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(-) Description

Title :  THE FOURTH FAS1 DOMAIN STRUCTURE OF HUMAN BIGH3
 
Authors :  J. -H. Yoo, H. -S. Cho
Date :  08 Jul 08  (Deposition) - 21 Jul 09  (Release) - 21 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rgd-Containing Collagen-Associated Protein, Fas1, Bigh3, Vision, Amyloid, Rgd-Cap, Secreted, Disease Mutation, Kerato-Epithelin, Fasciclin 1, Polymorphism, Cell Adhesion, Sensory Transduction, Extracellular Matrix (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. -H. Yoo, E. Kim, J. Kim, H. -S. Cho
The Structural Analysis Of The Fas1 Domain 4 Of Big-H3 For Relationship With Corneal Dystrophy
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSFORMING GROWTH FACTOR-BETA-INDUCED PROTEIN IG-H3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPRSET(A)
    FragmentFOURTH FAS1 DOMAIN, RESIDUES 502-633
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA IG-H3, KERATO-EPITHELIN, RGD-CONTAINING COLLAGEN-ASSOCIATED PROTEIN, RGD-CAP

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2VXP)

(-) Sites  (0, 0)

(no "Site" information available for 2VXP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VXP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VXP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (23, 46)

Asymmetric Unit (23, 46)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_031535V505DBGH3_HUMANDisease (CDL1)  ---A/BV505D
02UniProtVAR_031536L509RBGH3_HUMANDisease (EBMD)121909216A/BL509R
03UniProtVAR_012446L518PBGH3_HUMANDisease (CDL1)  ---A/BL518P
04UniProtVAR_018484L518RBGH3_HUMANDisease (CDL1)  ---A/BL518R
05UniProtVAR_005080L527RBGH3_HUMANDisease (CDL1)  ---A/BL527R
06UniProtVAR_018485T538RBGH3_HUMANDisease (CDL1)  ---A/BT538R
07UniProtVAR_031537V539DBGH3_HUMANUnclassified  ---A/BV539D
08UniProtVAR_031538F540SBGH3_HUMANDisease (CDL3A)121909214A/BF540S
09UniProtVAR_012447N544SBGH3_HUMANPolymorphism777288957A/BN544S
10UniProtVAR_031539A546DBGH3_HUMANDisease (CDL1)267607109A/BA546D
11UniProtVAR_012448A546TBGH3_HUMANDisease (CDL3A)  ---A/BA546T
12UniProtVAR_031540P551QBGH3_HUMANDisease (CDL1)267607110A/BP551Q
13UniProtVAR_005082R555QBGH3_HUMANDisease (CDTB)121909209A/BR555Q
14UniProtVAR_005083R555WBGH3_HUMANDisease (CDGG1)121909208A/BR555W
15UniProtVAR_031541L569RBGH3_HUMANDisease (CDL1)  ---A/BL569R
16UniProtVAR_031543H572RBGH3_HUMANDisease (CDL1)  ---A/BH572R
17UniProtVAR_031544G594VBGH3_HUMANUnclassified  ---A/BG594V
18UniProtVAR_012449N622HBGH3_HUMANUnclassified  ---A/BN622H
19UniProtVAR_018486N622KBGH3_HUMANDisease (CDL3A)  ---A/BN622K
20UniProtVAR_018487G623DBGH3_HUMANDisease (CDL1)121909215A/BG623D
21UniProtVAR_018488H626PBGH3_HUMANDisease (CDL1)  ---A/BH626P
22UniProtVAR_012450H626RBGH3_HUMANDisease (CDL1)  ---A/BH626R
23UniProtVAR_018489V631DBGH3_HUMANUnclassified  ---A/BV631D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (23, 23)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_031535V505DBGH3_HUMANDisease (CDL1)  ---AV505D
