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(-) Description

Title :  NMR STUDY OF THE TRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN-LIKE DOMAIN (TB MODULE/8-CYS DOMAIN), NMR, 21 STRUCTURES
 
Authors :  X. Yuan, A. K. Downing, V. Knott, P. A. Handford
Date :  22 Jul 97  (Deposition) - 28 Jan 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
Keywords :  Fibrillin Fragment, Microfibril, Tb Module, Marfan Syndrome, Connective Tissue, Novel Fold, Extracellular Matrix (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Yuan, A. K. Downing, V. Knott, P. A. Handford
Solution Structure Of The Transforming Growth Factor Beta-Binding Protein-Like Module, A Domain Associated With Matrix Fibrils.
Embo J. V. 16 6659 1997
PubMed-ID: 9362480  |  Reference-DOI: 10.1093/EMBOJ/16.22.6659
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBRILLIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE30
    Expression System StrainNM554
    Expression System Taxid562
    FragmentTRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN- LIKE DOMAIN 6(TB6), RESIDUES 2054 - 2125
    Fragment (source)TRANSFORMING GROWTH FACTOR BETA BINDING PROTEIN- LIKE DOMAIN 6(TB6), RESIDUES 2054-2125
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (21x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1APJ)

(-) Sites  (0, 0)

(no "Site" information available for 1APJ)

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:2061 -A:2083
2A:2070 -A:2096
3A:2084 -A:2099
4A:2085 -A:2111

(-) Cis Peptide Bonds  (1, 21)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21Glu A:2102 -Pro A:2103

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (10, 10)

NMR Structure (10, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_076113C2084WFBN1_HUMANDisease (MFS)  ---AC2084W
02UniProtVAR_076114C2084YFBN1_HUMANDisease (MFS)  ---AC2084Y
03UniProtVAR_023899C2085RFBN1_HUMANDisease (MFS)  ---AC2085R
04UniProtVAR_002333C2099WFBN1_HUMANDisease (MFS)  ---AC2099W
05UniProtVAR_018028T2101MFBN1_HUMANPolymorphism200816828AT2101M
06UniProtVAR_076115E2105KFBN1_HUMANDisease  ---AE2105K
07UniProtVAR_018029C2111RFBN1_HUMANDisease (MFS)363815AC2111R
08UniProtVAR_002334C2111YFBN1_HUMANDisease (MFS)  ---AC2111Y
09UniProtVAR_055732Y2113FFBN1_HUMANPolymorphism363816AY2113F
10UniProtVAR_076116I2118MFBN1_HUMANDisease (MFS)  ---AI2118M

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TBPS51364 TGF-beta binding (TB) domain profile.FBN1_HUMAN184-227
334-389
659-711
851-890
956-1008
1532-1589
1693-1748
2059-2111
2337-2390
  1-
-
-
-
-
-
-
A:2059-2111
-

