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- PDB-1kc5: CRYSTAL STRUCTURE OF ANTIBODY PC287 IN COMPLEX WITH PS1 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1kc5
TitleCRYSTAL STRUCTURE OF ANTIBODY PC287 IN COMPLEX WITH PS1 PEPTIDE
Components
  • (PC287 Immunoglobulin) x 2
  • PS1 peptide
KeywordsIMMUNE SYSTEM / ANTIBODY / PEPTIDE ANTIGEN / COMPLEX (ANTIBODY-PEPTIDE)
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / caveolin-mediated endocytosis of virus by host cell / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / caveolin-mediated endocytosis of virus by host cell / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / defense response to bacterium / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm
Similarity search - Function
Large envelope protein S / Major surface antigen from hepadnavirus / 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 ...Large envelope protein S / Major surface antigen from hepadnavirus / 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
: / Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form / : / Large envelope protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V. / Salunke, D.M.
Citation
Journal: J.Immunol. / Year: 2002
Title: Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response.
Authors: Nair, D.T. / Singh, K. / Siddiqui, Z. / Nayak, B.P. / Rao, K.V. / Salunke, D.M.
#1: Journal: J.IMMUNOL. / Year: 2000
Title: Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-antibody Recognition
Authors: Nair, D.T. / Singh, K. / Sahu, N. / Rao, K.V. / Salunke, D.M.
History
DepositionNov 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE An appropriate sequence database match for the Immunoglobulin was not available at the ...SEQUENCE An appropriate sequence database match for the Immunoglobulin was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PC287 Immunoglobulin
H: PC287 Immunoglobulin
P: PS1 peptide


Theoretical massNumber of molelcules
Total (without water)48,2693
Polymers48,2693
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-29 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.590, 71.588, 87.677
Angle α, β, γ (deg.)90.00, 98.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PC287 Immunoglobulin


Mass: 23478.830 Da / Num. of mol.: 1 / Fragment: light chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VC55, UniProt: P01837*PLUS
#2: Antibody PC287 Immunoglobulin


Mass: 23205.986 Da / Num. of mol.: 1 / Fragment: heavy chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01869
#3: Protein/peptide PS1 peptide


Mass: 1584.622 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Hepatitis B virus.
References: GenBank: 15419846, UniProt: Q91C35*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Temperature: 293 K / pH: 5
Details: Shimizu, T., (2001) Acta Crystallogr., Sect.D, 57, 1171.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium acetate1droppH5.0
210 mg/mlprotein1drop
350 mMsodium acetate1reservoirpH5.0
40.2 M1reservoirNaCl
512-17.5 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
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: 13521 / Num. obs: 13521 / Redundancy: 4.6 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 5.5
Reflection shellHighest resolution: 2.5 Å

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Processing

Software
NameVersionClassification
MARdata collection
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
MARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 119332.05 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1245 10.2 %RANDOM
Rwork0.195 ---
obs-13521 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.7715 Å2 / ksol: 0.297564 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å2-2.08 Å2
2---3.08 Å20 Å2
3---2.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 0 176 3517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d1.22
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 190 11 %
Rwork0.318 1535 -
obs-1288 65.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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