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Title :   CRYSTAL STRUCTURE OF SFI1P/CDC31P COMPLEX

Authors :   S. Li, A. M. Sandercock, P. T. Conduit, C. V. Robinson, R. L. Williams, J. V. Kilmartin

Date :   03 May 06 (Deposition) - 27 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Sfi1P, Centrin, Cdc31P, Spindle Pole Body, Centrosome, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Li, A. M. Sandercock, P. Conduit, C. V. Robinson, R. L. Williams, J. V. Kilmartin
Structural Role Of Sfi1P-Centrin Filaments In Budding Yeast Spindle Pole Body Duplication.
J. Cell Biol. V. 173 867 2006
PubMed-ID: 16785321 | Reference-DOI: 10.1083/JCB.200603153
(for further references see the PDB file header)

Molecule 1 - CELL DIVISION CONTROL PROTEIN 31
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CDC31
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	NUCLEOPORIN CDC31, NUCLEAR PORE PROTEIN CDC31

Molecule 2 - SFI1P
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6
	Expression System Strain	:	ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	SFI1
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 24)

No.	Name	Count	Type	Full Name
1	CA	7	Ligand/Ion	CALCIUM ION
2	MSE	17	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:33 , ASN A:35 , ASP A:37 , PHE A:39 , GLU A:44	BINDING SITE FOR RESIDUE CA A 162
2	AC2	SOFTWARE	ASP A:106 , ASP A:108 , THR A:110 , LYS A:112 , ASN A:117	BINDING SITE FOR RESIDUE CA A 163
3	AC3	SOFTWARE	ASP A:142 , ASP A:144 , ASP A:146 , GLU A:148 , ASN A:150 , GLU A:153	BINDING SITE FOR RESIDUE CA A 164
4	AC4	SOFTWARE	ASP B:33 , ASN B:35 , ASP B:37 , PHE B:39 , GLU B:44	BINDING SITE FOR RESIDUE CA B 162
5	AC5	SOFTWARE	ASP B:106 , ASP B:108 , THR B:110 , LYS B:112 , ASN B:117	BINDING SITE FOR RESIDUE CA B 163
6	AC6	SOFTWARE	ASP B:142 , ASP B:144 , ASP B:146 , GLU B:148 , GLU B:153	BINDING SITE FOR RESIDUE CA B 164
7	AC7	SOFTWARE	ASP C:33 , ASN C:35 , ASP C:37 , PHE C:39 , GLU C:44	BINDING SITE FOR RESIDUE CA C 162

(no "SS Bond" information available for 2DOQ)

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

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

Asymmetric/Biological Unit (2, 15)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CDC31_YEAST	20-55 93-128 129-161	9	A:20-55 B:20-55 C:20-55 A:93-128 B:93-128 C:93-126 A:129-160 B:129-161 C:136-157
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CDC31_YEAST	33-45 142-154	6	A:33-45 B:33-45 C:33-45 A:142-154 B:142-154 C:142-154

Asymmetric/Biological Unit (2, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLL003W	1	YLL003W.1	XII:143200-146040	2841	SFI1_YEAST	1-946	946	1	D:214-296 (gaps)	104

2.1	YOR257W	1	YOR257W.1	XV:811008-811493	486	CDC31_YEAST	1-161	161	3	A:15-160 B:13-161 C:14-157 (gaps)	146 149 144

Asymmetric/Biological Unit

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Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:146
 aligned with CDC31_YEAST | P06704 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:146
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154      
          CDC31_YEAST    15 SELLEEQKQEIYEAFSLFDMNNDGFLDYHELKVAMKALGFELPKREILDLIDEYDSEGRHLMKYDDFYIVMGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELGETLTDEELRAMIEEFDLDGDGEINENEFIAICTD 160
               SCOP domains d2doqa_ A: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh......eehhhhhhhhhhhh....hhhhhhhhhhhh.......eehhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----EF_HAND_2  PDB: A:20-55             -------------------------------------EF_HAND_2  PDB: A:93-128            EF_HAND_2  PDB: A:129-160        PROSITE (1)
                PROSITE (2) ------------------EF_HAND_1    ------------------------------------------------------------------------------------------------EF_HAND_1    ------ PROSITE (2)
               Transcript 2 Exon 2.1  PDB: A:15-160 UniProt: 1-161 [INCOMPLETE]                                                                                                Transcript 2
                 2doq A  15 SELLEEQKQEIYEAFSLFDmNNDGFLDYHELKVAmKALGFELPKREILDLIDEYDSEGRHLmKYDDFYIVmGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELGETLTDEELRAmIEEFDLDGDGEINENEFIAICTD 160
                                    24        34        44    |   54        64        74 |      84|       94       104       114       124       134  |    144       154      
                                              34-MSE         49-MSE                     76-MSE   85-MSE                                             137-MSE

