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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ARTHRITOGENIC ANTIBODY M2139 (FAB FRAGMENT) IN COMPLEX WITH THE TRIPLE-HELICAL J1 PEPTIDE
 
Authors :  B. Raposo, D. Dobritzsch, C. Ge, D. Ekman, I. Lindh, M. Foerster, H. Uysa G. Schneider, R. Holmdahl
Date :  26 Apr 13  (Deposition) - 05 Feb 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B,E,F,G
Keywords :  Immune System, Antibody, Rheumatoid Arthritis, Collagen Type Ii (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Raposo, D. Dobritzsch, C. Ge, D. Ekman, B. Xu, I. Lindh, M. Forster, H. Uysal, K. S. Nandakumar, G. Schneider, R. Holmdahl
Epitope-Specific Antibody Response Is Controlled By Immunoglobulin Vh Polymorphisms.
J. Exp. Med. V. 211 405 2014
PubMed-ID: 24534192  |  Reference-DOI: 10.1084/JEM.20130968

(-) Compounds

Molecule 1 - M2139 FAB FRAGMENT HEAVY CHAIN
    Cell LineMURINE HYBRIDOMA (NS0)
    ChainsA
    FragmentVH AND CH1
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsHEAVY CHAIN CLEAVED BY PAPAIN, EXACT TERMINI UNCLEAR
    StrainDBA/1
 
Molecule 2 - J1 EPITOPE
    ChainsE, F, G
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsTRIPLE-HELICAL SYNTHETIC PEPTIDE, CHAINS CROSSLINKED AT C-TERMINUS, CONTAINS J1-EPITOPE OF COLLAGEN TYPE II FROM MOUSE FLANKED BY GPO REPEATS
    SyntheticYES
 
Molecule 3 - M2139 FAB FRAGMENT LIGHT CHAIN
    Cell LineMURINE HYBRIDOMA (NS0)
    ChainsB
    FragmentVL AND CL
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainDBA/1

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 13)

Asymmetric/Biological Unit (1, 13)
No.NameCountTypeFull Name
1HYP13Mod. Amino Acid4-HYDROXYPROLINE

(-) Sites  (0, 0)

(no "Site" information available for 4BKL)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2A:143 -A:198
3B:23 -B:92
4B:138 -B:198

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe A:149 -Pro A:150
2Trp A:191 -Pro A:192
3Ser B:7 -Pro B:8
4His B:80 -Pro B:81
5Val B:98 -Pro B:99
6Tyr B:144 -Pro B:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BKL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BKL)

(-) Exons   (0, 0)

(no "Exon" information available for 4BKL)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee........eeeeeeee.....ee...eeeee........eeeee..........eeeeeeeeeee.....eeee........eeeeeeeee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bkl A   1 QVQLQQSGAELAKPGTSVKMSCKASGYTFISYWMNWVKQRPGQGLEWIGAINPSDGYTEYNQKFKDKAIMTADRSSSTAYMQLSSLTSEDSALYYCARYGGYFDYWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWSSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      

Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee....eeeee......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4bkl B   1 DIVLTQSPASLAVSLGQRATISCRASESVEYFGTSLMQWYQQKPGQPPKLLIYAASNVESGVPARFSGSGSGTDFSLNIHPVEEDDIAMYFCQQSREVPYTFGGGSKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      

Chain E from PDB  Type:PROTEIN  Length:25
 aligned with CO2A1_MOUSE | P28481 from UniProtKB/Swiss-Prot  Length:1487

    Alignment length:58
                                   748       758       768       778       788        
          CO2A1_MOUSE   739 PPGAQGPPGLQGMPGERGAAGIAGPKGDRGDVGEKGPEGAPGKDGGRGLTGPIGPPGP 796
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..---...---................---------------------------.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 4bkl E  11 Pp---GPp---GMpGERGAAGIAGPKG---------------------------PpGP  35
                             |   | | - | |    24      |  -         -         -    ||  
                             |  13 |  16 |           31                          32|  
                            12-HYP15-HYP18-HYP                                    33-HYP

