Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO R132K:L121E MUTANT OF CELLULAR RETINOIC ACID-BINDING PROTEIN II AT 1.68 ANGSTROM RESOLUTION
 
Authors :  X. Jia, C. T. Watson, J. H. Geiger
Date :  25 Jun 09  (Deposition) - 28 Jul 09  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crabpii, Retinoic Acid, Retinoid, Nucleus, Retinol-Binding, Transport, Vitamin A, Lipid Binding, Retinal Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Vasileiou, W. Wang, X. Jia, K. S. Lee, C. T. Watson, J. H. Geiger, B. Borhan
Elucidating The Exact Role Of Engineered Crabpii Residues For The Formation Of A Retinal Protonated Schiff Base.
Proteins V. 77 812 2009
PubMed-ID: 19603486  |  Reference-DOI: 10.1002/PROT.22495

(-) Compounds

Molecule 1 - CELLULAR RETINOIC ACID-BINDING PROTEIN 2
    ChainsB, A
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidCRABPII-PET17B-KE
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCRABP2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCELLULAR RETINOIC ACID-BINDING PROTEIN II, CRABP-II

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3I17)

(-) Sites  (0, 0)

(no "Site" information available for 3I17)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I17)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3I17)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I17)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FABPPS00214 Cytosolic fatty-acid binding proteins signature.RABP2_HUMAN6-23
 
  2A:5-22
B:5-22

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003682222aENSE00001446616chr1:156675393-156675169225RABP2_HUMAN1-24242A:1-23
B:1-23
23
23
1.3bENST000003682223bENSE00000959257chr1:156670844-156670666179RABP2_HUMAN24-83602A:23-82
B:23-82
60
60
1.4ENST000003682224ENSE00000959258chr1:156670450-156670334117RABP2_HUMAN84-122392A:83-121
B:83-121
39
39
1.5bENST000003682225bENSE00001446614chr1:156669868-156669398471RABP2_HUMAN123-138162A:122-137
B:122-137
16
16

(-) 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:137
 aligned with RABP2_HUMAN | P29373 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
          RABP2_HUMAN     2 PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE 138
               SCOP domains d3i17a_ A: Cellular retinoic-acid-binding protein (CRABP)                                                                                 SCOP domains
               CATH domains 3i17A00 A:1-137  [code=2.40.128.20, no name defined]                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhhh..hhhhhhhhhhhhhh.eeeeeee..eeeeeee....eeeeeee....eeee.....eeeeeeeeee..eeeeeeee.......eeeeeee....eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----FABP  PDB: A:5-22 ------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-23 -----------------------------------------------------------Exon 1.4  PDB: A:83-121 UniProt: 84-122Exon 1.5b        Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.3b  PDB: A:23-82 UniProt: 24-83                      ------------------------------------------------------- Transcript 1 (2)
                 3i17 A   1 PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELIETMTADDVVCTKVYVRE 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with RABP2_HUMAN | P29373 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       
          RABP2_HUMAN     2 PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE 138
               SCOP domains d3i17b_ B: Cellular retinoic-acid-binding protein (CRABP)                                                                                 SCOP domains
               CATH domains 3i17B00 B:1-137  [code=2.40.128.20, no name defined]                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeehhhhhhhhh..hhhhhhhhhhhh...eeeeeee..eeeeeee....eeeeeee....eeee.....eeeeeeeeee..eeeeeeee.......eeeeeee....eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----FABP  PDB: B:5-22 ------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:1-23 -----------------------------------------------------------Exon 1.4  PDB: B:83-121 UniProt: 84-122Exon 1.5b        Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.3b  PDB: B:23-82 UniProt: 24-83                      ------------------------------------------------------- Transcript 1 (2)
                 3i17 B   1 PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRPCKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELIETMTADDVVCTKVYVRE 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       

   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 3I17)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RABP2_HUMAN | P29373)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0016918    retinal binding    Interacting selectively and non-covalently with retinal, one of the forms of vitamin A. Retinal plays an important role in the visual process in most vertebrates, combining with opsins to form visual pigments in the retina.
    GO:0001972    retinoic acid binding    Interacting selectively and non-covalently with retinoic acid, 3,7-dimethyl-9-(2,6,-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid.
    GO:0005501    retinoid binding    Interacting selectively and non-covalently with retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
    GO:0019841    retinol binding    Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0035115    embryonic forelimb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
    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:0048672    positive regulation of collateral sprouting    Any process that activates or increases the frequency, rate or extent of collateral sprouting.
    GO:0048385    regulation of retinoic acid receptor signaling pathway    Any process that modulates the frequency, rate or extent of retinoic acid receptor signaling pathway activity.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042573    retinoic acid metabolic process    The chemical reactions and pathways involving retinoic acid, one of the three components that makes up vitamin A.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3i17)
 
  Sites
(no "Sites" information available for 3i17)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3i17)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3i17
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RABP2_HUMAN | P29373
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  RABP2_HUMAN | P29373
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RABP2_HUMAN | P293731blr 1bm5 1cbq 1cbs 1xca 2cbs 2fr3 2frs 2fs6 2fs7 2g78 2g79 2g7b 3cbs 3cr6 3cwk 3d95 3d96 3d97 3f8a 3f9d 3fa6 3fa7 3fa8 3fa9 3fek 3fel 3fen 3fep 4i9r 4i9s 4m6s 4m7m 4qgv 4qgw 4qgx 4ybp 4ybu 4yce 4ych 4yda 4ydb 4yfp 4yfq 4yfr 4ygg 4ygh 4ygz 4yh0 4ykm 4yko 5hzq

(-) Related Entries Specified in the PDB File

2fs6 APO WILD-TYPE CRABPII
2fs7 APO WILD-TYPE CRABPII
3fa7 ANOTHER APO CRABPII MUTANT