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Title :   STRUCTURE OF PIN DOMAIN OF HUMAN SMG5.

Authors :   F. Glavan, I. Behm-Ansmant, E. Izaurralde, E. Conti

Date :   02 Aug 06 (Deposition) - 14 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Rna Degradation, Decay, Nmd, Est1A, P Bodies, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Glavan, I. Behm-Ansmant, E. Izaurralde, E. Conti
Structures Of The Pin Domains Of Smg6 And Smg5 Reveal A Nuclease Within The Mrna Surveillance Complex.
Embo J. V. 25 5117 2006
PubMed-ID: 17053788 | Reference-DOI: 10.1038/SJ.EMBOJ.7601377
(for further references see the PDB file header)

Molecule 1 - PROTEIN SMG5
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGEXCS
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	PINC DOMAIN
	Gene	:	SMG5
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SMG-5 HOMOLOG, EST1-LIKE PROTEIN B, LPTS- INTERACTING PROTEIN, LPTS-RP1

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2HWY)

(no "Site" information available for 2HWY)

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

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

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_030828	N	1004	D	SMG5_HUMAN	Polymorphism	17853821	A/B	N	1004	D

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_030828	N	1004	D	SMG5_HUMAN	Polymorphism	17853821	A	N	1004	D

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_030828	N	1004	D	SMG5_HUMAN	Polymorphism	17853821	B	N	1004	D

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

(no "PROSITE Motif" information available for 2HWY)

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000361813	1a	ENSE00001446734	chr1:156252616-156252398	219	SMG5_HUMAN	1-25	25	0	-	-
1.2	ENST00000361813	2	ENSE00001196892	chr1:156248825-156248727	99	SMG5_HUMAN	25-58	34	0	-	-
1.3	ENST00000361813	3	ENSE00001075011	chr1:156247839-156247716	124	SMG5_HUMAN	58-99	42	0	-	-
1.4	ENST00000361813	4	ENSE00001075015	chr1:156247032-156246876	157	SMG5_HUMAN	100-152	53	0	-	-
1.5	ENST00000361813	5	ENSE00001075017	chr1:156244477-156244388	90	SMG5_HUMAN	152-182	31	0	-	-
1.6	ENST00000361813	6	ENSE00001054407	chr1:156243241-156243152	90	SMG5_HUMAN	182-212	31	0	-	-
1.7	ENST00000361813	7	ENSE00001054410	chr1:156242189-156242111	79	SMG5_HUMAN	212-238	27	0	-	-
1.8	ENST00000361813	8	ENSE00001054405	chr1:156238206-156238081	126	SMG5_HUMAN	238-280	43	0	-	-
1.9	ENST00000361813	9	ENSE00001054409	chr1:156237974-156237906	69	SMG5_HUMAN	280-303	24	0	-	-
1.10a	ENST00000361813	10a	ENSE00001054402	chr1:156237469-156237261	209	SMG5_HUMAN	303-373	71	0	-	-
1.11a	ENST00000361813	11a	ENSE00001054413	chr1:156236469-156236332	138	SMG5_HUMAN	373-419	47	0	-	-
1.12b	ENST00000361813	12b	ENSE00001054417	chr1:156236171-156235572	600	SMG5_HUMAN	419-619	201	0	-	-
1.13	ENST00000361813	13	ENSE00001054406	chr1:156233361-156233186	176	SMG5_HUMAN	619-677	59	0	-	-
1.14	ENST00000361813	14	ENSE00001054400	chr1:156231199-156231124	76	SMG5_HUMAN	678-703	26	0	-	-
1.15	ENST00000361813	15	ENSE00001054416	chr1:156230417-156230242	176	SMG5_HUMAN	703-761	59	0	-	-
1.16	ENST00000361813	16	ENSE00001054412	chr1:156228954-156228796	159	SMG5_HUMAN	762-814	53	0	-	-
1.17b	ENST00000361813	17b	ENSE00001054408	chr1:156223299-156223240	60	SMG5_HUMAN	815-834	20	0	-	-
1.18c	ENST00000361813	18c	ENSE00001054415	chr1:156222869-156222710	160	SMG5_HUMAN	835-888	54	2	A:855-888 B:855-888	34 34
1.19b	ENST00000361813	19b	ENSE00001054404	chr1:156222295-156222205	91	SMG5_HUMAN	888-918	31	2	A:888-918 (gaps) B:888-918 (gaps)	31 31
1.20a	ENST00000361813	20a	ENSE00001054403	chr1:156221268-156221194	75	SMG5_HUMAN	918-943	26	2	A:918-923 B:918-925	6 8
1.20d	ENST00000361813	20d	ENSE00001054418	chr1:156220787-156220649	139	SMG5_HUMAN	943-989	47	2	A:945-986 (gaps) B:944-983 (gaps)	42 40
1.21c	ENST00000361813	21c	ENSE00001446733	chr1:156220461-156219015	1447	SMG5_HUMAN	990-1016	27	2	A:991-1012 B:993-1013 (gaps)	22 21

