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Title :   CRYSTAL STRUCTURE OF THE C-TERMINAL MA3 DOMAIN OF PDCD4 (MOUSE); FORM 1

Authors :   A. Wlodawer, N. A. Laronde-Leblanc

Date :   10 Oct 06 (Deposition) - 14 Nov 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Alpha-Helical, Antitumor Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Laronde-Leblanc, A. N. Santhanam, A. R. Baker, A. Wlodawer, N. H. Colburn
Structural Basis For Inhibition Of Translation By The Tumor Suppressor Pdcd4.
Mol. Cell. Biol. V. 27 147 2007
PubMed-ID: 17060447 | Reference-DOI: 10.1128/MCB.00867-06

Molecule 1 - PROGRAMMED CELL DEATH 4, PDCD4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST14
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL MA3 DOMAIN, RESIDUES 323-448
	Gene	:	PDCD4, TIS
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		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 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2IOL)

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MI	PS51366	MI domain profile.	PDCD4_MOUSE	163-284 326-449	2	- A:326-448 B:326-448

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MI	PS51366	MI domain profile.	PDCD4_MOUSE	163-284 326-449	1	- A:326-448 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MI	PS51366	MI domain profile.	PDCD4_MOUSE	163-284 326-449	1	- - B:326-448

(no "Exon" information available for 2IOL)

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:127
 aligned with PDCD4_MOUSE | Q61823 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:127
                                   331       341       351       361       371       381       391       401       411       421       431       441       
          PDCD4_MOUSE   322 QPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCP 448
               SCOP domains d2iola1 A:322-448 Programmed cell death 4, PDCD4                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----MI  PDB: A:326-448 UniProt: 326-449                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iol A 322 QPVNHLVKEIDmLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVmVLESTGESAFKmILDLLKSLWKSSTITIDQmKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCP 448
                                   331 |     341       351       361       371       381|      391       401       411       421       431       441       
                                     333-MSE                              370-MSE     382-MSE            401-MSE

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with PDCD4_MOUSE | Q61823 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:127
                                   331       341       351       361       371       381       391       401       411       421       431       441       
          PDCD4_MOUSE   322 QPVNHLVKEIDMLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVMVLESTGESAFKMILDLLKSLWKSSTITIDQMKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCP 448
               SCOP domains d2iolb_ B: Programmed cell death 4, PDCD4                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----MI  PDB: B:326-448 UniProt: 326-449                                                                                         PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iol B 322 QPVNHLVKEIDmLLKEYLLSGDISEAEHCLKELEVPHFHHELVYEAIVmVLESTGESAFKmILDLLKSLWKSSTITIDQmKRGYERIYNEIPDINLDVPHSYSVLERFVEECFQAGIISKQLRDLCP 448
                                   331 |     341       351       361       371       381|      391       401       411       421       431       441       
                                     333-MSE                              370-MSE     382-MSE            401-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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: alpha-alpha superhelix (690)

Superfamily: ARM repeat (317)

Family: MIF4G domain-like (17)

Protein domain: Programmed cell death 4, PDCD4 (5)

Mouse (Mus musculus) [TaxId: 10090] (5)

1a	d2iola1	A:322-448
1b	d2iolb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PDCD4_MOUSE | Q61823)

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: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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	PDCD4_MOUSE \| Q61823	:	2hm8 2ion 2ios 2kzt 2nsz 3eiq

2ion	CRYSTAL STRUCTURE OF THE C-TERMINAL MA3 DOMAIN OF PDCD4 (MOUSE); FORM 2
2ios	CRYSTAL STRUCTURE OF THE C-TERMINAL MA3 DOMAIN OF PDCD4 (MOUSE); FORM 3

Description

Compounds

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Ligands, Modified Residues, Ions (1, 8)

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