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(-) Description

Title :  STRUCTURE OF PARATHYROID HORMONE-RELATED PROTEIN COMPLEXED TO A NEUTRALIZING MONOCLONAL ANTIBODY
 
Authors :  W. J. Mckinstry, G. Polekhina, H. Diefenbach-Jagger, P. W. M. Ho, K. Sat E. Onuma, M. T. Gillespie, T. J. Martin, M. W. Parker
Date :  03 Dec 08  (Deposition) - 28 Apr 09  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Pthrp Complexed To Fab, Cleavage On Pair Of Basic Residues, Hormone, Nucleus, Secreted, Immune System-Hormone Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. J. Mckinstry, G. Polekhina, H. Diefenbach-Jagger, P. W. M. Ho, K. Sato, E. Onuma, M. T. Gillespie, T. J. Martin, M. W. Parker
Structural Basis For Antibody Discrimination Between Two Hormones That Recognize The Parathyroid Hormone Receptor
J. Biol. Chem. V. 284 15557 2009
PubMed-ID: 19346515  |  Reference-DOI: 10.1074/JBC.M900044200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MONOCLONAL ANTIBODY, HEAVY CHAIN, FAB FRAGMENT
    ChainsA
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System CellHYBRIDOMA CELL
    Expression System Cellular LocationABDOMINAL CAVITY OF BALB/C
    Expression System CommonMOUSE
    Expression System Taxid10090
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - MONOCLONAL ANTIBODY, LIGHT CHAIN, FAB FRAGMENT
    ChainsB
    EngineeredYES
    Expression SystemMUS MUSCULUS
    Expression System CellHYBRIDOMA CELL
    Expression System Cellular LocationABDOMINAL CAVITY OF BALB/C
    Expression System CommonMOUSE
    Expression System Taxid10090
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - PARATHYROID HORMONE-RELATED PROTEIN
    ChainsP
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPTH-RP, PTHRP

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3FFD)

(-) Sites  (0, 0)

(no "Site" information available for 3FFD)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:96
2A:145 -A:200
3B:22 -B:92
4B:143 -B:201

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe A:151 -Pro A:152
2Glu A:153 -Pro A:154
3Ser B:149 -Pro B:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063712L60PPTHR_HUMANDisease (BDE2)267606985PL24P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FFD)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003958721bENSE00001523139chr12:28124903-2812486044PTHR_HUMAN-00--
1.2ENST000003958722ENSE00001647300chr12:28123200-28122958243PTHR_HUMAN-00--
1.4ENST000003958724ENSE00001756275chr12:28122449-28122327123PTHR_HUMAN1-34340--
1.5aENST000003958725aENSE00001188730chr12:28116703-28116281423PTHR_HUMAN34-1751421P:14-3118
1.7ENST000003958727ENSE00001523130chr12:28111501-28111017485PTHR_HUMAN175-17730--

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3ffdA01 A:1-118 Immunoglobulins                                                                                       3ffdA02 A:119-217 Immunoglobulins                                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeeehhh.eeeeee...hhhhheeeeeee........ee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh.....ee...eee..eeeeeeeeee..hhhhhh..eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ffd A   1 EVQLVESGGDLVKPGGSLKLSCAASGFTFSSYGMSWIRQTPDKRLEWVATISSGGSYTYYPDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMFYCARQTTMTYFAYWGQGTLVTVSAAKTTPPSVYPLAPMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIEPA 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130||     148       158       168       178       188       198       208       218
                                                                                                                                                            131|                                                                              
                                                                                                                                                             140                                                                              

Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d3ffdb1 B:1-116 automated matches                                                                                   d3ffdb2 B:117-217 automated matches                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeeee....eeeeeee.hhhh...eeeeee......eeeeee.....eee.......eeeeee..eeeeee...hhhhheeeeeeeeeee..eeeeee...eeeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eee...eee..eeeeeeeeeeehhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ffd B   1 QLVLTQSSSASFSLGASAKLTCTLSSQHSTYTIEWYQQQPLKPPKYVMDLKQDGSHSTGDGIPDRFSGSSSGADRYLSISNIQPEDEAMYICGVGDTIKEQFVYVFGGGTKVTVLGEPKSTPTLTVFPPSSEELKENKATLVCLISNFSPSGVTVAWKANGTPITQGVDTSNPTKEGNKFMASSFLHLTSDQWRSHNSFTCQVTHEGDTVEKSLSPA 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       

Chain P from PDB  Type:PROTEIN  Length:18
 aligned with PTHR_HUMAN | P12272 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:18
                                    59        
           PTHR_HUMAN    50 SIQDLRRRFFLHHLIAEI  67
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------P------- SAPs(SNPs)
                    PROSITE ------------------ PROSITE
               Transcript 1 Exon 1.5a          Transcript 1
                 3ffd P  14 SIQDLRRRFFLHHLIAEI  31
                                    23        

   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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FFD)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (PTHR_HUMAN | P12272)
molecular function
    GO:0005179    hormone activity    The action characteristic of a hormone, any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action. The term was originally applied to agents with a stimulatory physiological action in vertebrate animals (as opposed to a chalone, which has a depressant action). Usage is now extended to regulatory compounds in lower animals and plants, and to synthetic substances having comparable effects; all bind receptors and trigger some biological process.
    GO:0051428    peptide hormone receptor binding    Interacting selectively and non-covalently with a receptor for peptide hormones.
biological process
    GO:0007189    adenylate cyclase-activating G-protein coupled receptor signaling pathway    The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through activation of adenylyl cyclase activity and a subsequent increase in the concentration of cyclic AMP (cAMP).
    GO:0046058    cAMP metabolic process    The chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0008544    epidermis development    The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species.
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0032331    negative regulation of chondrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation.
    GO:0002076    osteoblast development    The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone.
    GO:0030819    positive regulation of cAMP biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0032330    regulation of chondrocyte differentiation    Any process that modulates the frequency, rate or extent of chondrocyte differentiation.
    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: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).
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PTHR_HUMAN | P122721bzg 1et3 1m5n 3h3g

(-) Related Entries Specified in the PDB File

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