2YG2 - JenaLib

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Title :   STRUCTURE OF APOLIOPROTEIN M IN COMPLEX WITH SPHINGOSINE 1-PHOSPHATE

Authors :   C. Christoffersen, H. Obinata, S. Gowda, S. Galvani, J. Ahnstrom, M. Se C. Egerer-Sieber, Y. A. Muller, T. Hla, L. Nielsen, B. Dahlback

Date :   11 Apr 11 (Deposition) - 01 Jun 11 (Release) - 22 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Lipid Transport, Lipocalin, Hdl (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Christoffersen, H. Obinata, S. B. Kumaraswamy, S. Galvani, J. Ahnstrom, M. Sevvana, C. Egerer-Sieber, Y. A. Muller, T. Hla, L. B. Nielsen, B. Dahlback
Endothelium-Protective Sphingosine-1-Phosphate Provided By Hdl-Associated Apolipoprotein M.
Proc. Natl. Acad. Sci. Usa V. 108 9613 2011
PubMed-ID: 21606363 | Reference-DOI: 10.1073/PNAS.1103187108

Molecule 1 - APOLIPOPROTEIN M
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	APO-M, APOM, PROTEIN G3A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	FLC	1	Ligand/Ion	CITRATE ANION
2	S1P	2	Ligand/Ion	(2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YLDIHYDROGEN PHOSPHATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FLC	1	Ligand/Ion	CITRATE ANION
2	S1P	1	Ligand/Ion	(2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YLDIHYDROGEN PHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	FLC	-1	Ligand/Ion	CITRATE ANION
2	S1P	1	Ligand/Ion	(2S,3R,4E)-2-AMINO-3-HYDROXYOCTADEC-4-EN-1-YLDIHYDROGEN PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:63 , PHE A:71 , MET A:73 , ARG A:98 , TRP A:100 , TYR A:102 , LEU A:111 , ARG A:116 , LEU A:134 , GLU A:136 , TYR A:147 , FLC A:401 , HOH A:2026 , HOH A:2027 , HOH A:2061 , HOH A:2075 , HOH A:2091 , HOH A:2121 , ASN B:179	BINDING SITE FOR RESIDUE S1P A 301
2	AC2	SOFTWARE	ARG A:116 , ASP A:118 , MET A:119 , TYR A:141 , S1P A:301 , HOH A:2027 , HOH A:2075 , HOH A:2088 , ASP B:67 , LYS B:91 , PRO B:177 , ASN B:179 , GLN B:180	BINDING SITE FOR RESIDUE FLC A 401
3	AC3	SOFTWARE	ASP A:35 , GLY A:107 , SER A:108 , PHE B:63 , PHE B:71 , MET B:73 , ARG B:98 , TRP B:100 , TYR B:102 , LEU B:111 , ARG B:116 , GLU B:136 , ARG B:143 , TYR B:147 , HOH B:2046 , HOH B:2056 , HOH B:2061 , HOH B:2077 , HOH B:2078	BINDING SITE FOR RESIDUE S1P B 301

Asymmetric Unit

No.	Residues
1	A:23	-	A:167
2	A:95	-	A:183
3	A:128	-	A:157
4	B:95	-	B:183
5	B:128	-	B:157

(no "Cis Peptide Bond" information available for 2YG2)

(no "SAP(SNP)/Variant" information available for 2YG2)

(no "PROSITE Motif" information available for 2YG2)

(no "Exon" information available for 2YG2)

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
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Chain A from PDB  Type:PROTEIN  Length:163
 aligned with APOM_HUMAN | O95445 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:166
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           APOM_HUMAN    23 CPEHSQLTTLGVDGKEFPEVHLGQWYFIAGAAPTKEELATFDPVDNIVFNMAAGSAPMQLHLRATIRMKDGLCVPRKWIYHLTEGSTDLRTEGRPDMKTELFSSSCPGGIMLNETGQGYQRFLLYNRSPHPPEKCVEEFKSLTSCLDSKAFLLTPRNQEACELSNN 188
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--..........-hhhhhh.eeeeeeeeee.hhhhhhhhh.eeeeeeeeee.....eeeeeeeeee....eeeeeeeeee......eee..eeeeeeeee......eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yg2 A  23 CP--SQLTTLGVDG-EFPEVHLGQWYFIAGAAPTKEELATFDPVDNIVFNMAAGSAPMQLHLRATIRMKDGLCVPRKWIYHLTEGSTDLRTEGRPDMKTELFSSSCPGGIMLNETGQGYQRFLLYNRSPHPPEKCVEEFKSLTSCLDSKAFLLTPRNQEACELSNN 188
                             |  |   32   | |  42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
                             | 27       36 |                                                                                                                                                      
                            24            38

