3EBM - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN TRANSLATIONALLY CONTROLLED TUMOUR ASSOCIATED PROTEIN (HTCTP) MUTANT E12V

Authors :   B. Yang, X. Dong, C. Zhong, J. Ding

Date :   28 Aug 08 (Deposition) - 30 Jun 09 (Release) - 10 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Tctp, E12V, Calcium, Cytoplasm, Phosphoprotein, Calcium- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Dong, B. Yang, Y. Li, C. Zhong, J. Ding
Molecular Basis Of The Acceleration Of The Gdp-Gtp Exchange Of Human Ras Homolog Enriched In Brain By Human Translationally Controlled Tumor Protein.
J. Biol. Chem. V. 284 23754 2009
PubMed-ID: 19570981 | Reference-DOI: 10.1074/JBC.M109.012823
(for further references see the PDB file header)

Molecule 1 - TRANSLATIONALLY-CONTROLLED TUMOR PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-22B+
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TPT1
	Mutation	:	YES
	Organism Common	:	MAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TRANSLATIONALLY CONTROLLED TUMOUR ASSOCIATED PROTEIN, HTCTP, TCTP, P23, HISTAMINE-RELEASING FACTOR, HRF, FORTILIN

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 3EBM)

Asymmetric Unit

No.	Residues
1	B:172	-	C:172

(no "Cis Peptide Bond" information available for 3EBM)

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052273	V	146	F	TCTP_HUMAN	Polymorphism	3087989	A/B/C/D	V	146	F

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052273	V	146	F	TCTP_HUMAN	Polymorphism	3087989	A	V	146	F

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052273	V	146	F	TCTP_HUMAN	Polymorphism	3087989	B	V	146	F

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

Biological Unit 3 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052273	V	146	F	TCTP_HUMAN	Polymorphism	3087989	C	V	146	F

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

Biological Unit 4 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052273	V	146	F	TCTP_HUMAN	Polymorphism	3087989	D	V	146	F

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TCTP_3	PS51797	Translationally controlled tumor protein (TCTP) domain profile.	TCTP_HUMAN	1-172	4	A:1-172 B:1-172 C:1-172 D:1-172
2	TCTP_2	PS01003	Translationally controlled tumor protein (TCTP) domain signature 2.	TCTP_HUMAN	129-151	4	A:129-151 B:129-151 C:129-151 D:129-151

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TCTP_3	PS51797	Translationally controlled tumor protein (TCTP) domain profile.	TCTP_HUMAN	1-172	1	A:1-172 - - -
2	TCTP_2	PS01003	Translationally controlled tumor protein (TCTP) domain signature 2.	TCTP_HUMAN	129-151	1	A:129-151 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TCTP_3	PS51797	Translationally controlled tumor protein (TCTP) domain profile.	TCTP_HUMAN	1-172	1	- B:1-172 - -
2	TCTP_2	PS01003	Translationally controlled tumor protein (TCTP) domain signature 2.	TCTP_HUMAN	129-151	1	- B:129-151 - -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TCTP_3	PS51797	Translationally controlled tumor protein (TCTP) domain profile.	TCTP_HUMAN	1-172	1	- - C:1-172 -
2	TCTP_2	PS01003	Translationally controlled tumor protein (TCTP) domain signature 2.	TCTP_HUMAN	129-151	1	- - C:129-151 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TCTP_3	PS51797	Translationally controlled tumor protein (TCTP) domain profile.	TCTP_HUMAN	1-172	1	- - - D:1-172
2	TCTP_2	PS01003	Translationally controlled tumor protein (TCTP) domain signature 2.	TCTP_HUMAN	129-151	1	- - - D:129-151

(no "Exon" information available for 3EBM)

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:147
 aligned with TCTP_HUMAN | P13693 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:176
                                                                                                                                                                                                     172    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 |    
           TCTP_HUMAN     1 MIIYRDLISHDEMFSDIYKIREIADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGPEGEGTESTVITGVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGLEMEKC----   -
               SCOP domains d3ebma_ A: Translationally controlled                              tumor protein TCTP (histamine-releasing factor)                                                               SCOP domains
               CATH domains 3ebmA00 A:1-176 Metal Binding Protein                             , Guanine Nucleotide Exchange Factor; Chain A                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee...eeeee....eeeee..ee.-----------------------------..eehhhhhhh.eee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhheeee..........eeeee......eeeeee...eeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------F------------------------------ SAPs(SNPs)
                PROSITE (1) TCTP_3  PDB: A:1-172 UniProt: 1-172                                                                                                                                         ---- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------TCTP_2  PDB: A:129-151 ------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebm A   1 MIIYRDLISHDVMFSDIYKIREIADGLCLEVEGKMVS-----------------------------ITGVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGLEMEKCLEHH 176
                                    10        20        30      |  -         -         -      | 70        80        90       100       110       120       130       140       150       160       170      
                                                               37                            67

