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- PDB-1mvu: SINGLE CHAIN FV OF C219 HEAVY CHAIN V101L MUTANT IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 1mvu
TitleSINGLE CHAIN FV OF C219 HEAVY CHAIN V101L MUTANT IN COMPLEX WITH SYNTHETIC EPITOPE PEPTIDE
Components
  • Ig VDJ-region (HEAVY CHAIN)
  • Ig kappa-chain VJ-region (Light chain)
  • P-GLYCOPROTEIN
KeywordsIMMUNE SYSTEM / SINGLE CHAIN FV / MONOCLONAL ANTIBODY / C219 / P-GLYCOPROTEIN / IMMUNOGLOBULIN / SITE-DIRECTED MUTAGENESIS
Function / homology
Function and homology information


oligopeptide export from mitochondrion / terpenoid transport / ceramide floppase activity / floppase activity / ABC-type oligopeptide transporter activity / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / xenobiotic transport across blood-brain barrier / intercellular canaliculus / xenobiotic detoxification by transmembrane export across the plasma membrane ...oligopeptide export from mitochondrion / terpenoid transport / ceramide floppase activity / floppase activity / ABC-type oligopeptide transporter activity / phosphatidylethanolamine flippase activity / phosphatidylcholine floppase activity / xenobiotic transport across blood-brain barrier / intercellular canaliculus / xenobiotic detoxification by transmembrane export across the plasma membrane / P-type phospholipid transporter / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / phospholipid translocation / immunoglobulin complex / efflux transmembrane transporter activity / adaptive immune response / mitochondrial inner membrane / apical plasma membrane / ATP hydrolysis activity / extracellular region / ATP binding / cytoplasm
Similarity search - Function
: / Type 1 protein exporter / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / Immunoglobulin V-Type / ABC transporter-like, conserved site / ABC transporters family signature. ...: / Type 1 protein exporter / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / Immunoglobulin V-Type / ABC transporter-like, conserved site / ABC transporters family signature. / Immunoglobulin V-set domain / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
: / : / ATP-dependent translocase ABCB1 / Igh protein / ScFv B8E5 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsChan, D.C.M. / Kuntz, D.A. / Rose, D.R.
Citation
Journal: To be Published
Title: Single Chain C219 V(101H)L Mutant Antibody Complexed with a Helical Peptide
Authors: Chan, D.C.M. / Hirama, T. / Mackenzie, C.R. / Kuntz, D.A. / Rose, D.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Antibody C19 Recognizes an Alpha-Helical Epitope on P-Glycoprotein
Authors: Van den Elsen, J.M. / Kuntz, D.A. / Hoedemaeker, F.J. / Rose, D.R.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: A Single Chain Fv Fragment of P-Glycoprotein-Specific Monoclonal Antibody C219. Design, Expression, and Crystal Structure at 2.4 A Resolution
Authors: Hoedemaeker, F.J. / Signorelli, T. / Johns, K. / Kuntz, D.A. / Rose, D.R.
History
DepositionSep 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Derived calculations
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AT THE TIME OF PROCESSING, NO DATABASE REFERENCE SEQUENCE WAS AVAILABLE FOR C219 ANTIBODY ...SEQUENCE AT THE TIME OF PROCESSING, NO DATABASE REFERENCE SEQUENCE WAS AVAILABLE FOR C219 ANTIBODY HEAVY CHAIN. AUTHORS INFORMED THAT RESIDUE 101 OF THIS CHAIN WAS MUTATED FROM VAL TO LEU.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig kappa-chain VJ-region (Light chain)
B: Ig VDJ-region (HEAVY CHAIN)
P: P-GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5394
Polymers27,4423
Non-polymers961
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-27 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.733, 50.967, 58.636
Angle α, β, γ (deg.)90.00, 93.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Ig kappa-chain VJ-region (Light chain) / C219 ANTIBODY LIGHT CHAIN


Mass: 12525.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LIGHT AND HEAVY CHAINS LINKED WITH A SYNTHETIC (GGGGS)3 LINKER
Source: (gene. exp.) Mus musculus (house mouse) / Cellular location: PERIPLASM / Plasmid: PSJF2 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: GenBank: 196563, UniProt: Q6KB05*PLUS
#2: Antibody Ig VDJ-region (HEAVY CHAIN) / C219 ANTIBODY HEAVY CHAIN


Mass: 13442.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LIGHT AND HEAVY CHAINS LINKED WITH A SYNTHETIC (GGGGS)3 LINKER
Source: (gene. exp.) Mus musculus (house mouse) / Cellular location: PERIPLASM / Plasmid: PSJF2 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q505N9*PLUS
#3: Protein/peptide P-GLYCOPROTEIN


Mass: 1473.654 Da / Num. of mol.: 1 / Fragment: ATP-binding domain (Residues 1-13) / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN CRICETULUS GRISEUS (CHINESE HAMSTER).
References: GenBank: 191155, UniProt: P21448*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG8000, lithium sulfate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 10, 2002 / Details: mirrors
RadiationMonochromator: Quartz crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→20 Å / Num. obs: 23268 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Biso Wilson estimate: 17 Å2
Reflection shellResolution: 1.78→1.84 Å / % possible all: 96.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→19.27 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 385673.56 / Data cutoff high rms absF: 385673.56 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1103 4.8 %RANDOM
Rwork0.197 ---
all0.2 23706 --
obs0.197 22806 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8686 Å2 / ksol: 0.402656 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1--8.32 Å20 Å20.96 Å2
2--4.52 Å20 Å2
3---3.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.78→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 5 190 2104
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 157 4.4 %
Rwork0.259 3419 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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