02UniProtVAR_031536L509RBGH3_HUMANDisease (EBMD)121909216AL509R
03UniProtVAR_012446L518PBGH3_HUMANDisease (CDL1)  ---AL518P
04UniProtVAR_018484L518RBGH3_HUMANDisease (CDL1)  ---AL518R
05UniProtVAR_005080L527RBGH3_HUMANDisease (CDL1)  ---AL527R
06UniProtVAR_018485T538RBGH3_HUMANDisease (CDL1)  ---AT538R
07UniProtVAR_031537V539DBGH3_HUMANUnclassified  ---AV539D
08UniProtVAR_031538F540SBGH3_HUMANDisease (CDL3A)121909214AF540S
09UniProtVAR_012447N544SBGH3_HUMANPolymorphism777288957AN544S
10UniProtVAR_031539A546DBGH3_HUMANDisease (CDL1)267607109AA546D
11UniProtVAR_012448A546TBGH3_HUMANDisease (CDL3A)  ---AA546T
12UniProtVAR_031540P551QBGH3_HUMANDisease (CDL1)267607110AP551Q
13UniProtVAR_005082R555QBGH3_HUMANDisease (CDTB)121909209AR555Q
14UniProtVAR_005083R555WBGH3_HUMANDisease (CDGG1)121909208AR555W
15UniProtVAR_031541L569RBGH3_HUMANDisease (CDL1)  ---AL569R
16UniProtVAR_031543H572RBGH3_HUMANDisease (CDL1)  ---AH572R
17UniProtVAR_031544G594VBGH3_HUMANUnclassified  ---AG594V
18UniProtVAR_012449N622HBGH3_HUMANUnclassified  ---AN622H
19UniProtVAR_018486N622KBGH3_HUMANDisease (CDL3A)  ---AN622K
20UniProtVAR_018487G623DBGH3_HUMANDisease (CDL1)121909215AG623D
21UniProtVAR_018488H626PBGH3_HUMANDisease (CDL1)  ---AH626P
22UniProtVAR_012450H626RBGH3_HUMANDisease (CDL1)  ---AH626R
23UniProtVAR_018489V631DBGH3_HUMANUnclassified  ---AV631D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (23, 23)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_031535V505DBGH3_HUMANDisease (CDL1)  ---BV505D
02UniProtVAR_031536L509RBGH3_HUMANDisease (EBMD)121909216BL509R
03UniProtVAR_012446L518PBGH3_HUMANDisease (CDL1)  ---BL518P
04UniProtVAR_018484L518RBGH3_HUMANDisease (CDL1)  ---BL518R
05UniProtVAR_005080L527RBGH3_HUMANDisease (CDL1)  ---BL527R
06UniProtVAR_018485T538RBGH3_HUMANDisease (CDL1)  ---BT538R
07UniProtVAR_031537V539DBGH3_HUMANUnclassified  ---BV539D
08UniProtVAR_031538F540SBGH3_HUMANDisease (CDL3A)121909214BF540S
09UniProtVAR_012447N544SBGH3_HUMANPolymorphism777288957BN544S
10UniProtVAR_031539A546DBGH3_HUMANDisease (CDL1)267607109BA546D
11UniProtVAR_012448A546TBGH3_HUMANDisease (CDL3A)  ---BA546T
12UniProtVAR_031540P551QBGH3_HUMANDisease (CDL1)267607110BP551Q
13UniProtVAR_005082R555QBGH3_HUMANDisease (CDTB)121909209BR555Q
14UniProtVAR_005083R555WBGH3_HUMANDisease (CDGG1)121909208BR555W
15UniProtVAR_031541L569RBGH3_HUMANDisease (CDL1)  ---BL569R
16UniProtVAR_031543H572RBGH3_HUMANDisease (CDL1)  ---BH572R
17UniProtVAR_031544G594VBGH3_HUMANUnclassified  ---BG594V
18UniProtVAR_012449N622HBGH3_HUMANUnclassified  ---BN622H
19UniProtVAR_018486N622KBGH3_HUMANDisease (CDL3A)  ---BN622K
20UniProtVAR_018487G623DBGH3_HUMANDisease (CDL1)121909215BG623D
21UniProtVAR_018488H626PBGH3_HUMANDisease (CDL1)  ---BH626P
22UniProtVAR_012450H626RBGH3_HUMANDisease (CDL1)  ---BH626R
23UniProtVAR_018489V631DBGH3_HUMANUnclassified  ---BV631D

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAS1PS50213 FAS1/BIgH3 domain profile.BGH3_HUMAN103-236
240-371
375-498
502-632
 
