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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SAPOSIN D
 
Authors :  T. Maier, M. Rossman, W. Saenger
Date :  18 Sep 07  (Deposition) - 29 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Lipid Binding Protein, Saposin, Activator Protein, Sap, Disease Mutation, Gaucher Disease, Glycoprotein, Gm2-Gangliosidosis, Lipid Metabolism, Lysosome, Metachromatic Leukodystrophy, Sphingolipid Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Rossmann, R. Schultz-Heienbrok, J. Behlke, N. Remmel, C. Alings, K. Sandhoff, W. Saenger, T. Maier
Crystal Structures Of Human Saposins C And D: Implications For Lipid Recognition And Membrane Interactions.
Structure V. 16 809 2008
PubMed-ID: 18462685  |  Reference-DOI: 10.1016/J.STR.2008.02.016

(-) Compounds

Molecule 1 - PROACTIVATOR POLYPEPTIDE
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9K
    Expression System StrainGS115
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GenePSAP, GLBA, SAP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:17 , HOH A:133 , HOH A:134 , HOH A:183 , HOH A:199BINDING SITE FOR RESIDUE SO4 A 100
2AC2SOFTWARETYR A:14 , ARG A:17 , ASN A:18 , HOH A:188 , ARG B:17BINDING SITE FOR RESIDUE SO4 A 101
3AC3SOFTWARELYS C:10 , ARG C:17 , HOH C:122 , HOH C:124 , HOH C:181BINDING SITE FOR RESIDUE SO4 C 100
4AC4SOFTWAREARG B:17 , PRO B:68 , HOH B:226 , HOH B:240BINDING SITE FOR RESIDUE GOL B 200
5AC5SOFTWAREGLU C:64 , ALA D:52 , HOH D:285BINDING SITE FOR RESIDUE GOL D 200

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:5 -A:78
2A:8 -A:72
3A:36 -A:47
4B:5 -B:78
5B:8 -B:72
6B:36 -B:47
7C:5 -C:78
8C:8 -C:72
9C:36 -C:47
10D:5 -D:78
11D:8 -D:72
12D:36 -D:47

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Cys A:78 -Pro A:79
2Cys B:78 -Pro B:79
3Cys D:78 -Pro D:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RB3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RB3)

(-) Exons   (3, 12)

Asymmetric Unit (3, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003949361aENSE00001858117chr10:73611126-73610939188SAP_HUMAN1-14140--
1.2ENST000003949362ENSE00001239781chr10:73594262-73594129134SAP_HUMAN14-58450--
1.3ENST000003949363ENSE00000987087chr10:73591677-7359160375SAP_HUMAN59-83250--
1.4bENST000003949364bENSE00000987088chr10:73591008-73590883126SAP_HUMAN84-125420--
1.5ENST000003949365ENSE00001239733chr10:73588834-73588634201SAP_HUMAN126-192670--
1.6ENST000003949366ENSE00000987090chr10:73587914-73587771144SAP_HUMAN193-240480--
1.7ENST000003949367ENSE00000987091chr10:73585650-7358559457SAP_HUMAN241-259190--
1.10cENST0000039493610cENSE00001239711chr10:73581764-73581633132SAP_HUMAN260-303440--
1.11ENST0000039493611ENSE00000987093chr10:73580092-7357999796SAP_HUMAN304-335320--
1.12bENST0000039493612bENSE00000987094chr10:73579657-73579471187SAP_HUMAN336-398630--
1.13ENST0000039493613ENSE00000987095chr10:73579379-73579222158SAP_HUMAN398-450534A:2-46
B:2-46
C:2-46
D:2-46
45
45
45
45
1.14bENST0000039493614bENSE00000987096chr10:73578868-7357878881SAP_HUMAN451-477274A:47-73
B:47-73
C:47-73
D:47-73
27
27
27
27
1.15bENST0000039493615bENSE00000987097chr10:73578481-73578374108SAP_HUMAN478-513364A:74-80
B:74-80
C:74-80
D:74-79
7
7
7
6
1.16eENST0000039493616eENSE00001917960chr10:73577233-735760551179SAP_HUMAN514-524110--

