3GF5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE P21 R1-R7 N-TERMINAL DOMAIN OF MURINE MVP

Authors :   J. Querol-Audi, A. Casanas, D. Luque, J. R. Caston, I. Fita, N. Verdague

Date :   26 Feb 09 (Deposition) - 10 Nov 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Beta Sheets, Phosphoprotein, Ribonucleoprotein, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Querol-Audi, A. Casanas, I. Uson, D. Luque, J. R. Caston, I. Fita, N. Verdaguer
The Mechanism Of Vault Opening From The High Resolution Structure Of The N-Terminal Repeats Of Mvp
Embo J. V. 28 3450 2009
PubMed-ID: 19779459 | Reference-DOI: 10.1038/EMBOJ.2009.274

Molecule 1 - MAJOR VAULT PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	R1-R7 DOMAIN, UNP RESIDUES 1-383
	Gene	:	MVP
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	MVP

		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 (1, 7)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:15 , PHE A:45	BINDING SITE FOR RESIDUE GOL A 384
2	AC2	SOFTWARE	ASP A:141 , GLU A:142 , PHE A:209	BINDING SITE FOR RESIDUE GOL A 385
3	AC3	SOFTWARE	TYR B:15 , VAL B:48	BINDING SITE FOR RESIDUE GOL B 384
4	AC4	SOFTWARE	LYS B:155 , GLU B:156	BINDING SITE FOR RESIDUE GOL B 385
5	AC5	SOFTWARE	TYR B:281 , GLN B:321 , ASP B:322 , TYR B:324 , HOH B:396	BINDING SITE FOR RESIDUE GOL B 386
6	AC6	SOFTWARE	ASP B:237 , ARG B:239 , VAL B:241 , HIS B:243 , LEU B:250 , ASP B:255	BINDING SITE FOR RESIDUE GOL B 388

(no "SS Bond" information available for 3GF5)

Asymmetric Unit

No.	Residues
1	Gly A:31	-	Pro A:32
2	Gly A:147	-	Pro A:148
3	Gly A:361	-	Pro A:362
4	Gly B:31	-	Pro B:32
5	Gly B:147	-	Pro B:148
6	Gly B:289	-	Pro B:290
7	Gly B:361	-	Pro B:362

(no "SAP(SNP)/Variant" information available for 3GF5)

Asymmetric Unit (1, 14)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MVP	PS51224	MVP (vault) repeat profile.	MVP_MOUSE	4-54 56-116 117-169 170-222 223-277 279-327 328-383 384-436	14	A:4-54 B:4-54 A:56-116 B:56-116 A:117-169 B:117-169 A:170-222 B:170-222 A:223-277 B:223-277 A:279-327 B:279-327 A:328-380 B:328-380 -

Biological Unit 1 (1, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MVP	PS51224	MVP (vault) repeat profile.	MVP_MOUSE	4-54 56-116 117-169 170-222 223-277 279-327 328-383 384-436	7	A:4-54 - A:56-116 - A:117-169 - A:170-222 - A:223-277 - A:279-327 - A:328-380 - -

Biological Unit 2 (1, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MVP	PS51224	MVP (vault) repeat profile.	MVP_MOUSE	4-54 56-116 117-169 170-222 223-277 279-327 328-383 384-436	7	- B:4-54 - B:56-116 - B:117-169 - B:170-222 - B:223-277 - B:279-327 - B:328-380 -

(no "Exon" information available for 3GF5)

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:378
 aligned with MVP_MOUSE | Q9EQK5 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:384
                                1                                                                                                                                                                                                                                                                                                                                                                                           
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376    
            MVP_MOUSE     - ----MATEEAIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPVRMVTVPPRHYCIVANPVSRDAQSSVLFDVTGQVRLRHADQEIRLAQDPFPLYPGELLEKDITPLQVVLPNTALHLKALLDFEDKNGDKVMAGDEWLFEGPGTYIPQKEVEVVEIIQATVIKQNQALRLRARKECFDRDGKERVTGEEWLVRSVGAYLPAVFEEVLDLVDAVILTEKTALHLRARQNFKDLRGVAHRTGEEWLVTVQDTEAHVPDVYEEVLGVVPITTLGPRHYCVILDPMGPDGKNQLGQKRVVKGEKSFFLQPGERLERGIQDVYVLSEQQGLLLKALQPLEEGEGEEKVAHQAGDRWLIRGPLEYVPSAKVEVVEERQAI 380
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeee...eeeeeee.....eeeee..eeee....eee....ee.......eeeeee.........................eeee............eeeeeeee.eee...eeeeeee...ee.....ee....eeeee..eee.....eeeeeeee.eee...eeeeeee...ee.....ee....eeee...eee.....eeeeeeee.ee....eeeeeee...ee.....ee....eeee......ee.....eeeeeeee.eee...eeeeee.............eeeee..eee......ee....ee.eee....eeeeee....------.........eeeee..eee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------MVP  PDB: A:4-54 UniProt: 4-54                     -MVP  PDB: A:56-116 UniProt: 56-116                           MVP  PDB: A:117-169 UniProt: 117-169                 MVP  PDB: A:170-222 UniProt: 170-222                 MVP  PDB: A:223-277 UniProt: 223-277                   -MVP  PDB: A:279-327 UniProt: 279-327             MVP  PDB: A:328-380 UniProt: 328-383                  PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gf5 A  -3 GPLGMATEEAIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPVRMVTVPPRHYCIVANPVSRDAQSSVLFDVTGQVRLRHADQEIRLAQDPFPLYPGELLEKDITPLQVVLPNTALHLKALLDFEDKNGDKVMAGDEWLFEGPGTYIPQKEVEVVEIIQATVIKQNQALRLRARKECFDRDGKERVTGEEWLVRSVGAYLPAVFEEVLDLVDAVILTEKTALHLRARQNFKDLRGVAHRTGEEWLVTVQDTEAHVPDVYEEVLGVVPITTLGPRHYCVILDPMGPDGKNQLGQKRVVKGEKSFFLQPGERLERGIQDVYVLSEQQGLLLKALQPL------ERVAHQAGDRWLIRGPLEYVPSAKVEVVEERQAI 380
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336   |     -|      356       366       376    
                                                                                                                                                                                                                                                                                                                                                                                 340    347

