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- PDB-1i8k: CRYSTAL STRUCTURE OF DSFV MR1 IN COMPLEX WITH THE PEPTIDE ANTIGEN... -

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Basic information

Entry
Database: PDB / ID: 1i8k
TitleCRYSTAL STRUCTURE OF DSFV MR1 IN COMPLEX WITH THE PEPTIDE ANTIGEN OF THE MUTANT EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII, AT LIQUID NITROGEN TEMPERATURE
Components
  • EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV HEAVY CHAIN
  • EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV LIGHT CHAIN
  • EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII PEPTIDE ANTIGEN
KeywordsIMMUNE SYSTEM / antibody-peptide complex / immunoglobulin fold / peptide antigen / type II' beta turn.
Function / homology
Function and homology information


immunoglobulin mediated immune response / immunoglobulin complex / antigen binding / adaptive immune response / immune response / extracellular region
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-III region PC 3741/TEPC 111 / Ig heavy chain V region 5-76 / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLandry, R.C. / Klimowicz, A.C. / Lavictoire, S.J. / Borisova, S. / Kottachchi, D.T. / Lorimer, I.A. / Evans, S.V.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Antibody recognition of a conformational epitope in a peptide antigen: Fv-peptide complex of an antibody fragment specific for the mutant EGF receptor, EGFRvIII.
Authors: Landry, R.C. / Klimowicz, A.C. / Lavictoire, S.J. / Borisova, S. / Kottachchi, D.T. / Lorimer, I.A. / Evans, S.V.
History
DepositionMar 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Residues 100 of chain A and 344 of chain B have been mutated to Cys residues to introduce ...SEQUENCE Residues 100 of chain A and 344 of chain B have been mutated to Cys residues to introduce a disulfide bridge between chains A and B. There is no sequence database match for chain C because the sequence of EGFRvIII has not yet been deposited in any database. The DNA sequence of the normal EGF receptor has been deposited (NM_005228).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV LIGHT CHAIN
B: EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV HEAVY CHAIN
C: EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII PEPTIDE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)26,8793
Polymers26,8793
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-16 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.500, 44.800, 108.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV LIGHT CHAIN / DSFV MR1 VARIABLE DOMAIN LIGHT CHAIN


Mass: 11745.038 Da / Num. of mol.: 1 / Mutation: D100C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q8R028, UniProt: P01660*PLUS
#2: Protein EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY MR1SCFV HEAVY CHAIN / DSFV MR1 VARIABLE DOMAIN HEAVY CHAIN


Mass: 13712.354 Da / Num. of mol.: 1 / Mutation: R344C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P18529
#3: Protein/peptide EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII PEPTIDE ANTIGEN / EPIDERMAL GROWTH FACTOR RECEPTOR / EGFRVIII PEPTIDE ANTIGEN


Mass: 1421.531 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT / Source method: obtained synthetically
Details: The peptide sequence is from the N-terminal of the mutant epidermal growth factor receptor, EGFRvIII
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: sodium chloride, MPD, PEG 10K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14 mg/mlpeptide1drop
240 mMADA buffer1droppH7.0
325 mM1dropNaCl
41 %(w/v)MPD1drop
56 %(w/v)PEG100001drop
6200 mMADA buffer1reservoirpH7.0
72-3 %MPD1reservoir
816 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 1999
RadiationMonochromator: collimating mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.8→6 Å / Num. all: 25057 / Num. obs: 24309 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.26 % / Biso Wilson estimate: 13.94 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.94 % / Rmerge(I) obs: 0.143 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 24641 / % possible obs: 98.5 % / Num. measured all: 25654
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→6 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: CHARMm
RfactorNum. reflectionSelection details
Rfree0.224 2406 RANDOM
Rwork0.172 --
all0.179 25057 -
obs0.175 24309 -
Displacement parametersBiso mean: 13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 260 2080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_bond_d0.014
LS refinement shellResolution: 1.8→1.88 Å
RfactorNum. reflection% reflection
Rfree0.276 310 -
Rwork0.216 --
obs-2603 99.37 %
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 6 Å / σ(F): 3 / Rfactor Rfree: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 13 Å2
LS refinement shell
*PLUS
Rfactor Rfree: 0.276 / Rfactor Rwork: 0.216

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