2ZN9 - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CA2+-BOUND FORM OF DES3-20ALG-2

Authors :   H. Suzuki, M. Kawasaki, T. Inuzuka, T. Kakiuchi, H. Shibata, S. Wakatsuki, M. Maki

Date :   22 Apr 08 (Deposition) - 09 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Penta-Ef-Hand Protein, Calcium Binding Protein, Apoptosis, Endoplasmic Reticulum, Membrane, Nucleus, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Suzuki, M. Kawasaki, T. Inuzuka, M. Okumura, T. Kakiuchi, H. Shibata, S. Wakatsuki, M. Maki
Structural Basis For Ca(2+)-Dependent Formation Of Alg-2/Alix Peptide Complex: Ca(2+)/Ef3-Driven Arginine Switch Mechanism
Structure V. 16 1562 2008
PubMed-ID: 18940611 | Reference-DOI: 10.1016/J.STR.2008.07.012
(for further references see the PDB file header)

Molecule 1 - PROGRAMMED CELL DEATH PROTEIN 6
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3D
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 20-191
	Gene	:	PDCD6, ALG2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	APOPTOSIS-LINKED GENE 2 PROTEIN, PROBABLE CALCIUM- BINDING PROTEIN ALG-2

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 9)

No.	Name	Count	Type	Full Name
1	12P	1	Ligand/Ion	DODECAETHYLENE GLYCOL
2	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
3	CA	7	Ligand/Ion	CALCIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	12P	1	Ligand/Ion	DODECAETHYLENE GLYCOL
2	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
3	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	12P	-1	Ligand/Ion	DODECAETHYLENE GLYCOL
2	2PE	1	Ligand/Ion	NONAETHYLENE GLYCOL
3	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:36 , ASP A:38 , SER A:40 , VAL A:42 , GLU A:47 , HOH A:927	BINDING SITE FOR RESIDUE CA A 901
2	AC2	SOFTWARE	ASP A:103 , ASP A:105 , SER A:107 , MET A:109 , GLU A:114	BINDING SITE FOR RESIDUE CA A 902
3	AC3	SOFTWARE	ASP A:169 , ASP A:171 , ASP A:173 , TRP A:175 , HOH A:924 , HOH A:928	BINDING SITE FOR RESIDUE CA A 903
4	AC4	SOFTWARE	ASN A:106 , HOH A:920 , ASN B:106 , HOH B:924	BINDING SITE FOR RESIDUE CA A 904
5	AC5	SOFTWARE	TYR A:91 , TRP A:95 , PHE A:122 , GLY A:123 , TYR A:124 , ARG A:166 , PRO B:23 , GLN B:25	BINDING SITE FOR RESIDUE 2PE A 1
6	AC6	SOFTWARE	ASP B:36 , ASP B:38 , SER B:40 , VAL B:42 , GLU B:47 , HOH B:915	BINDING SITE FOR RESIDUE CA B 901
7	AC7	SOFTWARE	ASP B:103 , ASP B:105 , SER B:107 , MET B:109 , GLU B:114	BINDING SITE FOR RESIDUE CA B 902
8	AC8	SOFTWARE	ASP B:169 , ASP B:171 , ASP B:173 , TRP B:175 , HOH B:914 , HOH B:925	BINDING SITE FOR RESIDUE CA B 903
9	AC9	SOFTWARE	ALA A:21 , PRO A:23 , GLN A:25 , LEU A:28 , THR A:86 , TYR B:91 , ASP B:94 , TRP B:95 , GLY B:123 , TYR B:124 , ARG B:166	BINDING SITE FOR RESIDUE 12P B 2

(no "SS Bond" information available for 2ZN9)

(no "Cis Peptide Bond" information available for 2ZN9)

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035459	G	123	C	PDCD6_HUMAN	Unclassified	---	A/B	G	123	C
2	CancerSNP	VAR_PDCD6_HUMAN_CCDS3854_1_01 *	G	123	C	PDCD6_HUMAN	Disease (Breast cancer)	---	A/B	G	123	C
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035459	G	123	C	PDCD6_HUMAN	Unclassified	---	A/B	G	123	C
2	CancerSNP	VAR_PDCD6_HUMAN_CCDS3854_1_01 *	G	123	C	PDCD6_HUMAN	Disease (Breast cancer)	---	A/B	G	123	C
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_035459	G	123	C	PDCD6_HUMAN	Unclassified	---	A/B	G	123	C
2	CancerSNP	VAR_PDCD6_HUMAN_CCDS3854_1_01 *	G	123	C	PDCD6_HUMAN	Disease (Breast cancer)	---	A/B	G	123	C
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	PDCD6_HUMAN	23-58 90-125 156-191	6	A:23-58 B:23-58 A:90-125 B:90-125 A:156-189 B:156-190
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	PDCD6_HUMAN	36-48 103-115	4	A:36-48 B:36-48 A:103-115 B:103-115

