1N69 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN SAPOSIN B

Authors :   V. E. Ahn, K. F. Faull, J. P. Whitelegge, A. L. Fluharty, G. G. Prive

Date :   08 Nov 02 (Deposition) - 07 Jan 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C  (2x)

Keywords :   Lipid Binding Protein, Glycosphingolipid Activator Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. E. Ahn, K. F. Faull, J. P. Whitelegge, A. L. Fluharty, G. G. Prive
Crystal Structure Of Saposin B Reveals A Dimeric Shell For Lipid Binding
Proc. Natl. Acad. Sci. Usa V. 100 38 2003
PubMed-ID: 12518053 | Reference-DOI: 10.1073/PNAS.0136947100
(for further references see the PDB file header)

Molecule 1 - SAPOSIN B
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-16(B)
	Expression System Strain	:	AD494(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PROSAPOSIN, PSAP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PROACTIVATOR POLYPEPTIDE, SAP-B, SPHINGOLIPID ACTIVATOR PROTEIN 1, SAP-1, CEREBROSIDE SULFATE ACTIVATOR, CSACT, CS-ACT, SULFATIDE/GM1 ACTIVATOR, GALACTOSYLCERBROSIDE ACTIVATOR

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PEH	1	Ligand/Ion	DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PEH	1	Ligand/Ion	DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	PEH	-1	Ligand/Ion	DI-STEAROYL-3-SN-PHOSPHATIDYLETHANOLAMINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:38 , LEU A:39 , MET A:43 , ILE A:51 , GLN A:66 , HOH A:515 , VAL B:29 , TYR B:50 , TYR B:54 , ILE B:59 , MET B:65	BINDING SITE FOR RESIDUE PEH A 300

Asymmetric Unit

No.	Residues
1	A:4	-	A:77
2	A:7	-	A:71
3	A:36	-	A:47
4	B:4	-	B:77
5	B:7	-	B:71
6	B:36	-	B:47
7	C:4	-	C:77
8	C:7	-	C:71
9	C:36	-	C:47

(no "Cis Peptide Bond" information available for 1N69)

Asymmetric Unit (4, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_031823	N	215	H	SAP_HUMAN	Disease (MLD-SAPB)	121918107	A/B/C	N	21	H
2	UniProt	VAR_031899	N	215	K	SAP_HUMAN	Disease (MLD-SAPB)	770171865	A/B/C	N	21	K
3	UniProt	VAR_006943	T	217	I	SAP_HUMAN	Disease (MLD-SAPB)	121918103	A/B/C	T	23	I
4	UniProt	VAR_006944	C	241	S	SAP_HUMAN	Disease (MLD-SAPB)	1130793	A/B/C	C	47	S

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

Biological Unit 1 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_031823	N	215	H	SAP_HUMAN	Disease (MLD-SAPB)	121918107	A/B	N	21	H
2	UniProt	VAR_031899	N	215	K	SAP_HUMAN	Disease (MLD-SAPB)	770171865	A/B	N	21	K
3	UniProt	VAR_006943	T	217	I	SAP_HUMAN	Disease (MLD-SAPB)	121918103	A/B	T	23	I
4	UniProt	VAR_006944	C	241	S	SAP_HUMAN	Disease (MLD-SAPB)	1130793	A/B	C	47	S

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

Biological Unit 2 (4, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_031823	N	215	H	SAP_HUMAN	Disease (MLD-SAPB)	121918107	C	N	21	H
2	UniProt	VAR_031899	N	215	K	SAP_HUMAN	Disease (MLD-SAPB)	770171865	C	N	21	K
3	UniProt	VAR_006943	T	217	I	SAP_HUMAN	Disease (MLD-SAPB)	121918103	C	T	23	I
4	UniProt	VAR_006944	C	241	S	SAP_HUMAN	Disease (MLD-SAPB)	1130793	C	C	47	S

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAP_B	PS50015	Saposin B type domain profile.	SAP_HUMAN	59-142 194-275 311-392 405-486	1	- B:2-78 - -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAP_B	PS50015	Saposin B type domain profile.	SAP_HUMAN	59-142 194-275 311-392 405-486	1	- B:2-78 - -

Biological Unit 2 (, 0)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SAP_B	PS50015	Saposin B type domain profile.	SAP_HUMAN	59-142 194-275 311-392 405-486	0	- - - -