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with APOM_HUMAN | O95445 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:157
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       
           APOM_HUMAN    29 LTTLGVDGKEFPEVHLGQWYFIAGAAPTKEELATFDPVDNIVFNMAAGSAPMQLHLRATIRMKDGLCVPRKWIYHLTEGSTDLRTEGRPDMKTELFSSSCPGGIMLNETGQGYQRFLLYNRSPHPPEKCVEEFKSLTSCLDSKAFLLTPRNQEACEL 185
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ApoM-2   yg2B01 B:29-185                                                                                                                                      Pfam domains (1)
           Pfam domains (2) ApoM-2   yg2B02 B:29-185                                                                                                                                      Pfam domains (2)
         Sec.struct. author ......---hhhhhhheeeeeeeeee.hhhhhhhhh.eeeeeeeee.---..eeeeeeeeee....eeeeeeeee.......eee..eeeeeeeeee.....eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yg2 B  29 LTTLGV---EFPEVHLGQWYFIAGAAPTKEELATFDPVDNIVFNMAA---PMQLHLRATIRMKDGLCVPRKWIYHLTEGSTDLRTEGRPDMKTELFSSSCPGGIMLNETGQGYQRFLLYNRSPHPPEKCVEEFKSLTSCLDSKAFLLTPRNQEACEL 185
                                 |  38        48        58        68      |  -|       88        98       108       118       128       138       148       158       168       178       
                                34  38                                   75  79

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 '\|'

(no "SCOP Domain" information available for 2YG2)

(no "CATH Domain" information available for 2YG2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Calycin (163)

Family: ApoM (3)

Homo sapiens (Human) (2)

1a	ApoM-2yg2B01	B:29-185
1b	ApoM-2yg2B02	B:29-185

Asymmetric Unit(hide GO term definitions)

Chain A,B (APOM_HUMAN | O95445)

molecular function
	GO:0016209	antioxidant activity	Inhibition of the reactions brought about by dioxygen (O2) or peroxides. Usually the antioxidant is effective because it can itself be more easily oxidized than the substance protected. The term is often applied to components that can trap free radicals, thereby breaking the chain reaction that normally leads to extensive biological damage.
	GO:0005319	lipid transporter activity	Enables the directed movement of lipids into, out of or within a cell, or between cells.
	GO:0005543	phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0033344	cholesterol efflux	The directed movement of cholesterol, cholest-5-en-3-beta-ol, out of a cell or organelle.
	GO:0042632	cholesterol homeostasis	Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
	GO:0034380	high-density lipoprotein particle assembly	The non-covalent aggregation and arrangement of proteins and lipids to form a high-density lipoprotein particle.
	GO:0034384	high-density lipoprotein particle clearance	The process in which a high-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
	GO:0034375	high-density lipoprotein particle remodeling	The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
	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:0042157	lipoprotein metabolic process	The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids.
	GO:0034445	negative regulation of plasma lipoprotein oxidation	Any process that stops, prevents, or reduces the frequency, rate or extent of lipoprotein particle oxidation, occurring in the blood plasma.
	GO:0009749	response to glucose	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 glucose stimulus.
	GO:0001523	retinoid metabolic process	The chemical reactions and pathways involving 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:0043691	reverse cholesterol transport	The directed movement of peripheral cell cholesterol, cholest-5-en-3-beta-ol, towards the liver for catabolism.
	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:0034365	discoidal high-density lipoprotein particle	A newly formed high-density lipoprotein particle; consists of a phospholipid bilayer surrounded by two or more APOA1 molecules. The discoidal HDL particle is formed when lipid-free or lipid-poor APOA1 acquires phospholipids and unesterified cholesterol from either cell membranes or triglyceride-rich lipoproteins (undergoing lipolysis by lipoprotein lipase).
	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:0034364	high-density lipoprotein particle	A lipoprotein particle with a high density (typically 1.063-1.21 g/ml) and a diameter of 5-10 nm that contains APOAs and may contain APOCs and APOE; found in blood and carries lipids from body tissues to the liver as part of the reverse cholesterol transport process.
	GO:0005887	integral component of plasma membrane	The component of the plasma 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:0034362	low-density lipoprotein particle	A lipoprotein particle, rich in cholesterol esters and low in triglycerides that is typically composed of APOB100 and APOE and has a density of 1.02-1.06 g/ml and a diameter of between 20-25 nm. LDL particles are formed from VLDL particles (via IDL) by the loss of triglyceride and gain of cholesterol ester. They transport endogenous cholesterol (and to some extent triglycerides) from peripheral tissues back to the liver.
	GO:0034366	spherical high-density lipoprotein particle	A mature high-density lipoprotein (HDL) particle, converted from discoidal HDL particles following the esterification of cholesterol in the particle by phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT).
	GO:0034361	very-low-density lipoprotein particle	A triglyceride-rich lipoprotein particle that is typically composed of APOB100, APOE and APOCs and has a density of about 1.006 g/ml and a diameter of between 20-80 nm. It is found in blood and transports endogenous products (newly synthesized cholesterol and triglycerides) from the liver.

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	2yg2
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	APOM_HUMAN \| O95445	:	2wew 2wex

2wew	CRYSTAL STRUCTURE OF HUMAN APOM IN COMPLEX WITH MYRISTIC ACID
2wex	CRYSTAL STRUCTURE OF HUMAN APOM IN COMPLEX WITH GLYCEROL 1- MYRISTIC ACID

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