3GDQ - JenaLib

Title :   CRYSTAL STRUCTURE OF THE HUMAN 70KDA HEAT SHOCK PROTEIN 1-LIKE ATPASE DOMAIN IN COMPLEX WITH ADP AND INORGANIC PHOSPHATE

Authors :   M. Wisniewska, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. C L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Ham A. Johansson, I. Johansson, T. Karlberg, T. Kotenyova, L. Lehtio, M. E P. Nordlund, T. Nyman, C. Persson, J. Sagemark, P. Schutz, M. Siponen, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Welin, H. Schueler, Structural Genomics Consortium (Sgc)

Date :   24 Feb 09 (Deposition) - 14 Apr 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Helix, Structural Genomics, Structural Genomics Consortium, Sgc, Atp- Binding, Nucleotide-Binding, Transcription, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Wisniewska, T. Karlberg, L. Lehtio, I. Johansson, T. Kotenyova, M. Moche, H. Schuler
Crystal Structures Of The Atpase Domains Of Four Human Hsp7 Isoforms: Hspa1L/Hsp70-Hom, Hspa2/Hsp70-2, Hspa6/Hsp70B', And Hspa5/Bip/Grp78
Plos One V. 5 E8625 2010
PubMed-ID: 20072699 | Reference-DOI: 10.1371/JOURNAL.PONE.0008625

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , THR A:15 , LYS A:73 , PRO A:149 , GLU A:177 , THR A:206 , ADP A:388 , MN A:390 , HOH A:418 , HOH A:427 , HOH A:448 , HOH A:462 , HOH A:499 , HOH A:528	BINDING SITE FOR RESIDUE PO4 A 387
2	AC2	SOFTWARE	THR A:15 , THR A:16 , TYR A:17 , GLY A:203 , GLY A:204 , GLY A:232 , GLU A:270 , LYS A:273 , ARG A:274 , SER A:277 , GLY A:340 , GLY A:341 , SER A:342 , ARG A:344 , ILE A:345 , ASP A:368 , PO4 A:387 , MN A:390 , HOH A:391 , HOH A:412 , HOH A:418 , HOH A:427 , HOH A:436 , HOH A:447 , HOH A:448 , HOH A:451 , HOH A:459 , HOH A:557 , HOH A:618 , HOH A:681	BINDING SITE FOR RESIDUE ADP A 388
3	AC3	SOFTWARE	THR A:15 , LYS A:73 , ARG A:74 , TYR A:151 , PHE A:152 , GLN A:156 , THR A:206 , THR A:228 , HOH A:445 , HOH A:558	BINDING SITE FOR RESIDUE GOL A 389
4	AC4	SOFTWARE	PO4 A:387 , ADP A:388 , HOH A:418 , HOH A:447 , HOH A:448 , HOH A:462	BINDING SITE FOR RESIDUE MN A 390

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:376
 aligned with HS71L_HUMAN | P34931 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:379
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375         
          HS71L_HUMAN     6 GIAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPQNTVFDAKRLIGRKFNDPVVQADMKLWPFQVINEGGKPKVLVSYKGENKAFYPEEISSMVLTKLKETAEAFLGHPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDKGGQGERHVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVSHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQANLEIDSLYEGIDFYTSITRARFEELCADLFRGTLEPVEKALRDAKMDKAKIHDIVLVGGSTRIPKVQRLLQDYFNGRDLNKSINPDEAVAYGAAVQAAILMG 384
               SCOP domains d3gdqa1 A:6-189 automated matches                                                                                                                                                       ---d3gdqa2 A:193-384 automated matches                                                                                                                                                              SCOP domains
               CATH domains 3gdqA01 A:6-69,A:125-189,A:363-383                              3gdqA02 A:70-124  [code=3.30.30.30, no name defined]   3gdqA01 A:6-69,A:125-189,A:363-383                               ---3gdqA03 A:193-230,A:315-362           3gdqA04 A:231-314 Actin; Chain A, domain 4                                          3gdqA03 A:193-230,A:315-362                     3gdqA01              - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeeeeee..eeee.........ee..eee....eeehhhhhhhhhhhhh.ee.hhhhhh.....hhhhhhhhh....eeeee..eeeeeeee..eeeeehhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhh..eeeeeeehhhhhhhhh....---..eeeeeeee....eeeeeeeee..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeehhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --P-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-------------------------G------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----HSP70_1 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HSP70_2       ---------------------------------------------------------------------------------------------------------------------------HSP70_3        ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gdq A   6 GIAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPQNTVFDAKRLIGRKFNDPVVQADMKLWPFQVINEGGKPKVLVSYKGENKAFYPEEISSMVLTKLKETAEAFLGHPVTNAVITVPAYFNDSQRQATKDAGVIAGLNVLRIINEPTAAAIAYGLDK---GERHVLIFDLGGGTFDVSILTIDDGIFEVKATAGDTHLGGEDFDNRLVSHFVEEFKRKHKKDISQNKRAVRRLRTACERAKRTLSSSTQANLEIDSLYEGIDFYTSITRARFEELCADLFRGTLEPVEKALRDAKMDKAKIHDIVLVGGSTRIPKVQRLLQDYFNGRDLNKSINPDEAVAYGAAVQAAILMG 384
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   |   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375         
                                                                                                                                                                                                                 189 193

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, 2)

CATH Domains (3, 4)

Pfam Domains (0, 0)

Gene Ontology (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HS71L_HUMAN | P34931)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0031072	heat shock protein binding	Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	GO:0007339	binding of sperm to zona pellucida	The process in which the sperm binds to the zona pellucida glycoprotein layer of the egg. The process begins with the attachment of the sperm plasma membrane to the zona pellucida and includes attachment of the acrosome inner membrane to the zona pellucida after the acrosomal reaction takes place.
	GO:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	GO:0042026	protein refolding	The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
	GO:1900034	regulation of cellular response to heat	Any process that modulates the frequency, rate or extent of cellular response to heat.
	GO:0006986	response to unfolded protein	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 an unfolded protein stimulus.
cellular component
	GO:0008180	COP9 signalosome	A protein complex that catalyzes the deneddylation of proteins, including the cullin component of SCF ubiquitin E3 ligase; deneddylation increases the activity of cullin family ubiquitin ligases. The signalosome is involved in many regulatory process, including some which control development, in many species; also regulates photomorphogenesis in plants; in many species its subunits are highly similar to those of the proteasome.
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	GO:0044297	cell body	The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
	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:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	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.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0002199	zona pellucida receptor complex	A multisubunit complex comprising the chaperonin-containing T-complex and several other components involved in mediating sperm-oocyte Interaction.

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