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with CDC31_YEAST | P06704 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:149
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152         
          CDC31_YEAST    13 LNSELLEEQKQEIYEAFSLFDMNNDGFLDYHELKVAMKALGFELPKREILDLIDEYDSEGRHLMKYDDFYIVMGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELGETLTDEELRAMIEEFDLDGDGEINENEFIAICTDS 161
               SCOP domains d2doqb_ B: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------EF_HAND_2  PDB: B:20-55             -------------------------------------EF_HAND_2  PDB: B:93-128            EF_HAND_2  PDB: B:129-161         PROSITE (1)
                PROSITE (2) --------------------EF_HAND_1    ------------------------------------------------------------------------------------------------EF_HAND_1    ------- PROSITE (2)
               Transcript 2 Exon 2.1  PDB: B:13-161 UniProt: 1-161 [INCOMPLETE]                                                                                                   Transcript 2
                 2doq B  13 LNSELLEEQKQEIYEAFSLFDmNNDGFLDYHELKVAmKALGFELPKREILDLIDEYDSEGRHLmKYDDFYIVmGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELGETLTDEELRAmIEEFDLDGDGEINENEFIAICTDS 161
                                    22        32 |      42      | 52        62        72   |    82  |     92       102       112       122       132    |  142       152         
                                                34-MSE         49-MSE                     76-MSE   85-MSE                                             137-MSE

Chain C from PDB  Type:PROTEIN  Length:130
 aligned with CDC31_YEAST | P06704 from UniProtKB/Swiss-Prot  Length:161

    Alignment length:144
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153    
          CDC31_YEAST    14 NSELLEEQKQEIYEAFSLFDMNNDGFLDYHELKVAMKALGFELPKREILDLIDEYDSEGRHLMKYDDFYIVMGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELGETLTDEELRAMIEEFDLDGDGEINENEFIAI 157
               SCOP domains d2doqc_ C: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh......eehhhhhhhhhhh.....hhhhhhhhhhhhh......eehhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhh..---------..hhhhh..-----hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ------EF_HAND_2  PDB: C:20-55             -------------------------------------EF_HAND_2  PDB: C:93-126            EF_HAND_2  PDB: C:136-157     PROSITE (1)
                PROSITE (2) -------------------EF_HAND_1    ------------------------------------------------------------------------------------------------EF_HAND_1    --- PROSITE (2)
               Transcript 2 Exon 2.1  PDB: C:14-157 (gaps) UniProt: 1-161 [INCOMPLETE]                                                                                       Transcript 2
                 2doq C  14 NSELLEEQKQEIYEAFSLFDmNNDGFLDYHELKVAmKALGFELPKREILDLIDEYDSEGRHLmKYDDFYIVmGEKILKRDPLDEIKRAFQLFDDDHTGKISIKNLRRVAKELG---------AmIEEFDLD-----NENEFIAI 157
                                    23        33|       43     |  53        63        73  |     83 |      93       103       113       123  |      -  ||   143|     |153    
                                               34-MSE         49-MSE                     76-MSE   85-MSE                                  126       136|    144   150       
                                                                                                                                                     137-MSE

Chain D from PDB  Type:PROTEIN  Length:83
 aligned with SFI1_YEAST | Q12369 from UniProtKB/Swiss-Prot  Length:946

    Alignment length:104
                                   202       212       222       232       242       252       262       272       282       292    
           SFI1_YEAST   193 SLAEYTYAKNKIRRHFNHWKTVCELNEEANRFANQAKLRVQEAVFYIWSDKTLKYSQMANDEAESFRNTWLLFRSFQQWITLTQTLKEQSRLADQAFLNKMFRK 296
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....---------------------...hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:214-296 (gaps) UniProt: 1-946 [INCOMPLETE]                                              Transcript 1
                 2doq D 214 PLGS---------------------NEEANRFANQAKLRVQEAVFYIWSDKTLKYSQmANDEAESFRNTWLLFRSFQQWITLTQTFKEQSRLADQAFLNKmFRK 296
                               |     -         -     | 222       232       242       252       262       272       282       292|   
                             217                   218                             250-MSE                                    293-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: automated matches (65)

Protein domain: automated matches (65)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (2)

1a	d2doqa_	A:
1b	d2doqb_	B:
1c	d2doqc_	C:

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

(no "Pfam Domain" information available for 2DOQ)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (CDC31_YEAST | P06704)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005200	structural constituent of cytoskeleton	The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007020	microtubule nucleation	The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation).
	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
	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:0043549	regulation of kinase activity	Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0030474	spindle pole body duplication	Construction of a new spindle pole body.
	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: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:0005825	half bridge of spindle pole body	Structure adjacent to the plaques of the spindle pole body.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0000111	nucleotide-excision repair factor 2 complex	One of several protein complexes involved in nucleotide-excision repair; possesses damaged DNA binding activity. In S. cerevisiae, it is composed of Rad4p and Rad23p.
	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:0005816	spindle pole body	The microtubule organizing center in fungi; functionally homologous to the animal cell centrosome.
	GO:0070390	transcription export complex 2	A protein complex that couples SAGA-dependent gene expression to mRNA export at the inner side of the nuclear pore complex (NPC). The TREX-2 complex is tethered to the inner side of the NPC via the nucleoporins Nup1 and Nup60; in S. cerevisiae it contains Sac3p, Thp1p, Sus1p and Cdc31p.

Chain D (SFI1_YEAST | Q12369)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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:0000086	G2/M transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
	GO:0007049	cell cycle	The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
	GO:0051301	cell division	The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
	GO:0051225	spindle assembly	The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart.
	GO:0030474	spindle pole body duplication	Construction of a new spindle pole body.
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:0005825	half bridge of spindle pole body	Structure adjacent to the plaques of the spindle pole body.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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(no "Related Entries Specified in the PDB File" available for 2DOQ)

Description

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Ligands, Modified Residues, Ions (2, 24)

Sites (7, 7)

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Cis Peptide Bonds (0, 0)

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