1M4M - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   MOUSE SURVIVIN

Authors :   S. W. Muchmore, J. Chen, C. Jakob, D. Zakula, E. D. Matayoshi, W. Wu, H. Zh S. C. Ng, D. C. Altieri

Date :   03 Jul 02 (Deposition) - 25 Sep 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)
Biol. Unit 3: A  (2x)

Keywords :   Zn Finger Baculovirus Iap Repeat, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. W. Muchmore, J. Chen, C. Jakob, D. Zakula, E. D. Matayoshi, W. Wu, H. Zhang, F. Li, S. C. Ng, D. C. Altieri
Crystal Structure And Mutagenic Analysis Of The Inhibitor-Of-Apoptosis Protein Survivin
Mol. Cell V. 6 173 2000
PubMed-ID: 10949038 | Reference-DOI: 10.1016/S1097-2765(00)00018-6

Molecule 1 - BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-4T-1
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	APOPTOSIS INHIBITOR SURVIVIN, APOPTOSIS INHIBITOR 4, TIAP

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:76 , HIS A:80	BINDING SITE FOR RESIDUE ZN A 501
2	AC2	SOFTWARE	CYS A:57 , CYS A:60 , HIS A:77 , CYS A:84	BINDING SITE FOR RESIDUE ZN A 502

Asymmetric Unit

No.	Residues
1	A:60	-	A:84

(no "Cis Peptide Bond" information available for 1M4M)

(no "SAP(SNP)/Variant" information available for 1M4M)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIR_REPEAT_2	PS50143	BIR repeat profile.	BIRC5_MOUSE	18-88	1	A:18-88

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIR_REPEAT_2	PS50143	BIR repeat profile.	BIRC5_MOUSE	18-88	1	A:18-88

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIR_REPEAT_2	PS50143	BIR repeat profile.	BIRC5_MOUSE	18-88	2	A:18-88

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIR_REPEAT_2	PS50143	BIR repeat profile.	BIRC5_MOUSE	18-88	2	A:18-88

Asymmetric Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENSMUST00000081387	1a	ENSMUSE00000151749	chr11:117710565-117710775	211	BIRC5_MOUSE	1-37	37	1	A:7-37	31
1.2	ENSMUST00000081387	2	ENSMUSE00000151751	chr11:117711068-117711177	110	BIRC5_MOUSE	38-74	37	1	A:38-74	37
1.3a	ENSMUST00000081387	3a	ENSMUSE00000506620	chr11:117713977-117714094	118	BIRC5_MOUSE	74-113	40	1	A:74-113	40
1.3c	ENSMUST00000081387	3c	ENSMUSE00000508223	chr11:117716539-117717046	508	BIRC5_MOUSE	114-140	27	1	A:114-118	5

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:112
 aligned with BIRC5_MOUSE | O70201 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:112
                                    16        26        36        46        56        66        76        86        96       106       116  
          BIRC5_MOUSE     7 PQIWQLYLKNYRIATFKNWPFLEDCACTPERMAEAGFIHCPTENEPDLAQCFFCFKELEGWEPDDNPIEEHRKHSPGCAFLTVKKQMEELTVSEFLKLDRQRAKNKIAKETN 118
               SCOP domains d1m4ma_ A: Anti-apoptotic protein survivin                                                                       SCOP domains
               CATH domains 1m4mA00 A:7-118 Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A                                           CATH domains
               Pfam domains -----------BIR-1m4mA01 A:18-88                                                    ------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh............hhhhhhhh.eee.........eee.....ee.......hhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------BIR_REPEAT_2  PDB: A:18-88 UniProt: 18-88                              ------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:7-37         Exon 1.2  PDB: A:38-74 UniProt: 38-74---------------------------------------1.3c  Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------Exon 1.3a  PDB: A:74-113 UniProt: 74-113----- Transcript 1 (2)
                 1m4m A   7 PQIWQLYLKNYRIATFKNWPFLEDCACTPERMAEAGFIHCPTENEPDLAQCFFCFKELEGWEPDDNPIEEHRKHSPGCAFLTVKKQMEELTVSEFLKLDRQRAKNKIAKETN 118
                                    16        26        36        46        56        66        76        86        96       106       116

Legend:		→ Mismatch	(orange background)
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		→ 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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Small proteins (3458)