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
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Chain A from PDB  Type:PROTEIN  Length:116
 aligned with SMG5_HUMAN | Q9UPR3 from UniProtKB/Swiss-Prot  Length:1016

    Alignment length:158
                                   864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004        
          SMG5_HUMAN    855 PYLVPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLKKEHPGARDGIRYLEAEFKKGNRYIRCQKEVGKSFERHKLKRQDADAWTLYKILDSCKQLTLAQGAGEEDPSGMVTIITGLPLDNPSVLSGPMQAALQAAAHASVDIKNVLDFYKQW 1012
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh-.hhhhhhhhhhhhhhhhhh...eee.---------------------hhhhhhhhhhhh...----------------.eeee......----hhhhhhh...ee.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------D-------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18c  PDB: A:855-888        -----------------------------Exon 1.20a  PDB: A:918-923----------------------------------------------Exon 1.21c [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.19b UniProt: 888-918    ------------------------Exon 1.20d  PDB: A:945-986 (gaps) [INCOMPLETE] ----------------------- Transcript 1 (2)
                2hwy A  855 PYLVPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLK-EHPGARDGIRYLEAEFKKGNRYIRCQ---------------------LYKILDSCKQLTLAQ----------------LPLDNPSVLSG----ALQAAAHASVDIKNVLDFYKQW 1012
                                   864       874       884       894 | |   904       914        |-         -         -|      954    |    -         - |     984 |    |994      1004        
                                                                   896 |                      923                   945           959              976       986  991                     
                                                                     898

Chain B from PDB  Type:PROTEIN  Length:111
 aligned with SMG5_HUMAN | Q9UPR3 from UniProtKB/Swiss-Prot  Length:1016

    Alignment length:159
                                   864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004         
          SMG5_HUMAN    855 PYLVPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLKKEHPGARDGIRYLEAEFKKGNRYIRCQKEVGKSFERHKLKRQDADAWTLYKILDSCKQLTLAQGAGEEDPSGMVTIITGLPLDNPSVLSGPMQAALQAAAHASVDIKNVLDFYKQWK 1013
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhh-.hhhhhhhhhhhhhhhhh....eee...------------------..hhhhhhhhhhhhhh------------------.ee...----------....-.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------D--------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.18c  PDB: B:855-888        -----------------------------Exon 1.20a  PDB: B:918-925----------------------------------------------Exon 1.21c [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------Exon 1.19b UniProt: 888-918    ------------------------Exon 1.20d  PDB: B:944-983 (gaps) [INCOMPLETE] ------------------------ Transcript 1 (2)
                2hwy B  855 PYLVPDTQALCHHLPVIRQLATSGRFIVIIPRTVIDGLDLLK-EHPGARDGIRYLEAEFKKGNRYIRCQKE------------------TLYKILDSCKQLTLAQ------------------LDNPSV----------AAAH-SVDIKNVLDFYKQWK 1013
                                   864       874       884       894 | |   904       914       924|        -       944       954    |    -         -   |    |-       993  | | 1004         
                                                                   896 |                        925                944            959                978  983        993  | |              
                                                                     898                                                                                                996 |              
                                                                                                                                                                          999

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

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

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (SMG5_HUMAN | Q9UPR3)

molecular function
	GO:0070182	DNA polymerase binding	Interacting selectively and non-covalently with a DNA polymerase.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	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:0051721	protein phosphatase 2A binding	Interacting selectively and non-covalently with the enzyme protein phosphatase 2A.
	GO:0042162	telomeric DNA binding	Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0006406	mRNA export from nucleus	The directed movement of mRNA from the nucleus to the cytoplasm.
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0035303	regulation of dephosphorylation	Any process that modulates the frequency, rate or extent of removal of phosphate groups from a molecule.
	GO:0032204	regulation of telomere maintenance	Any process that modulates the frequency, rate or extent of a process that affects and monitors the activity of telomeric proteins and the length of telomeric DNA.
	GO:0032210	regulation of telomere maintenance via telomerase	Any process that modulates the frequency, rate or extent of the addition of telomeric repeats by telomerase.
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: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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