Chain B from PDB  Type:PROTEIN  Length:147
 aligned with TCTP_HUMAN | P13693 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:177
                                                                                                                                                                                                     172     
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 |     
           TCTP_HUMAN     1 MIIYRDLISHDEMFSDIYKIREIADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGPEGEGTESTVITGVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGLEMEKC-----   -
               SCOP domains d3ebmb_ B: Translationally controlled                               tumor protein TCTP (histamine-releasing factor)                                                               SCOP domains
               CATH domains 3ebmB00 B:1-177 Metal Binding Protein,                               Guanine Nucleotide Exchange Factor; Chain A                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee....eeee....eeeee......------------------------------.hhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhheeee..........eeeee......eeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------F------------------------------- SAPs(SNPs)
                PROSITE (1) TCTP_3  PDB: B:1-172 UniProt: 1-172                                                                                                                                         ----- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------TCTP_2  PDB: B:129-151 -------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebm B   1 MIIYRDLISHDVMFSDIYKIREIADGLCLEVEGKMVSR------------------------------GVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGLEMEKCLEHHH 177
                                    10        20        30       | -         -         -        70        80        90       100       110       120       130       140       150       160       170       
                                                                38                             69

Chain C from PDB  Type:PROTEIN  Length:145
 aligned with TCTP_HUMAN | P13693 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:176
                                                                                                                                                                                                     172    
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 |    
           TCTP_HUMAN     1 MIIYRDLISHDEMFSDIYKIREIADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGPEGEGTESTVITGVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGLEMEKC----   -
               SCOP domains d3ebmc_ C: Translationally controlle                               d tumor protein TCTP (histamine-releasing factor)                                                             SCOP domains
               CATH domains 3ebmC00 C:1-176 Metal Binding Protei                               n, Guanine Nucleotide Exchange Factor; Chain A                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee...eeeeehhh.eeeee....-------------------------------..hhhhhhhh.eee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhheeee..........eeeee......eeeeee...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------F------------------------------ SAPs(SNPs)
                PROSITE (1) TCTP_3  PDB: C:1-172 UniProt: 1-172                                                                                                                                         ---- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------TCTP_2  PDB: C:129-151 ------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebm C   1 MIIYRDLISHDVMFSDIYKIREIADGLCLEVEGKMV-------------------------------TGVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGLEMEKCLEHH 176
                                    10        20        30     |   -         -         -       |70        80        90       100       110       120       130       140       150       160       170      
                                                              36                              68

Chain D from PDB  Type:PROTEIN  Length:144
 aligned with TCTP_HUMAN | P13693 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:174
                                                                                                                                                                                                     172  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170 |  
           TCTP_HUMAN     1 MIIYRDLISHDEMFSDIYKIREIADGLCLEVEGKMVSRTEGNIDDSLIGGNASAEGPEGEGTESTVITGVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGLEMEKC--   -
               SCOP domains d3ebmd_ D: Translationally controlled                               tumor protein TCTP (histamine-releasing factor)                                                            SCOP domains
               CATH domains 3ebmD00 D:1-174 Metal Binding Protein                              , Guanine Nucleotide Exchange Factor; Chain A                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....eeee...eeeee....eeeee..ee.------------------------------.eehhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhheeee..........eeeee......eeeeee...eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------F---------------------------- SAPs(SNPs)
                PROSITE (1) TCTP_3  PDB: D:1-172 UniProt: 1-172                                                                                                                                         -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------TCTP_2  PDB: D:129-151 ----------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ebm D   1 MIIYRDLISHDVMFSDIYKIREIADGLCLEVEGKMVS------------------------------TGVDIVMNHHLQETSFTKEAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGENMNPDGMVALLDYREDGVTPYMIFFKDGLEMEKCLE 174
                                    10        20        30      |  -         -         -       |70        80        90       100       110       120       130       140       150       160       170    
                                                               37                             68

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 Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Mss4-like (27)

Superfamily: Mss4-like (17)

Family: Translationally controlled tumor protein TCTP (histamine-releasing factor) (7)

Protein domain: Translationally controlled tumor protein TCTP (histamine-releasing factor) (5)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d3ebma_	A:
1b	d3ebmb_	B:
1c	d3ebmc_	C:
1d	d3ebmd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Complex (381)

Topology: Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A (12)

Homologous Superfamily: Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A (9)

Man (Homo sapiens) (1)

1a	3ebmD00	D:1-174
1b	3ebmC00	C:1-176
1c	3ebmA00	A:1-176
1d	3ebmB00	B:1-177

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TCTP_HUMAN | P13693)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	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:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006874	cellular calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
	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:1902230	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage.
	GO:0042981	regulation of apoptotic process	Any process that modulates the occurrence or rate of cell death by apoptotic process.
	GO:0009615	response to virus	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 stimulus from a virus.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005771	multivesicular body	A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
	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:0045298	tubulin complex	A heterodimer of tubulins alpha and beta that constitutes the protomer for microtubule assembly.

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	TCTP_HUMAN \| P13693	:	1yz1 2hr9 4z9v

1yz1	THE STRUCTURE OF WILD TYPE PROTEIN

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (1, 1)

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