Fold: Inhibitor of apoptosis (IAP) repeat (71)

Superfamily: Inhibitor of apoptosis (IAP) repeat (71)

Family: Inhibitor of apoptosis (IAP) repeat (70)

Protein domain: Anti-apoptotic protein survivin (10)

Mouse (Mus musculus) [TaxId: 10090] (1)

d1m4ma_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A (42)

Homologous Superfamily: Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A (42)

House mouse (Mus musculus) (1)

1m4mA00

A:7-118

Asymmetric Unit

Clans(

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Families(

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Organisms( (-)

)

Clan: BIR-like (25)

Family: BIR (25)

Mus musculus (Mouse) (1)

BIR-1m4mA01

A:18-88

Asymmetric Unit(hide GO term definitions)

Chain A (BIRC5_MOUSE | O70201)

molecular function
	GO:0008536	Ran GTPase binding	Interacting selectively and non-covalently with Ran, a conserved Ras-like GTP-binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly.
	GO:0051087	chaperone binding	Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
	GO:0048037	cofactor binding	Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
	GO:0004869	cysteine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0043027	cysteine-type endopeptidase inhibitor activity involved in apoptotic process	Stops, prevents or reduces the activity of a cysteine-type endopeptidase involved in the apoptotic process.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	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:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	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:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0015631	tubulin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of tubulin, including microtubules.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	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:0000910	cytokinesis	The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
	GO:0051303	establishment of chromosome localization	The directed movement of a chromosome to a specific location.
	GO:1990001	inhibition of cysteine-type endopeptidase activity involved in apoptotic process	Any process that prevents the activation of an inactive cysteine-type endopeptidase involved in an apoptotic process.
	GO:0000226	microtubule cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
	GO:0090307	mitotic spindle assembly	The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0043154	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
	GO:0043524	negative regulation of neuron apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0031536	positive regulation of exit from mitosis	Any process that activates or increases the rate of progression from anaphase/telophase (high mitotic CDK activity) to G1 (low mitotic CDK activity).
	GO:0045931	positive regulation of mitotic cell cycle	Any process that activates or increases the rate or extent of progression through the mitotic cell cycle.
	GO:0031503	protein complex localization	A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
	GO:0061178	regulation of insulin secretion involved in cellular response to glucose stimulus	Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
	GO:0007346	regulation of mitotic cell cycle	Any process that modulates the rate or extent of progress through the mitotic cell cycle.
	GO:0009966	regulation of signal transduction	Any process that modulates the frequency, rate or extent of signal transduction.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0061469	regulation of type B pancreatic cell proliferation	Any process that modulates the frequency, rate or extent of type B pancreatic cell proliferation.
	GO:0031577	spindle checkpoint	A cell cycle checkpoint that originates from the mitotic or meiotic spindle.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005814	centriole	A cellular organelle, found close to the nucleus in many eukaryotic cells, consisting of a small cylinder with microtubular walls, 300-500 nm long and 150-250 nm in diameter. It contains nine short, parallel, peripheral microtubular fibrils, each fibril consisting of one complete microtubule fused to two incomplete microtubules. Cells usually have two centrioles, lying at right angles to each other. At division, each pair of centrioles generates another pair and the twin pairs form the pole of the mitotic spindle.
	GO:0005694	chromosome	A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
	GO:0032133	chromosome passenger complex	A eukaryotically conserved protein complex that localizes to kinetochores in early mitosis, the spindle mid-zone in anaphase B and to the telophase midbody. It has been proposed that the passenger complex coordinates various events based on its location to different structures during the course of mitosis. Complex members include the BIR-domain-containing protein Survivin, Aurora kinase, INCENP and Borealin.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005881	cytoplasmic microtubule	Any microtubule in the cytoplasm of a cell.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0031021	interphase microtubule organizing center	A microtubule organizing center found in interphase cells, which organize a longitudinal array of three to five MT bundles from the nuclear envelope during interphase. Each MT bundle is composed of two to seven MTs arranged in an antiparallel configuration, with the dynamic MT plus ends extending toward the cell tips and stable minus ends near the nucleus.
	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:0005874	microtubule	Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
	GO:0030496	midbody	A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
	GO:0000228	nuclear chromosome	A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
	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:0005819	spindle	The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
	GO:0005876	spindle microtubule	Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.

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