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Yorodumi- PDB-4bkl: Crystal structure of the arthritogenic antibody M2139 (Fab fragme... -
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-Basic information
Entry | Database: PDB / ID: 4bkl | ||||||
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Title | Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1 peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ANTIBODY / RHEUMATOID ARTHRITIS / COLLAGEN TYPE II | ||||||
Function / homology | Function and homology information Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / MET activates PTK2 signaling / anterior head development ...Non-integrin membrane-ECM interactions / Extracellular matrix organization / NCAM1 interactions / Signaling by PDGF / Collagen biosynthesis and modifying enzymes / Collagen chain trimerization / collagen type II trimer / collagen type XI trimer / MET activates PTK2 signaling / anterior head development / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / embryonic skeletal joint morphogenesis / otic vesicle development / ECM proteoglycans / proteoglycan metabolic process / platelet-derived growth factor binding / Integrin cell surface interactions / notochord development / limb bud formation / extracellular matrix structural constituent conferring tensile strength / cartilage development involved in endochondral bone morphogenesis / limb morphogenesis / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / endochondral ossification / collagen trimer / collagen fibril organization / cartilage development / skeletal system morphogenesis / proteoglycan binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cartilage condensation / inner ear morphogenesis / roof of mouth development / inner ear development / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / ossification / extracellular matrix / skeletal system development / central nervous system development / sensory perception of sound / bone development / regulation of gene expression / collagen-containing extracellular matrix / protein homodimerization activity / extracellular space / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | ||||||
Authors | Raposo, B. / Dobritzsch, D. / Ge, C. / Ekman, D. / Lindh, I. / Foerster, M. / Uysal, H. / Schneider, G. / Holmdahl, R. | ||||||
Citation | Journal: J.Exp.Med. / Year: 2014 Title: Epitope-Specific Antibody Response is Controlled by Immunoglobulin Vh Polymorphisms. Authors: Raposo, B. / Dobritzsch, D. / Ge, C. / Ekman, D. / Xu, B. / Lindh, I. / Forster, M. / Uysal, H. / Nandakumar, K.S. / Schneider, G. / Holmdahl, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bkl.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bkl.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 4bkl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bkl_validation.pdf.gz | 466.1 KB | Display | wwPDB validaton report |
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Full document | 4bkl_full_validation.pdf.gz | 478.2 KB | Display | |
Data in XML | 4bkl_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 4bkl_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bkl ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bkl | HTTPS FTP |
-Related structure data
Related structure data | 2y5tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: HYP / End label comp-ID: HYP / Refine code: _
NCS ensembles :
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-Components
#1: Antibody | Mass: 24689.611 Da / Num. of mol.: 1 / Fragment: VH AND CH1 / Source method: isolated from a natural source Details: HEAVY CHAIN CLEAVED BY PAPAIN, EXACT TERMINI UNCLEAR Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA (NS0) / Strain: DBA/1 | ||
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#2: Antibody | Mass: 23963.469 Da / Num. of mol.: 1 / Fragment: VL AND CL / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA (NS0) / Strain: DBA/1 | ||
#3: Protein/peptide | Mass: 3314.599 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: TRIPLE-HELICAL SYNTHETIC PEPTIDE, CHAINS CROSSLINKED AT C-TERMINUS, CONTAINS J1-EPITOPE OF COLLAGEN TYPE II FROM MOUSE FLANKED BY GPO REPEATS Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P28481*PLUS Sequence details | THE ANTIBODY UNDERWENT SOMATIC MUTATION SEQUENCE IS LARGELY IDENTICAL WITH THAT OF IGHV1-4 THE ...THE ANTIBODY UNDERWENT SOMATIC MUTATION SEQUENCE IS LARGELY IDENTICAL WITH THAT OF IGHV1-4 THE ANTIBODY UNDERWENT SOMATIC MUTATION SEQUENCE IS LARGELY IDENTICAL WITH THAT OF IGKV3-1 ONE OF THE THREE PEPTIDE CHAINS HAS ADDITIONAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.4 % / Description: NONE |
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Crystal grow | pH: 7 Details: 1.7 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7.0, 10 % DIOXANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.975 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→82.5 Å / Num. obs: 16327 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 3.25→3.43 Å / Redundancy: 4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Y5T Resolution: 3.25→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 21.877 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R: 2.289 / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY ONE OF THE TWO ALTERNATIVE CONFORMATION OF LOOP A158-164 WAS MODELED SEVERAL RESIDUES AT THE C-TERMINUS OF FAB HEAVY AND LIGHT CHAIN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY ONE OF THE TWO ALTERNATIVE CONFORMATION OF LOOP A158-164 WAS MODELED SEVERAL RESIDUES AT THE C-TERMINUS OF FAB HEAVY AND LIGHT CHAIN AND AT N- AND C-TERMINI OF THE PEPTIDE CHAINS ARE NOT MODELED DUE TO LACK OF ELECTRON DENSITY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 117.469 Å2
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Refinement step | Cycle: LAST / Resolution: 3.25→50 Å
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Refine LS restraints |
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