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

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Basic information

Entry
Database: PDB / ID: 4gag
TitleStructure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 412-423)
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 mitochondrial membrane / host cell lipid droplet / cysteine-type peptidase activity / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell endoplasmic reticulum membrane ...: / host cell mitochondrial membrane / host cell lipid droplet / cysteine-type peptidase activity / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane
Similarity search - Function
Hepatitis C virus core protein, chain A superfamily / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus capsid protein / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / 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 ...Hepatitis C virus core protein, chain A superfamily / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus capsid protein / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / 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: 1.8 Å
AuthorsPotter, J.A. / Owsianka, A. / Angus, A.G.N. / Jeffery, N. / Matthews, D. / Keck, Z. / Lau, P. / Foung, S.K.H. / 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 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1495
Polymers48,9653
Non-polymers1842
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-31 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.649, 56.903, 81.802
Angle α, β, γ (deg.)90.00, 113.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-402-

HOH

DetailsThe asymmetric unit contains one biological unit

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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 / Core protein p21 / Capsid protein C / p21 / Core protein p19 / Envelope glycoprotein E1 / gp32 / ...Core protein p21 / Capsid protein C / p21 / Core protein p19 / Envelope glycoprotein E1 / gp32 / gp35 / Envelope glycoprotein E2 / NS1 / gp68 / gp70 / p7 / Protease NS2-3 / p23


Mass: 1366.459 Da / Num. of mol.: 1 / Fragment: Residues 412-423 of HCV E2 / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus (isolate Glasgow)
References: UniProt: Q5EG65, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.77 Å3/Da / Density % sol: 55.65 %
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: Jul 5, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 49991 / Num. obs: 49991 / % possible obs: 98.28 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→23.11 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21092 2492 5.1 %RANDOM
Rwork0.17765 ---
obs0.17935 46640 98.28 %-
all-49991 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.877 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-0.33 Å2
2---0.11 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 12 346 3742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223520
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.9514823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1975450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55224.42138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29615548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.41513
X-RAY DIFFRACTIONr_chiral_restr0.1960.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212649
X-RAY DIFFRACTIONr_mcbond_it1.4691.52215
X-RAY DIFFRACTIONr_mcangle_it2.46623628
X-RAY DIFFRACTIONr_scbond_it3.45531303
X-RAY DIFFRACTIONr_scangle_it5.4744.51184
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 147 -
Rwork0.27 2859 -
obs--82.18 %

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