrystal structure of hiv-1 neutralizing human fab 4e10 in complex with an aib-induced 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 / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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: 2.2 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: Version format compliance
Revision 1.3Jan 22, 2014Group: Atomic model
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 999No database reference is currently available for light and heavy chains (Chains L and H).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab 4E10
H: Fab 4E10
M: Fab 4E10
I: Fab 4E10
N: Fab 4E10
J: Fab 4E10
O: Fab 4E10
K: Fab 4E10
P: Fragment of HIV glycoprotein (GP41)
Q: Fragment of HIV glycoprotein (GP41)
R: Fragment of HIV glycoprotein (GP41)
S: Fragment of HIV glycoprotein (GP41)


Theoretical massNumber of molelcules
Total (without water)195,04512
Polymers195,04512
Non-polymers00
Water10,809600
1
L: Fab 4E10
H: Fab 4E10
P: Fragment of HIV glycoprotein (GP41)


Theoretical massNumber of molelcules
Total (without water)48,7613
Polymers48,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-37 kcal/mol
Surface area19790 Å2
MethodPISA
2
M: Fab 4E10
I: Fab 4E10
Q: Fragment of HIV glycoprotein (GP41)


Theoretical massNumber of molelcules
Total (without water)48,7613
Polymers48,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-37 kcal/mol
Surface area20360 Å2
MethodPISA
3
N: Fab 4E10
J: Fab 4E10
R: Fragment of HIV glycoprotein (GP41)


Theoretical massNumber of molelcules
Total (without water)48,7613
Polymers48,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-40 kcal/mol
Surface area19960 Å2
MethodPISA
4
O: Fab 4E10
K: Fab 4E10
S: Fragment of HIV glycoprotein (GP41)


Theoretical massNumber of molelcules
Total (without water)48,7613
Polymers48,7613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-37 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.454, 113.253, 149.961
Angle α, β, γ (deg.)90.00, 94.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Fab 4E10


Mass: 23292.705 Da / Num. of mol.: 4 / 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: 23860.848 Da / Num. of mol.: 4 / 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: 1607.814 Da / Num. of mol.: 4 / Fragment: Peptide Epitope of 4E10 / Mutation: Y681R, I682R / Source method: obtained synthetically
Details: This sequence includes a fragment of the HIV envelope protein gp41
References: UniProt: P05880
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 36% MPEG 5000, 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2005
RadiationMonochromator: Double Crystal,Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 90395 / Num. obs: 86354 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 20.6 Å2 / Rsym value: 0.155 / Net I/σ(I): 7.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 7988 / Rsym value: 0.654 / % possible all: 88.9

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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: 2.2→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 4333 -RANDOM
Rwork0.235 ---
all-90345 --
obs-86139 95.3 %-
Solvent computationBsol: 47.2238 Å2 / ksol: 0.338274 e/Å3
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.877 Å20 Å20.568 Å2
2--3.982 Å20 Å2
3----3.105 Å2
Refine analyzeLuzzati coordinate error obs: 0.318 Å
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13740 0 0 600 14340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcangle_it2.326
X-RAY DIFFRACTIONc_mcbond_it1.434
X-RAY DIFFRACTIONc_scangle_it3.016
X-RAY DIFFRACTIONc_scbond_it2.097
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.2-2.210.352760.301X-RAY DIFFRACTION1466
2.21-2.230.352810.301X-RAY DIFFRACTION1588

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