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Title :   CRYSTAL STRUCTURE OF HUMAN SPLA/RYANODINE RECEPTOR DOMAIN AND SOCS BOX CONTAINING 1 (SPSB1) IN COMPLEX WITH A 20-RESIDUE VASA PEPTIDE

Authors :   P. Filippakopoulos, T. Sharpe, T. Keates, J. W. Murray, P. Savitsky, A. A. C. W. Pike, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt C. Bountra, S. Knapp, A. Bullock, Structural Genomics Consortium

Date :   30 Oct 08 (Deposition) - 09 Dec 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Apoptosis, Nucleus, Transcription Regulation, Sgc, Structural Genomics Consortium, Phosphoprotein, Ubl Conjugation Pathway, Atp- Binding, Developmental Protein, Differentiation, Helicase, Hydrolase, Nucleotide-Binding, Oogenesis, Apoptosis-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Filippakopoulos, A. Low, T. D. Sharpe, J. Uppenberg, S. Yao, Z. Kuang, P. Savitsky, R. S. Lewis, S. E. Nicholson, R. S. Norton, A. N. Bullock
Structural Basis For Par-4 Recognition By The Spry Domain- And Socs Box-Containing Proteins Spsb1, Spsb2, And Spsb4.
J. Mol. Biol. V. 401 389 2010
PubMed-ID: 20561531 | Reference-DOI: 10.1016/J.JMB.2010.06.017

Molecule 1 - SPRY DOMAIN-CONTAINING SOCS BOX PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC28-BSA4
	Expression System Strain	:	BL21(DE3)-R3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-233
	Gene	:	SPSB1, SSB1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SSB-1

Molecule 2 - 20-MER PEPTIDE FROM ATP-DEPENDENT RNA HELICASE VASA
	Chains	:	C, D
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN DROSOPHILA MELANOGASTER (FRUIT FLY)
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3F2O)

(no "Site" information available for 3F2O)

(no "SS Bond" information available for 3F2O)

Asymmetric Unit

No.	Residues
1	Tyr A:161	-	Pro A:162
2	Tyr B:161	-	Pro B:162

(no "SAP(SNP)/Variant" information available for 3F2O)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	B302_SPRY	PS50188	B30.2/SPRY domain profile.	SPSB1_HUMAN	33-231	2	A:33-231 B:33-231
2	SOCS	PS50225	SOCS box domain profile.	SPSB1_HUMAN	221-273	2	A:221-233 B:221-233

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	B302_SPRY	PS50188	B30.2/SPRY domain profile.	SPSB1_HUMAN	33-231	1	A:33-231 -
2	SOCS	PS50225	SOCS box domain profile.	SPSB1_HUMAN	221-273	1	A:221-233 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	B302_SPRY	PS50188	B30.2/SPRY domain profile.	SPSB1_HUMAN	33-231	1	- B:33-231
2	SOCS	PS50225	SOCS box domain profile.	SPSB1_HUMAN	221-273	1	- B:221-233

(no "Exon" information available for 3F2O)

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:203
 aligned with SPSB1_HUMAN | Q96BD6 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:203
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230   
          SPSB1_HUMAN    31 YCKPTRLDLLLDMPPVSYDVQLLHSWNNNDRSLNVFVKEDDKLIFHRHPVAQSTDAIRGKVGYTRGLHVWQITWAMRQRGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRNRLYHDGKNQPSKTYPAFLEPDETFIVPDSFLVALDMDDGTLSFIVDGQYMGVAFRGLKGKKLYPVVSAVWGHCEIRMRYLNGLDPE 233
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...hhhhhhhhheeeeee...eee......eeee.....eeeeeee.......eeeeeee.hhhhh....eeeee......eee...........eeeee....eeee.......ee...............eeeeeee....eeeeee..eeeeeee........eeeeee.....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --B302_SPRY  PDB: A:33-231 UniProt: 33-231                                                                                                                                                               -- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOCS          PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f2o A  31 YCKPTRLDLLLDMPPVSYDVQLLHSWNNNDRSLNVFVKEDDKLIFHRHPVAQSTDAIRGKVGYTRGLHVWQITWAMRQRGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRNRLYHDGKNQPSKTYPAFLEPDETFIVPDSFLVALDMDDGTLSFIVDGQYMGVAFRGLKGKKLYPVVSAVWGHCEIRMRYLNGLDPE 233
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with SPSB1_HUMAN | Q96BD6 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:204
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
          SPSB1_HUMAN    30 DYCKPTRLDLLLDMPPVSYDVQLLHSWNNNDRSLNVFVKEDDKLIFHRHPVAQSTDAIRGKVGYTRGLHVWQITWAMRQRGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRNRLYHDGKNQPSKTYPAFLEPDETFIVPDSFLVALDMDDGTLSFIVDGQYMGVAFRGLKGKKLYPVVSAVWGHCEIRMRYLNGLDPE 233
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhh...hhhhhhhh.eeeeee...eeee..eeeeeee.....eeeeeee.......eeeeeeee.hhhh....eeeee......eee...........eeeee....eeee.......ee...............eeeeeee....eeeeee..eeeeeee........eeeeee.....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---B302_SPRY  PDB: B:33-231 UniProt: 33-231                                                                                                                                                               -- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SOCS          PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3f2o B  30 DYCKPTRLDLLLDMPPVSYDVQLLHSWNNNDRSLNVFVKEDDKLIFHRHPVAQSTDAIRGKVGYTRGLHVWQITWAMRQRGTHAVVGVATADAPLHSVGYTTLVGNNHESWGWDLGRNRLYHDGKNQPSKTYPAFLEPDETFIVPDSFLVALDMDDGTLSFIVDGQYMGVAFRGLKGKKLYPVVSAVWGHCEIRMRYLNGLDPE 233
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229

Chain C from PDB  Type:PROTEIN  Length:18
 aligned with VASA1_DROME | P09052 from UniProtKB/Swiss-Prot  Length:661

    Alignment length:18
                                   193        
          VASA1_DROME   184 DINNNNNIVEDVERKREF 201
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author ..........hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 3f2o C 184 DINNNNNIVEDVERKREF 201
                                   193

Chain D from PDB  Type:PROTEIN  Length:15
 aligned with VASA1_DROME | P09052 from UniProtKB/Swiss-Prot  Length:661

    Alignment length:15
                                   193     
          VASA1_DROME   184 DINNNNNIVEDVERK 198
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ............... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 3f2o D 184 DINNNNNIVEDVERK 198
                                   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 '\|'

(no "SCOP Domain" information available for 3F2O)

(no "CATH Domain" information available for 3F2O)

(no "Pfam Domain" information available for 3F2O)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SPSB1_HUMAN | Q96BD6)

molecular function
	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:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
biological process
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0000209	protein polyubiquitination	Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a 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.

Chain C,D (VASA1_DROME | P09052)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004004	ATP-dependent RNA helicase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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).
biological process
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:0008104	protein localization	Any process in which a protein is transported to, or maintained in, a specific location.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(no "Sites" information available for 3f2o)

	Cis Peptide Bonds
		Tyr A:161 - Pro A:162	[ RasMol ]
		Tyr B:161 - Pro B:162	[ RasMol ]

Biological Units
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	3f2o
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	VASA1_DROME \| P09052
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	3.6.1.-
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UniProtKB/Swiss-Prot
	SPSB1_HUMAN \| Q96BD6	:	2jk9
	VASA1_DROME \| P09052	:	2db3 2ihs 3emw 5nt7

(no "Related Entries Specified in the PDB File" available for 3F2O)

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