3PSO - 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)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE VPS29 COMPLEXED WITH ZN2+

Authors :   J. Swarbrick, D. Shaw, S. Chhabra, R. Ghai, E. Valkov, S. Norwood, B. Col

Date :   02 Dec 10 (Deposition) - 15 Dec 10 (Release) - 15 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Phosphatase Fold, Scaffold, Membrane Trafficking, Vps35, Tbc1D5, Snx1, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Swarbrick, D. Shaw, S. Chhabra, R. Ghai, E. Valkov, S. Norwood, B. Collins
Conformational Dynamics And Biomolecular Interactions Of Vps29 Studied By Nmr And X-Ray Crystallography
To Be Published
PubMed: search

Molecule 1 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	VPS29
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	VESICLE PROTEIN SORTING 29, VPS29

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 7)

No.	Name	Count	Type	Full Name
1	ZN	7	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:8 , HIS A:10 , ASN A:39 , HIS A:117 , ZN A:602	BINDING SITE FOR RESIDUE ZN A 601
2	AC2	SOFTWARE	ASP A:8 , ASN A:39 , ASP A:62 , HIS A:86 , HIS A:115 , ZN A:601	BINDING SITE FOR RESIDUE ZN A 602
3	AC3	SOFTWARE	HIS A:33 , ASP A:55 , HIS A:57 , VAL A:75	BINDING SITE FOR RESIDUE ZN A 603
4	AC4	SOFTWARE	HIS A:10 , CYS A:41	BINDING SITE FOR RESIDUE ZN A 604
5	AC5	SOFTWARE	ASP B:8 , HIS B:10 , ASN B:39 , HIS B:117 , ZN B:702	BINDING SITE FOR RESIDUE ZN B 701
6	AC6	SOFTWARE	ASN B:39 , ASP B:62 , HIS B:86 , HIS B:115 , ZN B:701	BINDING SITE FOR RESIDUE ZN B 702
7	AC7	SOFTWARE	HIS B:33 , ASP B:55 , HIS B:57 , VAL B:75	BINDING SITE FOR RESIDUE ZN B 703

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

Asymmetric Unit

No.	Residues
1	Ile A:11	-	Pro A:12
2	Ile B:11	-	Pro B:12

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

(no "PROSITE Motif" information available for 3PSO)

(no "Exon" information available for 3PSO)

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:182
 aligned with VPS29_MOUSE | Q9QZ88 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
          VPS29_MOUSE     1 MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS 182
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee............hhhhhh........eeee.....hhhhhhhhhhhh.eeee.............eeeeee..eeeeee.........hhhhhhh........eeee......eeee....eeee.................eeeeeeee..eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pso A   1 MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with VPS29_MOUSE | Q9QZ88 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180  
          VPS29_MOUSE     1 MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS 182
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Metallophos_2-3psoB01 B:1-158                                                                                                                                 ------------------------ Pfam domains (1)
           Pfam domains (2) Metallophos_2-3psoB02 B:1-158                                                                                                                                 ------------------------ Pfam domains (2)
         Sec.struct. author .eeeee............hhhhhh........eeee.....hhhhhhhhhhhh.eeee.............eeeeee..eeeeee.........hhhhhhh........eeee......eeee....eeee.................eeeeeeee..eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pso B   1 MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKS 182
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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 3PSO)

(no "CATH Domain" information available for 3PSO)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Calcineurin (56)

Family: Metallophos_2 (10)

Mus musculus (Mouse) (4)

1a	Metallophos_2-3psoB01	B:1-158
1b	Metallophos_2-3psoB02	B:1-158

Asymmetric Unit(hide GO term definitions)

Chain A,B (VPS29_MOUSE | Q9QZ88)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
	GO:0006896	Golgi to vacuole transport	The directed movement of substances from the Golgi to the vacuole.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0042147	retrograde transport, endosome to Golgi	The directed movement of membrane-bounded vesicles from endosomes back to the trans-Golgi network where they are recycled for further rounds of transport.
	GO:1990126	retrograde transport, endosome to plasma membrane	The directed movement of membrane-bounded vesicles from endosomes back to the plasma membrane, a trafficking pathway that promotes the recycling of internalized transmembrane proteins.
	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:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	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:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030904	retromer complex	A conserved hetero-pentameric membrane-associated complex involved in retrograde transport from endosomes to the Golgi apparatus. The budding yeast retromer comprises Vps35p, Vps29p, Vps26p, Vps5p, and Vps17p. The mammalian complex shows slight variation in composition compared to yeast, and comprises SNX1 or SNX2, SNX5 or SNX6, VPS26A or VPS26B, VPS29, and VPS35.

Asymmetric Unit
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	Cis Peptide Bonds
		Ile A:11 - Pro A:12	[ RasMol ]
		Ile B:11 - Pro B:12	[ RasMol ]

Biological Units
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	3pso
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	VPS29_MOUSE \| Q9QZ88
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	VPS29_MOUSE \| Q9QZ88	:	1z2w 1z2x 3psn

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Pfam Domains (1, 2)

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