2RG8 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PROGRAMMED FOR CELL DEATH 4 MIDDLE MA3 DOMAIN

Authors :   R. Garces, C. Suzuki, G. Wagner

Date :   03 Oct 07 (Deposition) - 04 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Ma3 Domain, Heat Repeats, Anti-Oncogene, Apoptosis, Cell Cycle, Cytoplasm, Nucleus, Phosphorylation, Polymorphism, Rna-Binding, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Suzuki, R. G. Garces, K. A. Edmonds, S. Hiller, S. G. Hyberts, A. Marintchev, G. Wagner
Pdcd4 Inhibits Translation Initiation By Binding To Eif4A Using Both Its Ma3 Domains.
Proc. Natl. Acad. Sci. Usa V. 105 3274 2008
PubMed-ID: 18296639 | Reference-DOI: 10.1073/PNAS.0712235105
(for further references see the PDB file header)

Molecule 1 - PROGRAMMED CELL DEATH PROTEIN 4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	MA3 DOMAIN
	Gene	:	PDCD4, H731
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUCLEAR ANTIGEN H731-LIKE, NEOPLASTIC TRANSFORMATION INHIBITOR PROTEIN, PROTEIN 197/15A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
3	NA	3	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 5)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:160 , ARG A:162 , ALA A:163 , LYS A:297 , ASN B:192	BINDING SITE FOR RESIDUE CL A 1
2	AC2	SOFTWARE	GLY B:284 , THR B:285 , ARG B:292	BINDING SITE FOR RESIDUE CL B 2
3	AC3	SOFTWARE	SER B:220 , ASP B:271 , HOH B:307	BINDING SITE FOR RESIDUE NA B 3
4	AC4	SOFTWARE	SER A:220 , ARG A:267 , ASP A:271 , HOH A:308	BINDING SITE FOR RESIDUE NA A 4
5	AC5	SOFTWARE	HOH A:310 , ARG B:216 , LEU B:260 , GLN B:263 , PHE B:264 , HOH B:312	BINDING SITE FOR RESIDUE NA B 5

(no "SS Bond" information available for 2RG8)

Asymmetric Unit

No.	Residues
1	Leu B:157	-	Pro B:158

(no "SAP(SNP)/Variant" information available for 2RG8)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MI	PS51366	MI domain profile.	PDCD4_HUMAN	163-284 326-449	2	A:163-284 B:163-284 -

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MI	PS51366	MI domain profile.	PDCD4_HUMAN	163-284 326-449	1	A:163-284 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MI	PS51366	MI domain profile.	PDCD4_HUMAN	163-284 326-449	1	- B:163-284 -

Asymmetric Unit (4, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000280154	1a	ENSE00001922986	chr10:112631565-112631776	212	PDCD4_HUMAN	-	0	0	-	-
1.2	ENST00000280154	2	ENSE00002190882	chr10:112635724-112635828	105	PDCD4_HUMAN	1-15	15	0	-	-
1.6a	ENST00000280154	6a	ENSE00001380538	chr10:112640991-112641293	303	PDCD4_HUMAN	15-116	102	0	-	-
1.7	ENST00000280154	7	ENSE00000995567	chr10:112642761-112642855	95	PDCD4_HUMAN	116-147	32	0	-	-
1.8c	ENST00000280154	8c	ENSE00001094657	chr10:112645011-112645124	114	PDCD4_HUMAN	148-185	38	2	A:156-185 B:157-185	30 29
1.9e	ENST00000280154	9e	ENSE00002200197	chr10:112647423-112647644	222	PDCD4_HUMAN	186-259	74	2	A:186-259 B:186-259	74 74
1.10	ENST00000280154	10	ENSE00001788034	chr10:112649291-112649388	98	PDCD4_HUMAN	260-292	33	2	A:260-292 B:260-292	33 33
1.11a	ENST00000280154	11a	ENSE00001772839	chr10:112650314-112650428	115	PDCD4_HUMAN	292-330	39	2	A:292-305 B:292-305	14 14
1.12b	ENST00000280154	12b	ENSE00001599108	chr10:112653849-112653956	108	PDCD4_HUMAN	331-366	36	0	-	-
1.13	ENST00000280154	13	ENSE00001674744	chr10:112654170-112654280	111	PDCD4_HUMAN	367-403	37	0	-	-
1.14b	ENST00000280154	14b	ENSE00001636249	chr10:112655706-112655845	140	PDCD4_HUMAN	404-450	47	0	-	-
1.15e	ENST00000280154	15e	ENSE00001840051	chr10:112657786-112659764	1979	PDCD4_HUMAN	450-469	20	0	-	-

