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- PDB-1i8i: CRYSTAL STRUCTURE OF DSFV MR1 IN COMPLEX WITH THE PEPTIDE ANTIGEN... -

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Basic information

Entry
Database: PDB / ID: 1i8i
TitleCRYSTAL STRUCTURE OF DSFV MR1 IN COMPLEX WITH THE PEPTIDE ANTIGEN OF THE MUTANT EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII, AT ROOM 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 6, 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
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-17 kcal/mol
Surface area10130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.600, 45.300, 110.400
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-terminus of the mutant epidermal growth factor receptor, EGFRvIII.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
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: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Apr 21, 2000
RadiationMonochromator: Supper focussing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→6 Å / Num. all: 9686 / Num. obs: 9119 / % possible obs: 91.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 40.12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 2.46 % / Rmerge(I) obs: 0.115 / % possible all: 62.3
Reflection
*PLUS
Num. obs: 9684 / % possible obs: 86.6 % / Num. measured all: 10214 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 58.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MERLOTphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→6 Å / σ(F): 3 / σ(I): 3 / Stereochemistry target values: CHARMm
RfactorNum. reflectionSelection details
Rfree0.262 997 RANDOM
Rwork0.156 --
all0.176 9686 -
obs0.173 9119 -
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 0 85 1896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_bond_d0.017
LS refinement shellResolution: 2.4→2.5 Å
RfactorNum. reflection% reflection
Rfree0.344 83 -
Rwork0.245 678 -
obs-8170 65.3 %
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 6 Å / σ(F): 3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg3.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.344 / Rfactor Rwork: 0.245

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