Chain B from PDB  Type:PROTEIN  Length:380
 aligned with MVP_MOUSE | Q9EQK5 from UniProtKB/Swiss-Prot  Length:861

    Alignment length:383
                               1                                                                                                                                                                                                                                                                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377   
            MVP_MOUSE     - ---MATEEAIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPVRMVTVPPRHYCIVANPVSRDAQSSVLFDVTGQVRLRHADQEIRLAQDPFPLYPGELLEKDITPLQVVLPNTALHLKALLDFEDKNGDKVMAGDEWLFEGPGTYIPQKEVEVVEIIQATVIKQNQALRLRARKECFDRDGKERVTGEEWLVRSVGAYLPAVFEEVLDLVDAVILTEKTALHLRARQNFKDLRGVAHRTGEEWLVTVQDTEAHVPDVYEEVLGVVPITTLGPRHYCVILDPMGPDGKNQLGQKRVVKGEKSFFLQPGERLERGIQDVYVLSEQQGLLLKALQPLEEGEGEEKVAHQAGDRWLIRGPLEYVPSAKVEVVEERQAI 380
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee...eeeeeee....eeeeee..eeee....eee....ee.......eeeeee.........................eeee............eeeeeeee.eee...eeeeeee...ee.....ee....eeeee..eee.....eeeeeeee.eee...eeeeeee...ee.....ee....eeee...eee.....eeeeeeee.ee....eeeeeee...ee.....ee....eeee......ee.....eeeeeeee.eee...eeeeee.............eeeee..eee......ee....ee.eee....eeeeee.......---.........eeeee..eee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------MVP  PDB: B:4-54 UniProt: 4-54                     -MVP  PDB: B:56-116 UniProt: 56-116                           MVP  PDB: B:117-169 UniProt: 117-169                 MVP  PDB: B:170-222 UniProt: 170-222                 MVP  PDB: B:223-277 UniProt: 223-277                   -MVP  PDB: B:279-327 UniProt: 279-327             MVP  PDB: B:328-380 UniProt: 328-383                  PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gf5 B  -2 PLGMATEEAIIRIPPYHYIHVLDQNSNVSRVEVGPKTYIRQDNERVLFAPVRMVTVPPRHYCIVANPVSRDAQSSVLFDVTGQVRLRHADQEIRLAQDPFPLYPGELLEKDITPLQVVLPNTALHLKALLDFEDKNGDKVMAGDEWLFEGPGTYIPQKEVEVVEIIQATVIKQNQALRLRARKECFDRDGKERVTGEEWLVRSVGAYLPAVFEEVLDLVDAVILTEKTALHLRARQNFKDLRGVAHRTGEEWLVTVQDTEAHVPDVYEEVLGVVPITTLGPRHYCVILDPMGPDGKNQLGQKRVVKGEKSFFLQPGERLERGIQDVYVLSEQQGLLLKALQPLEEG---ERVAHQAGDRWLIRGPLEYVPSAKVEVVEERQAI 380
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337     | 347       357       367       377   
                                                                                                                                                                                                                                                                                                                                                                                   343 347

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 3GF5)

(no "CATH Domain" information available for 3GF5)

(no "Pfam Domain" information available for 3GF5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MVP_MOUSE | Q9EQK5)

molecular function
	GO:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
biological process
	GO:0038127	ERBB signaling pathway	A series of molecular signals initiated by binding of a ligand to a member of the ERBB family of receptor tyrosine kinases on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0031953	negative regulation of protein autophosphorylation	Any process that stops, prevents or decreases the rate of the phosphorylation by a protein of one or more of its own residues.
	GO:0061099	negative regulation of protein tyrosine kinase activity	Any process that decreases the rate, frequency, or extent of protein tyrosine kinase activity.
	GO:0023057	negative regulation of signaling	Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
	GO:0072376	protein activation cascade	A response to a stimulus that consists of a sequential series of modifications to a set of proteins where the product of one reaction acts catalytically in the following reaction. The magnitude of the response is typically amplified at each successive step in the cascade. Modifications typically include proteolysis or covalent modification, and may also include binding events.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:147 - Pro A:148	[ RasMol ]
		Gly A:31 - Pro A:32	[ RasMol ]
		Gly A:361 - Pro A:362	[ RasMol ]
		Gly B:147 - Pro B:148	[ RasMol ]
		Gly B:289 - Pro B:290	[ RasMol ]
		Gly B:31 - Pro B:32	[ RasMol ]
		Gly B:361 - Pro B:362	[ RasMol ]

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	3gf5
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UniProtKB/Swiss-Prot
	MVP_MOUSE \| Q9EQK5	:	3gnf 3gng

3gnf	P1 R1-R7 STRUCTURE
3gng	P21B R1-R7 STRUCTURE

Description

Compounds

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Ligands, Modified Residues, Ions (1, 7)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (7, 7)

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