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:150
 aligned with PDCD4_HUMAN | Q53EL6 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:150
                                   165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
          PDCD4_HUMAN   156 VLPLDERAFEKTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVMSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSYKGTVDCVQARAALDKATVLLSMS 305
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------MI  PDB: A:163-284 UniProt: 163-284                                                                                       --------------------- PROSITE
           Transcript 1 (1) Exon 1.8c  PDB: A:156-185     Exon 1.9e  PDB: A:186-259 UniProt: 186-259                                Exon 1.10  PDB: A:260-292        ------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------Exon 1.11a     Transcript 1 (2)
                 2rg8 A 156 GLPLDERAFEKTLTPIIQEYFEHGDTNEVAEmLRDLNLGEmKSGVPVLAVSLALEGKASHREmTSKLLSDLCGTVmSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSYKGTVDCVQARAALDKATVLLSmS 305
                                   165       175       185 |     195|      205       215  |    225     | 235       245       255       265       275       285       295       305
                                                         187-MSE  196-MSE               218-MSE      231-MSE                                                                  304-MSE

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with PDCD4_HUMAN | Q53EL6 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:149
                                   166       176       186       196       206       216       226       236       246       256       266       276       286       296         
          PDCD4_HUMAN   157 LPLDERAFEKTLTPIIQEYFEHGDTNEVAEMLRDLNLGEMKSGVPVLAVSLALEGKASHREMTSKLLSDLCGTVMSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSYKGTVDCVQARAALDKATVLLSMS 305
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------MA3-2rg8B01 B:164-275                                                                                           ------------------------------ Pfam domains (1)
           Pfam domains (2) -------MA3-2rg8B02 B:164-275                                                                                           ------------------------------ Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------MI  PDB: B:163-284 UniProt: 163-284                                                                                       --------------------- PROSITE
           Transcript 1 (1) Exon 1.8c  PDB: B:157-185    Exon 1.9e  PDB: B:186-259 UniProt: 186-259                                Exon 1.10  PDB: B:260-292        ------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------Exon 1.11a     Transcript 1 (2)
                 2rg8 B 157 LPLDERAFEKTLTPIIQEYFEHGDTNEVAEmLRDLNLGEmKSGVPVLAVSLALEGKASHREmTSKLLSDLCGTVmSTTDVEKSFDKLLKDLPELALDTPRAPQLVGQFIARAVGDGILCNTYIDSYKGTVDCVQARAALDKATVLLSmS 305
                                   166       176       186|      196       206       216 |     226    |  236       246       256       266       276       286       296       | 
                                                        187-MSE  196-MSE               218-MSE      231-MSE                                                                  304-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 '\|'

(no "SCOP Domain" information available for 2RG8)

(no "CATH Domain" information available for 2RG8)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TPR (230)

Family: MA3 (5)

Homo sapiens (Human) (5)

1a	MA3-2rg8B01	B:164-275
1b	MA3-2rg8B02	B:164-275

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDCD4_HUMAN | Q53EL6)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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: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:0007569	cell aging	An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
	GO:0043508	negative regulation of JUN kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of JUN kinase activity.
	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:0045786	negative regulation of cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
	GO:1904761	negative regulation of myofibroblast differentiation	Any process that stops, prevents or reduces the frequency, rate or extent of myofibroblast differentiation.
	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:0034393	positive regulation of smooth muscle cell apoptotic process	Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process.
	GO:0051246	regulation of protein metabolic process	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a 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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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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(no "Related Entries Specified in the PDB File" available for 2RG8)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (4, 8)

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