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003166231ENSE00001525471chr15:48937918-48937772147FBN1_HUMAN-00--
1.2ENST000003166232ENSE00002176401chr15:48937147-48936803345FBN1_HUMAN1-55550--
1.3ENST000003166233ENSE00001761744chr15:48905289-4890520783FBN1_HUMAN55-83290--
1.4ENST000003166234ENSE00001729100chr15:48903023-4890292599FBN1_HUMAN83-116340--
1.5ENST000003166235ENSE00001737946chr15:48892431-4889233696FBN1_HUMAN116-148330--
1.6ENST000003166236ENSE00001783191chr15:48888575-4888848096FBN1_HUMAN148-180330--
1.7ENST000003166237ENSE00001764592chr15:48830005-48829808198FBN1_HUMAN180-246670--
1.8ENST000003166238ENSE00001793339chr15:48826402-48826277126FBN1_HUMAN246-288430--
1.9ENST000003166239ENSE00001771562chr15:48818452-48818327126FBN1_HUMAN288-330430--
1.10ENST0000031662310ENSE00001744589chr15:48813014-48812856159FBN1_HUMAN330-383540--
1.11ENST0000031662311ENSE00001699841chr15:48808559-48808380180FBN1_HUMAN383-443610--
1.12ENST0000031662312ENSE00001599991chr15:48807724-48807584141FBN1_HUMAN443-490480--
1.13ENST0000031662313ENSE00001788059chr15:48805865-48805746120FBN1_HUMAN490-530410--
1.14ENST0000031662314ENSE00001675795chr15:48802366-48802241126FBN1_HUMAN530-572430--
1.15ENST0000031662315ENSE00001666782chr15:48800901-48800779123FBN1_HUMAN572-613420--
1.16ENST0000031662316ENSE00001721875chr15:48797344-48797222123FBN1_HUMAN613-654420--
1.17ENST0000031662317ENSE00001715942chr15:48796136-48795984153FBN1_HUMAN654-705520--
1.18ENST0000031662318ENSE00001640683chr15:48791235-4879118254FBN1_HUMAN705-723190--
1.19ENST0000031662319ENSE00001612341chr15:48789588-48789463126FBN1_HUMAN723-765430--
1.20ENST0000031662320ENSE00001630897chr15:48788422-48788297126FBN1_HUMAN765-807430--
1.21ENST0000031662321ENSE00001772761chr15:48787785-48787666120FBN1_HUMAN807-847410--
1.22ENST0000031662322ENSE00001661869chr15:48787457-48787320138FBN1_HUMAN847-893470--
1.23ENST0000031662323ENSE00001788284chr15:48786451-4878640151FBN1_HUMAN893-910180--
1.24ENST0000031662324ENSE00001769793chr15:48784783-48784658126FBN1_HUMAN910-952430--
1.25ENST0000031662325ENSE00001717687chr15:48782275-48782048228FBN1_HUMAN952-1028770--
1.26ENST0000031662326ENSE00001613423chr15:48780690-48780565126FBN1_HUMAN1028-1070430--
1.27ENST0000031662327ENSE00001762721chr15:48780438-48780310129FBN1_HUMAN1070-1113440--
1.28ENST0000031662328ENSE00001641154chr15:48779634-48779509126FBN1_HUMAN1113-1155430--
1.29ENST0000031662329ENSE00001800492chr15:48779397-48779272126FBN1_HUMAN1155-1197430--
1.30ENST0000031662330ENSE00001620699chr15:48777693-48777571123FBN1_HUMAN1197-1238420--
1.31ENST0000031662331ENSE00001613453chr15:48776140-48776015126FBN1_HUMAN1238-1280430--
1.32ENST0000031662332ENSE00001753582chr15:48773977-48773852126FBN1_HUMAN1280-1322430--
1.33ENST0000031662333ENSE00001628258chr15:48766847-48766725123FBN1_HUMAN1322-1363420--
1.34ENST0000031662334ENSE00001770461chr15:48766574-48766452123FBN1_HUMAN1363-1404420--
1.35ENST0000031662335ENSE00001613724chr15:48764873-48764748126FBN1_HUMAN1404-1446430--
1.36ENST0000031662336ENSE00000884505chr15:48762953-48762831123FBN1_HUMAN1446-1487420--
1.37ENST0000031662337ENSE00000884504chr15:48760731-48760609123FBN1_HUMAN1487-1528420--
1.38ENST0000031662338ENSE00000686984chr15:48760299-48760135165FBN1_HUMAN1528-1583560--
1.39ENST0000031662339ENSE00000686980chr15:48758055-4875798769FBN1_HUMAN1583-1606240--
1.40ENST0000031662340ENSE00000686976chr15:48757890-48757765126FBN1_HUMAN1606-1648430--
1.41ENST0000031662341ENSE00000884503chr15:48756218-48756096123FBN1_HUMAN1648-1689420--
1.42ENST0000031662342ENSE00000686967chr15:48755437-48755279159FBN1_HUMAN1689-1742540--
1.43ENST0000031662343ENSE00001175019chr15:48752514-4875244372FBN1_HUMAN1742-1766250--
1.44ENST0000031662344ENSE00000884501chr15:48748959-48748834126FBN1_HUMAN1766-1808430--
1.45ENST0000031662345ENSE00000884500chr15:48744881-48744759123FBN1_HUMAN1808-1849420--
1.46ENST0000031662346ENSE00001181714chr15:48741090-48740965126FBN1_HUMAN1849-1891430--
1.47ENST0000031662347ENSE00001175887chr15:48739019-48738903117FBN1_HUMAN1891-1930400--
1.48ENST0000031662348ENSE00000884497chr15:48737701-48737573129FBN1_HUMAN1930-1973440--
1.49ENST0000031662349ENSE00000884496chr15:48736857-48736738120FBN1_HUMAN1973-2013410--
1.50ENST0000031662350ENSE00000884495chr15:48734043-48733918126FBN1_HUMAN2013-2055431A:1-2055 (gaps)8
1.51ENST0000031662351ENSE00000884494chr15:48730114-48729965150FBN1_HUMAN2055-2105511A:2055-210551
1.52ENST0000031662352ENSE00000884493chr15:48729584-4872951966FBN1_HUMAN2105-2127231A:2105-212521
1.53ENST0000031662353ENSE00000884492chr15:48729274-48729158117FBN1_HUMAN2127-2166400--
1.54ENST0000031662354ENSE00001721904chr15:48726910-48726791120FBN1_HUMAN2166-2206410--
1.55ENST0000031662355ENSE00001759584chr15:48725185-48725063123FBN1_HUMAN2206-2247420--
1.56ENST0000031662356ENSE00000884489chr15:48722999-48722868132FBN1_HUMAN2247-2291450--
1.57ENST0000031662357ENSE00000884488chr15:48720668-48720543126FBN1_HUMAN2291-2333430--
1.59ENST0000031662359ENSE00001682471chr15:48719970-48719764207FBN1_HUMAN2333-2402700--
1.60ENST0000031662360ENSE00001657678chr15:48718061-48717936126FBN1_HUMAN2402-2444430--
1.61ENST0000031662361ENSE00001705569chr15:48717688-48717566123FBN1_HUMAN2444-2485420--
1.62ENST0000031662362ENSE00001770578chr15:48714265-48714149117FBN1_HUMAN2485-2524400--
1.63ENST0000031662363ENSE00001771268chr15:48713883-48713755129FBN1_HUMAN2524-2567440--
1.64ENST0000031662364ENSE00001767848chr15:48713003-48712884120FBN1_HUMAN2567-2607410--
1.65ENST0000031662365ENSE00001743300chr15:48707964-48707733232FBN1_HUMAN2607-2684780--
1.66ENST0000031662366ENSE00001804196chr15:48704940-48704766175FBN1_HUMAN2684-2742590--
1.67ENST0000031662367ENSE00001662441chr15:48703576-487005053072FBN1_HUMAN2743-28711290--

