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Title :   CRYSTAL STRUCTURE OF THE YEAST KINETOCHORE SPC24/SPC25 GLOBULAR DOMAIN

Authors :   R. R. Wei, S. C. Harrison

Date :   25 Jan 06 (Deposition) - 13 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Alpha-Beta, Complex, Coiled-Coil, Structural Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. R. Wei, S. C. Harrison, J. R. Schnell, J. J. Chou
Atomic Structure Of The Kinetochore Spc24P/Spc25P Globular Domain Reveals A Novel Fold
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL 25.2 KDA PROTEIN IN AFG3-SEB2 INTERGENIC REGION
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	ROSETTA
	Expression System Plasmid	:	PET3ATR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SPC25P GLOBULAR DOMAIN
	Gene	:	YER018C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

Molecule 2 - HYPOTHETICAL 24.6 KDA PROTEIN IN ILV2-ADE17 INTERGENIC REGION
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	ROSETTA
	Expression System Plasmid	:	PET3ATR
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SPC24P GLOBULAR DOMAIN
	Gene	:	YMR117C, YM9718.16C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE
2	NA	1	Ligand/Ion	SODIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:25 , HOH A:50 , THR A:195 , HIS A:198 , HOH B:40 , ARG B:210 , LYS B:213	BINDING SITE FOR RESIDUE PO4 A 222

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

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

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

(no "PROSITE Motif" information available for 2FTX)

Asymmetric/Biological Unit (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YER018C	1	YER018C.1	V:192623-191958	666	SPC25_YEAST	1-221	221	1	A:132-221	90

2.1	YMR117C	1	YMR117C.1	XIII:501890-501249	642	SPC24_YEAST	1-213	213	1	B:155-213	59

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
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Chain A from PDB  Type:PROTEIN  Length:90
 aligned with SPC25_YEAST | P40014 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:90
                                   141       151       161       171       181       191       201       211       221
          SPC25_YEAST   132 GNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL 221
               SCOP domains -d2ftxa1 A:133-221 Kinetochore protein Spc25                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheeeee.......eeeee.....eeeee.......eeeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:132-221 UniProt: 1-221 [INCOMPLETE]                                       Transcript 1
                 2ftx A 132 mNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAmHGDHVIGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDmLLASL 221
                            |      141       151       161       171   |   181       191       201       211    |  221
                          132-MSE                                    175-MSE                                  216-MSE

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with SPC24_YEAST | Q04477 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:59
                                   164       174       184       194       204         
          SPC24_YEAST   155 ANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK 213
               SCOP domains d2ftxb1 B:155-213 Kinetochore protein Spc24                 SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeeehhh.eeee........eeee.....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:155-213 UniProt: 1-213 [INCOMPLETE]        Transcript 2
                 2ftx B 155 ANENILKLKLYRSLGVILDLENDQVLINRKNDGNIDILPLDNNLSDFYKTKYIWERLGK 213
                                   164       174       184       194       204

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 "CATH Domain" information available for 2FTX)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SPC25_YEAST | P40014)

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: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:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	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).
cellular component
	GO:0031262	Ndc80 complex	A protein complex conserved among eukaryotes that forms part of the kinetochore and plays an essential role in forming stable kinetochore-microtubule attachments. The complex contains proteins known in several species, including budding and fission yeasts, as Ndc80p, Nuf2p, Spc24p, and Spc25p. In vertebrates it is part of the outer plate of the kinetochore.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000777	condensed chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
	GO:0000778	condensed nuclear chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules.
	GO:0000780	condensed nuclear chromosome, centromeric region	The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000776	kinetochore	A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	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.

Chain B (SPC24_YEAST | Q04477)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0007059	chromosome segregation	The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
	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).
cellular component
	GO:0031262	Ndc80 complex	A protein complex conserved among eukaryotes that forms part of the kinetochore and plays an essential role in forming stable kinetochore-microtubule attachments. The complex contains proteins known in several species, including budding and fission yeasts, as Ndc80p, Nuf2p, Spc24p, and Spc25p. In vertebrates it is part of the outer plate of the kinetochore.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000777	condensed chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
	GO:0000778	condensed nuclear chromosome kinetochore	A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules.
	GO:0000780	condensed nuclear chromosome, centromeric region	The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	GO:0000776	kinetochore	A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	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.

Asymmetric/Biological Unit
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	SPC25_YEAST \| P40014
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	SPC24_YEAST \| Q04477	:	2fv4 4geq 5t6j 5tcs 5td8
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Description

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Ligands, Modified Residues, Ions (3, 5)

Sites (1, 1)

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