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- PDB-4gaj: Structure of the broadly neutralizing antibody AP33 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4gaj
TitleStructure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 411-424)
Components
  • Genome polyprotein
  • NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
  • NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / antibody Fab / neutralizing antibody / HCV E2 binding
Function / homology
Function and homology information


host cell lipid droplet / lipid droplet / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Hepatitis C virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsPotter, J.A. / Owsianka, A. / Taylor, G.L. / Patel, A.H.
CitationJournal: J.Virol. / Year: 2012
Title: Toward a Hepatitis C Virus Vaccine: the Structural Basis of Hepatitis C Virus Neutralization by AP33, a Broadly Neutralizing Antibody.
Authors: Potter, J.A. / Owsianka, A.M. / Jeffery, N. / Matthews, D.J. / Keck, Z.Y. / Lau, P. / Foung, S.K. / Taylor, G.L. / Patel, A.H.
History
DepositionJul 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_atoms / Item: _audit_author.name
Revision 1.3Oct 16, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
H: NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN
L: NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN
P: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)49,2673
Polymers49,2673
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-33 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.910, 40.670, 73.770
Angle α, β, γ (deg.)90.00, 112.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody NEUTRALIZING ANTIBODY AP33 HEAVY CHAIN


Mass: 23677.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody NEUTRALIZING ANTIBODY AP33 LIGHT CHAIN


Mass: 23921.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide Genome polyprotein


Mass: 1667.867 Da / Num. of mol.: 1 / Fragment: unp residues 94-107 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: Q9IY15
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 18% PEG 8K, 0.1M TrisHCl, 0.2M CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 2, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 16538 / Num. obs: 16538 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.64 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→20 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.866 / SU B: 11.941 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.772 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31983 815 5 %RANDOM
Rwork0.24015 ---
obs0.24405 15613 99.33 %-
all-15613 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.435 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å21.04 Å2
2--0.13 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 0 6 3349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223459
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.9474739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0295441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88724.485136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.69115541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.51512
X-RAY DIFFRACTIONr_chiral_restr0.1030.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212600
X-RAY DIFFRACTIONr_mcbond_it0.8251.52182
X-RAY DIFFRACTIONr_mcangle_it1.53423568
X-RAY DIFFRACTIONr_scbond_it1.97431275
X-RAY DIFFRACTIONr_scangle_it3.2694.51161
LS refinement shellResolution: 2.509→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 50 -
Rwork0.366 1076 -
obs--93.6 %

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