Chain F from PDB  Type:PROTEIN  Length:26
 aligned with CO2A1_MOUSE | P28481 from UniProtKB/Swiss-Prot  Length:1487

    Alignment length:128
                                   677       687       697       707       717       727       737       747       757       767       777       787        
          CO2A1_MOUSE   668 PGPPGPPGEGGKQGDQGIPGEAGAPGLVGPRGERGFPGERGSPGAQGLQGPRGLPGTPGTDGPKGAAGPDGPPGAQGPPGLQGMPGERGAAGIAGPKGDRGDVGEKGPEGAPGKDGGRGLTGPIGPPG 795
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........---------------------------------------------------------------------------...............---------------------------... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bkl F   9 pGPpGPpG---------------------------------------------------------------------------MpGERGAAGIAGPKG---------------------------PpG  34
                            |  |  || -         -         -         -         -         -         -         -   ||   23       | -         -         -     || 
                            |  |  ||                                                                          17|           31                          32| 
                            9-HYP ||                                                                           18-HYP                                    33-HYP
                              12-HYP                                                                                                                        
                                 15-HYP                                                                                                                     
                                  16                                                                                                                        

Chain G from PDB  Type:PROTEIN  Length:25
 aligned with CO2A1_MOUSE | P28481 from UniProtKB/Swiss-Prot  Length:1487

    Alignment length:58
                                   747       757       767       777       787        
          CO2A1_MOUSE   738 GPPGAQGPPGLQGMPGERGAAGIAGPKGDRGDVGEKGPEGAPGKDGGRGLTGPIGPPG 795
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ...---...---................---------------------------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 4bkl G  10 GPp---GPp---GMpGERGAAGIAGPKG---------------------------PpG  34
                              |   | |-  | |   23       | -         -         -     || 
                              |  13 |  16 |           31                          32| 
                             12-HYP15-HYP18-HYP                                    33-HYP

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4BKL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BKL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BKL)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E,F,G   (CO2A1_MOUSE | P28481)
molecular function
    GO:0005201    extracellular matrix structural constituent    The action of a molecule that contributes to the structural integrity of the extracellular matrix.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0048407    platelet-derived growth factor binding    Interacting selectively and non-covalently with platelet-derived growth factor.
biological process
    GO:0060348    bone development    The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components.
    GO:0001502    cartilage condensation    The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0060351    cartilage development involved in endochondral bone morphogenesis    The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones.
    GO:0071773    cellular response to BMP stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bone morphogenetic protein (BMP) stimulus.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0002062    chondrocyte differentiation    The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage.
    GO:0030199    collagen fibril organization    Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix.
    GO:0060272    embryonic skeletal joint morphogenesis    The process in which the anatomical structures of skeletal joints are generated and organized during the embryonic phase. A skeletal joint is the connecting structure between the bones of the skeleton.
    GO:0001958    endochondral ossification    Replacement ossification wherein bone tissue replaces cartilage.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0048839    inner ear development    The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure.
    GO:0042472    inner ear morphogenesis    The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively.
    GO:0060174    limb bud formation    The process pertaining to the initial formation of a limb bud from unspecified parts. This process begins with the formation of a local condensation of mesenchyme cells within the prospective limb field, and ends when a limb bud is recognizable.
    GO:0035108    limb morphogenesis    The process in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping.
    GO:2001240    negative regulation of extrinsic apoptotic signaling pathway in absence of ligand    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
    GO:0030903    notochord development    The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0071599    otic vesicle development    The process whose specific outcome is the progression of the otic vesicle over time, from its formation to the mature structure. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0006029    proteoglycan metabolic process    The chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
    GO:0010468    regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0048705    skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized.
    GO:0001894    tissue homeostasis    A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    GO:0005585    collagen type II trimer    A collagen homotrimer of alpha1(II) chains; type II collagen triple helices associate to form fibrils.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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        CO2A1_MOUSE | P284812w65

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