(-) Sequences/Alignments

NMR Structure
   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:74
 aligned with FBN1_HUMAN | P35555 from UniProtKB/Swiss-Prot  Length:2871

    Alignment length:78
                                  2057      2067      2077      2087      2097      2107      2117        
          FBN1_HUMAN   2048 SSGRRCQDLRMSYCYAKFEGGKCSSPKSRNHSKQECCCALKGEGWGDPCELCPTEPDEAFRQICPYGSGIIVGPDDSA 2125
               SCOP domains d1    apja_ A: Fibrillin                                                       SCOP domains
               CATH domains 1a    pjA00 A:1-2125 Extracellular Matrix Fibrillin                            CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..----....ee.eeeee....eeee....eehhhhh......ee....ee......hhhhhh............... Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------WR-------------W-M---K-----R-F----M------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------Y--------------------------Y-------------- SAPs(SNPs) (2)
                    PROSITE -----------TB  PDB: A:2059-2111 UniProt: 2059-2111              -------------- PROSITE
           Transcript 1 (1) 1.50    -------------------------------------------------Exon 1.52             Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.51  PDB: A:2055-2105 UniProt: 2055-2105     -------------------- Transcript 1 (2)
                1apj A    1 SA----QDLRMSYCYAKFEGGKCSSPKSRNHSKQECCCALKGEGWGDPCELCPTEPDEAFRQICPYGSGIIVGPDDSA 2125
                             |    2057      2067      2077      2087      2097      2107      2117        
                             2 2054                                                                       

   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, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1APJ)

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (FBN1_HUMAN | P35555)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0030023    extracellular matrix constituent conferring elasticity    A component of the extracellular matrix that enables the matrix to recoil after transient stretching.
    GO:0005201    extracellular matrix structural constituent    The action of a molecule that contributes to the structural integrity of the extracellular matrix.
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0043010    camera-type eye development    The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field.
    GO:1990314    cellular response to insulin-like growth factor 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 an insulin-like growth factor stimulus.
    GO:0071560    cellular response to transforming growth factor beta 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 transforming growth factor beta stimulus.
    GO:0048048    embryonic eye morphogenesis    The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0001656    metanephros development    The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine.
    GO:0048050    post-embryonic eye morphogenesis    The process, occurring after embryonic development, by which the anatomical structures of the eye are generated and organized. The eye is the organ of sight.
    GO:0090287    regulation of cellular response to growth factor stimulus    Any process that modulates the rate, frequency, or extent of a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
    GO:0035582    sequestering of BMP in extracellular matrix    Confining a bone morphogenetic protein (BMP) to the extracellular matrix (ECM), such that it is separated from other components of the signaling pathway, including its cell surface receptor. Bone morphogenetic proteins (BMPs) are secreted as homodimers, non-covalently associated with N-terminal pro-peptides, and are targeted to the extracellular matrix through interaction with matrix proteins.
    GO:0035583    sequestering of TGFbeta in extracellular matrix    Confining TGFbeta to the extracellular matrix (ECM) such that it is separated from other components of the signaling pathway, including its cell surface receptor. TGFbeta is secreted as part of a latent complex that is targeted to the extracellular matrix through latent-TGFbeta-binding protein (LTBP)-mediated association with matrix proteins.
    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: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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0001527    microfibril    Extracellular matrix components occurring independently or along with elastin. Thought to have force-bearing functions in tendon. In addition to fibrillins, microfibrils may contain other associated proteins.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        FBN1_HUMAN | P355551emn 1emo 1lmj 1uzj 1uzk 1uzp 1uzq 2m74 2w86

(-) Related Entries Specified in the PDB File

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