Asymmetric Unit (4, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000394936	1a	ENSE00001858117	chr10:73611126-73610939	188	SAP_HUMAN	1-14	14	0	-	-
1.2	ENST00000394936	2	ENSE00001239781	chr10:73594262-73594129	134	SAP_HUMAN	14-58	45	0	-	-
1.3	ENST00000394936	3	ENSE00000987087	chr10:73591677-73591603	75	SAP_HUMAN	59-83	25	0	-	-
1.4b	ENST00000394936	4b	ENSE00000987088	chr10:73591008-73590883	126	SAP_HUMAN	84-125	42	0	-	-
1.5	ENST00000394936	5	ENSE00001239733	chr10:73588834-73588634	201	SAP_HUMAN	126-192	67	1	- B:-1-1 -	- 3 -
1.6	ENST00000394936	6	ENSE00000987090	chr10:73587914-73587771	144	SAP_HUMAN	193-240	48	3	A:1-46 B:2-46 C:1-46	46 45 46
1.7	ENST00000394936	7	ENSE00000987091	chr10:73585650-73585594	57	SAP_HUMAN	241-259	19	3	A:47-65 B:47-65 C:47-65	19 19 19
1.10c	ENST00000394936	10c	ENSE00001239711	chr10:73581764-73581633	132	SAP_HUMAN	260-303	44	3	A:66-78 B:66-78 C:66-78	13 13 13
1.11	ENST00000394936	11	ENSE00000987093	chr10:73580092-73579997	96	SAP_HUMAN	304-335	32	0	-	-
1.12b	ENST00000394936	12b	ENSE00000987094	chr10:73579657-73579471	187	SAP_HUMAN	336-398	63	0	-	-
1.13	ENST00000394936	13	ENSE00000987095	chr10:73579379-73579222	158	SAP_HUMAN	398-450	53	0	-	-
1.14b	ENST00000394936	14b	ENSE00000987096	chr10:73578868-73578788	81	SAP_HUMAN	451-477	27	0	-	-
1.15b	ENST00000394936	15b	ENSE00000987097	chr10:73578481-73578374	108	SAP_HUMAN	478-513	36	0	-	-
1.16e	ENST00000394936	16e	ENSE00001917960	chr10:73577233-73576055	1179	SAP_HUMAN	514-524	11	0	-	-

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:78
 aligned with SAP_HUMAN | P07602 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:78
                                   204       214       224       234       244       254       264        
            SAP_HUMAN   195 GDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGFCD 272
               SCOP domains d1n69a_ A: Saposin B                                                           SCOP domains
               CATH domains 1n69A00 A:1-78 NK-Lysin                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) --------------------H-I-----------------------S------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------K--------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE SAP_B  PDB: - UniProt: 194-275                                                 PROSITE
               Transcript 1 Exon 1.6  PDB: A:1-46 UniProt: 193-240        Exon 1.7           Exon 1.10c    Transcript 1
                 1n69 A   1 GDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGFCD  78
                                    10        20        30        40        50        60        70

Chain B from PDB  Type:PROTEIN  Length:80
 aligned with SAP_HUMAN | P07602 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:91
                                   191       201       211       221       231       241       251       261       271 
            SAP_HUMAN   182 QDGPRSKPQPKDNGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGFCD 272
               SCOP domains d1n           69b_ B: Saposin B                                                             SCOP domains
               CATH domains 1n6           9B00 B:-1-78 NK-Lysin                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-----------hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.... Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------H-I-----------------------S------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------K--------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------SAP_B  PDB: B:2-78 UniProt: 194-275                                             PROSITE
               Transcript 1 Exon 1.5   Exon 1.6  PDB: B:2-46 UniProt: 193-240          Exon 1.7           Exon 1.10c    Transcript 1
                 1n69 B  -1 MDG-----------DVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGFCD  78
                              |      -    |    7        17        27        37        47        57        67        77 
                              1           2

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

    Alignment length:78
                                   204       214       224       234       244       254       264        
            SAP_HUMAN   195 GDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGFCD 272
               SCOP domains d1n69c_ C: Saposin B                                                           SCOP domains
               CATH domains 1n69C00 C:1-78 NK-Lysin                                                        CATH domains
           Pfam domains (1) SapB_1-1n69C01 C:1-40                   ---SapB_2-1n69C04 C:44-77            - Pfam domains (1)
           Pfam domains (2) SapB_1-1n69C02 C:1-40                   ---SapB_2-1n69C05 C:44-77            - Pfam domains (2)
           Pfam domains (3) SapB_1-1n69C03 C:1-40                   ---SapB_2-1n69C06 C:44-77            - Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh... Sec.struct. author
             SAPs(SNPs) (1) --------------------H-I-----------------------S------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------K--------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE SAP_B  PDB: - UniProt: 194-275                                                 PROSITE
               Transcript 1 Exon 1.6  PDB: C:1-46 UniProt: 193-240        Exon 1.7           Exon 1.10c    Transcript 1
                 1n69 C   1 GDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGFCD  78
                                    10        20        30        40        50        60        70

Legend:		→ Mismatch	(orange background)
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	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Saposin-like (21)

Superfamily: Saposin (17)

Family: Saposin B (1)

Protein domain: Saposin B (1)

Human (Homo sapiens) [TaxId: 9606] (1)

1a	d1n69a_	A:
1b	d1n69b_	B:
1c	d1n69c_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: NK-Lysin (9)

Homologous Superfamily: NK-Lysin (9)

Human (Homo sapiens) (7)

1a	1n69A00	A:1-78
1b	1n69C00	C:1-78
1c	1n69B00	B:-1-78

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SapB_1] (11)

Family: SapB_1 (11)

Homo sapiens (Human) (7)

1a	SapB_1-1n69C01	C:1-40
1b	SapB_1-1n69C02	C:1-40
1c	SapB_1-1n69C03	C:1-40

Clan: no clan defined [family: SapB_2] (17)

Family: SapB_2 (17)

Homo sapiens (Human) (11)

2a	SapB_2-1n69C04	C:44-77
2b	SapB_2-1n69C05	C:44-77
2c	SapB_2-1n69C06	C:44-77

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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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	1n69
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	SAP_HUMAN \| P07602	:	1m12 1sn6 2dob 2gtg 2qyp 2r0r 2r1q 2rb3 2z9a 3bqp 3bqq 4ddj 4uex 4v2o

(no "Related Entries Specified in the PDB File" available for 1N69)

Description

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Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (9, 9)

Cis Peptide Bonds (0, 0)

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Exons (4, 10)

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