  2-
-
-
A:502-632
B:502-632
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAS1PS50213 FAS1/BIgH3 domain profile.BGH3_HUMAN103-236
240-371
375-498
502-632
 
  1-
-
-
A:502-632
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAS1PS50213 FAS1/BIgH3 domain profile.BGH3_HUMAN103-236
240-371
375-498
502-632
 
  1-
-
-
-
B:502-632

(-) Exons   (0, 0)

(no "Exon" information available for 2VXP)

(-) Sequences/Alignments

Asymmetric 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:131
 aligned with BGH3_HUMAN | Q15582 from UniProtKB/Swiss-Prot  Length:683

    Alignment length:131
                                   511       521       531       541       551       561       571       581       591       601       611       621       631 
           BGH3_HUMAN   502 MGTVMDVLKGDNRFSMLVAAIQSAGLTETLNREGVYTVFAPTNEAFRALPPRERSRLLGDAKELANILKYHIGDEILVSGGIGALVRLKSLQGDKLEVSLKNNVVSVNKEPVAEPDIMATNGVVHVITNVL 632
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh....hhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeee.....eeeeeee..eeee......eeeeee..eeeeee.... Sec.struct. author
             SAPs(SNPs) (1) ---D---R--------P--------R----------RDS---S-D----Q---Q-------------R--R---------------------V---------------------------HD--P----D- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------R---------------------------T--------W------------------------------------------------------------------K---R------ SAPs(SNPs) (2)
                    PROSITE FAS1  PDB: A:502-632 UniProt: 502-632                                                                                               PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxp A 502 MGTVMDVLKGDNRFSMLVAAIQSAGLTETLNREGVYTVFAPTNEAFRALPPRERSRLLGDAKELANILKYHIGDEILVSGGIGALVRLKSLQGDKLEVSLKNNVVSVNKEPVAEPDIMATNGVVHVITNVL 632
                                   511       521       531       541       551       561       571       581       591       601       611       621       631 

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with BGH3_HUMAN | Q15582 from UniProtKB/Swiss-Prot  Length:683

    Alignment length:131
                                   511       521       531       541       551       561       571       581       591       601       611       621       631 
           BGH3_HUMAN   502 MGTVMDVLKGDNRFSMLVAAIQSAGLTETLNREGVYTVFAPTNEAFRALPPRERSRLLGDAKELANILKYHIGDEILVSGGIGALVRLKSLQGDKLEVSLKNNVVSVNKEPVAEPDIMATNGVVHVITNVL 632
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Fasciclin-2vxpB01 B:513-632                                                                                              Pfam domains (1)
           Pfam domains (2) -----------Fasciclin-2vxpB02 B:513-632                                                                                              Pfam domains (2)
         Sec.struct. author ..hhhhhhhhh..hhhhhhhhhhh.hhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee............eeee.....eeeeee....eee.........ee...eeeeee.... Sec.struct. author
             SAPs(SNPs) (1) ---D---R--------P--------R----------RDS---S-D----Q---Q-------------R--R---------------------V---------------------------HD--P----D- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------R---------------------------T--------W------------------------------------------------------------------K---R------ SAPs(SNPs) (2)
                    PROSITE FAS1  PDB: B:502-632 UniProt: 502-632                                                                                               PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vxp B 502 MGTVMDVLKGDNRFSMLVAAIQSAGLTETLNREGVYTVFAPTNEAFRALPPRERSRLLGDAKELANILKYHIGDEILVSGGIGALVRLKSLQGDKLEVSLKNNVVSVNKEPVAEPDIMATNGVVHVITNVL 632
                                   511       521       531       541       551       561       571       581       591       601       611       621       631 

   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 2VXP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VXP)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BGH3_HUMAN | Q15582)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0050840    extracellular matrix binding    Interacting selectively and non-covalently with a component 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).
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    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: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:0007162    negative regulation of cell adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion.
    GO:0050896    response to stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    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: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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and 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.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BGH3_HUMAN | Q155821x3b 2ltb 2ltc

(-) Related Entries Specified in the PDB File

1x3b SOLUTION STRUCTURE OF THE FAS1 DOMAIN OF THE TRANSFORMINGGROWTH FACTOR-BETA INDUCED PROTEIN IG-H3