Biological Unit 1 (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	PDCD6_HUMAN	23-58 90-125 156-191	6	A:23-58 B:23-58 A:90-125 B:90-125 A:156-189 B:156-190
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	PDCD6_HUMAN	36-48 103-115	4	A:36-48 B:36-48 A:103-115 B:103-115

Biological Unit 2 (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	PDCD6_HUMAN	23-58 90-125 156-191	6	A:23-58 B:23-58 A:90-125 B:90-125 A:156-189 B:156-190
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	PDCD6_HUMAN	36-48 103-115	4	A:36-48 B:36-48 A:103-115 B:103-115

(no "Exon" information available for 2ZN9)

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:169
 aligned with PDCD6_HUMAN | O75340 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:169
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         
          PDCD6_HUMAN    21 ALPDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFS 189
               SCOP domains d2zn9a_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh......eehhhhhh..........hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------------------------------------------------------C------------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------C------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (1) --EF_HAND_2  PDB: A:23-58             -------------------------------EF_HAND_2  PDB: A:90-125            ------------------------------EF_HAND_2  PDB: A:156-189          PROSITE (1)
                PROSITE (2) ---------------EF_HAND_1    ------------------------------------------------------EF_HAND_1    -------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zn9 A  21 ALPDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFS 189
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with PDCD6_HUMAN | O75340 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:170
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
          PDCD6_HUMAN    21 ALPDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSI 190
               SCOP domains d2zn9b_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------EF_hand_6-2zn9B03 B:39-90                           EF_hand_5-2zn9B01 B:91-155                                       ----------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------EF_hand_6-2zn9B04 B:39-90                           EF_hand_5-2zn9B02 B:91-155                                       ----------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhh.......hhhhhhhhh........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------------------------------------------------------C------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------C------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) --EF_HAND_2  PDB: B:23-58             -------------------------------EF_HAND_2  PDB: B:90-125            ------------------------------EF_HAND_2  PDB: B:156-190           PROSITE (1)
                PROSITE (2) ---------------EF_HAND_1    ------------------------------------------------------EF_HAND_1    --------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zn9 B  21 ALPDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSI 190
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

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	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(

)

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)

Human (Homo sapiens) [TaxId: 9606] (35)

1a	d2zn9a_	A:
1b	d2zn9b_	B:

(no "CATH Domain" information available for 2ZN9)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: EF_hand_5 (126)

Homo sapiens (Human) (31)

1a	EF_hand_5-2zn9B01	B:91-155
1b	EF_hand_5-2zn9B02	B:91-155

Family: EF_hand_6 (75)

Homo sapiens (Human) (34)

2a	EF_hand_6-2zn9B03	B:39-90
2b	EF_hand_6-2zn9B04	B:39-90

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDCD6_HUMAN | O75340)

molecular function
	GO:0060090	binding, bridging	The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004198	calcium-dependent cysteine-type endopeptidase activity	Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
	GO:0048306	calcium-dependent 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), in the presence of calcium.
	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:0043495	protein anchor	Interacting selectively and non-covalently with both a protein or protein complex and a membrane, in order to maintain the localization of the protein at a specific membrane location.
	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:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0006919	activation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
	GO:0001525	angiogenesis	Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
	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:0097190	apoptotic signaling pathway	A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered.
	GO:0034605	cellular response to heat	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0006886	intracellular protein transport	The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
	GO:0032007	negative regulation of TOR signaling	Any process that stops, prevents, or reduces the frequency, rate or extent of TOR signaling.
	GO:0051898	negative regulation of protein kinase B signaling	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
	GO:0030948	negative regulation of vascular endothelial growth factor receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0043280	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
	GO:0010595	positive regulation of endothelial cell migration	Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0001938	positive regulation of endothelial cell proliferation	Any process that activates or increases the rate or extent of endothelial cell proliferation.
	GO:0051592	response to calcium ion	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 a calcium ion stimulus.
	GO:0036324	vascular endothelial growth factor receptor-2 signaling pathway	Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor-2 (VEGFR-2) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0070971	endoplasmic reticulum exit site	An endoplasmic reticulum part at which COPII-coated vesicles are produced.
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	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.

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	2zn9
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UniProtKB/Swiss-Prot
	PDCD6_HUMAN \| O75340	:	2zn8 2znd 2zne 2zrs 2zrt 3aaj 3aak 3wxa 5gqq

2zn8	CRYSTAL STRUCTURE OF ZN2+-BOUND FORM OF ALG-2
2znd	CRYSTAL STRUCTURE OF CA2+-FREE FORM OF DES3-20ALG-2
2zne	CRYSTAL STRUCTURE OF ZN2+-BOUND FORM OF DES3-23ALG-2 COMPLEXED WITH ALIX ABS PEPTIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

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Exons (0, 0)

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SCOP Domains (1, 2)

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