(-) 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:79
 aligned with SAP_HUMAN | P07602 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:79
                                   415       425       435       445       455       465       475         
            SAP_HUMAN   406 GGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACPS 484
               SCOP domains d2rb3a_ A: Saposin C                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.13  PDB: A:2-46 UniProt: 398-450      Exon 1.14b  PDB: A:47-73   1.15b   Transcript 1
                 2rb3 A   2 AGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACPS  80
                                    11        21        31        41        51        61        71         

Chain B from PDB  Type:PROTEIN  Length:79
 aligned with SAP_HUMAN | P07602 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:79
                                   415       425       435       445       455       465       475         
            SAP_HUMAN   406 GGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACPS 484
               SCOP domains d2rb3b_ B: Saposin C                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.13  PDB: B:2-46 UniProt: 398-450      Exon 1.14b  PDB: B:47-73   1.15b   Transcript 1
                 2rb3 B   2 AGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACPS  80
                                    11        21        31        41        51        61        71         

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with SAP_HUMAN | P07602 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:79
                                   415       425       435       445       455       465       475         
            SAP_HUMAN   406 GGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACPS 484
               SCOP domains d2rb3c_ C: Saposin C                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.13  PDB: C:2-46 UniProt: 398-450      Exon 1.14b  PDB: C:47-73   1.15b   Transcript 1
                 2rb3 C   2 AGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACPS  80
                                    11        21        31        41        51        61        71         

Chain D from PDB  Type:PROTEIN  Length:78
 aligned with SAP_HUMAN | P07602 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:78
                                   415       425       435       445       455       465       475        
            SAP_HUMAN   406 GGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACP 483
               SCOP domains d2rb3d_ D: Saposin C                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -SapB_1-2rb3D01 D:3-40                 ---SapB_2-2rb3D05 D:44-78             - Pfam domains (1)
           Pfam domains (2) -SapB_1-2rb3D02 D:3-40                 ---SapB_2-2rb3D06 D:44-78             - Pfam domains (2)
           Pfam domains (3) -SapB_1-2rb3D03 D:3-40                 ---SapB_2-2rb3D07 D:44-78             - Pfam domains (3)
           Pfam domains (4) -SapB_1-2rb3D04 D:3-40                 ---SapB_2-2rb3D08 D:44-78             - Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.13  PDB: D:2-46 UniProt: 398-450      Exon 1.14b  PDB: D:47-73   1.15b  Transcript 1
                 2rb3 D   2 AGFCEVCKKLVGYLDRNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIGACP  79
                                    11        21        31        41        51        61        71        

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RB3)

(-) Pfam Domains  (2, 8)

Asymmetric Unit

(-) Gene Ontology  (29, 29)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SAP_HUMAN | P07602)
molecular function
    GO:0001664    G-protein coupled receptor binding    Interacting selectively and non-covalently with a G-protein coupled receptor.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    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).
biological process
    GO:0007193    adenylate cyclase-inhibiting 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 inhibition of adenylyl cyclase activity and a subsequent decrease in the concentration of cyclic AMP (cAMP).
    GO:0071310    cellular response to organic substance    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 organic substance stimulus.
    GO:0048589    developmental growth    The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
    GO:0060742    epithelial cell differentiation involved in prostate gland development    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell of the prostate gland.
    GO:0006687    glycosphingolipid metabolic process    The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:1903206    negative regulation of hydrogen peroxide-induced cell death    Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen peroxide-induced cell death.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0043410    positive regulation of MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the MAPK cascade.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0060736    prostate gland growth    The increase in size or mass of the prostate gland where the increase in size or mass has the specific outcome of the progression of the gland, from its formation to its mature state.
    GO:0043408    regulation of MAPK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the MAP kinase (MAPK) cascade.
    GO:0010506    regulation of autophagy    Any process that modulates the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0019216    regulation of lipid metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids.
    GO:0006665    sphingolipid metabolic process    The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SAP_HUMAN | P076021m12 1n69 1sn6 2dob 2gtg 2qyp 2r0r 2r1q 2z9a 3bqp 3bqq 4ddj 4uex 4v2o

(-) Related Entries Specified in the PDB File

2qyp 2r0r 2r1q 2z9a