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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN SMG7
 
Authors :  N. Fukuhara, J. Ebert, L. Unterholzner, D. Lindner, E. Izaurralde, E. Conti
Date :  17 Dec 04  (Deposition) - 15 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Helical Repeat, Tetratricopetide Repeat (Tpr), 14-3-3, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Fukuhara, J. Ebert, L. Unterholzner, D. Lindner, E. Izaurralde, E. Conti
Smg7 Is A 14-3-3-Like Adaptor In The Nonsense-Mediated Mrna Decay Pathway.
Mol. Cell V. 17 537 2005
PubMed-ID: 15721257  |  Reference-DOI: 10.1016/J.MOLCEL.2005.01.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SMG-7 TRANSCRIPT VARIANT 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PPROEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN (1-497)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:66 , ARG A:163 , TYR A:164BINDING SITE FOR RESIDUE SO4 A 498
2AC2SOFTWARELYS B:66 , ARG B:163 , TYR B:164 , HOH B:669BINDING SITE FOR RESIDUE SO4 B 498
3AC3SOFTWARESER B:184 , GLY B:423 , ARG B:428 , HOH B:581BINDING SITE FOR RESIDUE SO4 B 499

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YA0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YA0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YA0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YA0)

(-) Exons   (14, 28)

Asymmetric Unit (14, 28)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1eENST000003476151eENSE00002181443chr1:183441637-183441784148SMG7_HUMAN1-10102A:1-10
B:1-10		10
10
1.6aENST000003476156aENSE00001675624chr1:183481972-18348200332SMG7_HUMAN10-21122A:10-21
B:10-21		12
12
1.7bENST000003476157bENSE00002159151chr1:183485009-183485126118SMG7_HUMAN21-60402A:21-60
B:21-60		40
40
1.8bENST000003476158bENSE00001067886chr1:183486823-183486955133SMG7_HUMAN60-104452A:60-104
B:60-104		45
45
1.10cENST0000034761510cENSE00001067882chr1:183495731-183495902172SMG7_HUMAN105-162582A:105-162 (gaps)
B:105-162 (gaps)		58
58
1.12ENST0000034761512ENSE00002188851chr1:183497091-18349716272SMG7_HUMAN162-186252A:162-186
B:162-186		25
25
1.13bENST0000034761513bENSE00001607532chr1:183498027-183498177151SMG7_HUMAN186-236512A:186-236
B:186-236		51
51
1.14bENST0000034761514bENSE00001598042chr1:183498533-183498668136SMG7_HUMAN236-281462A:236-281
B:236-281		46
46
1.15ENST0000034761515ENSE00001743469chr1:183502299-183502461163SMG7_HUMAN282-336552A:282-336
B:282-336		55
55
1.16ENST0000034761516ENSE00001723317chr1:183502811-183502967157SMG7_HUMAN336-388532A:336-388 (gaps)
B:336-388 (gaps)		53
53
1.17ENST0000034761517ENSE00001766732chr1:183506280-18350635071SMG7_HUMAN388-412252A:388-412 (gaps)
B:388-412		25
25
1.18ENST0000034761518ENSE00001664594chr1:183507515-18350757561SMG7_HUMAN412-432212A:412-432
B:412-432		21
21
1.19ENST0000034761519ENSE00001627281chr1:183510119-183510238120SMG7_HUMAN432-472412A:432-472 (gaps)
B:432-472 (gaps)		41
41
1.20bENST0000034761520bENSE00001264233chr1:183511211-183511637427SMG7_HUMAN472-6141432A:472-497
B:472-497		26
26
1.21ENST0000034761521ENSE00001744227chr1:183513488-183513632145SMG7_HUMAN615-663490--
1.22ENST0000034761522ENSE00001696991chr1:183514065-183514447383SMG7_HUMAN663-7901280--
1.23cENST0000034761523cENSE00001067890chr1:183515101-183515472372SMG7_HUMAN791-9141240--
1.25bENST0000034761525bENSE00000774233chr1:183518343-18351842381SMG7_HUMAN915-941270--
1.26aENST0000034761526aENSE00000774234chr1:183518899-183519058160SMG7_HUMAN942-995540--
1.27aENST0000034761527aENSE00000774235chr1:183519886-183520056171SMG7_HUMAN995-1052580--
1.28ENST0000034761528ENSE00000774236chr1:183520180-183520325146SMG7_HUMAN1052-1100490--
1.29bENST0000034761529bENSE00001822143chr1:183520953-1835233212369SMG7_HUMAN1101-1137370--

(-) Sequences/Alignments

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:458
 aligned with SMG7_HUMAN | Q92540 from UniProtKB/Swiss-Prot  Length:1137

    Alignment length:497
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       
           SMG7_HUMAN     1 MSLQSAQYLRQAEVLKADMTDSKLGPAEVWTSRQALQDLYQKMLVTDLEYALDKKVEQDLWNHAFKNQITTLQGQAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALESRDEVKTKWGVSDFIKAFIKFHGHVYLSKSLEKLSPLREKLEEQFKRLLFQKAFNSQQLVHVTVINLFQLHHLRDFSNETEQHTYSQDEQLCWTQLLALFMSFLGILCKCPLQNESQEESYNAYPLPAVKVSMDWLRLRPRVFQEAVVDERQYIWPWLISLLNSFHPHEEDLSSISATPLPEEFELQGFLALRPSFRNLDFSKGHQGITGDKEGQQRRIRQQRLISIGKWIADNQPRLIQCENEVGKLLFITEIPELILEDP 497
               SCOP domains d1ya0a1 A:1-497 SMG-7                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.-------------------------------.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.-.........hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh......-......hhhhhhh..hhhhhhhhh........------.hhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1e ----------Exon 1.7b  PDB: A:21-60 UniProt: 21-60  --------------------------------------------Exon 1.10c  PDB: A:105-162 (gaps) UniProt: 105-162        -----------------------Exon 1.13b  PDB: A:186-236 UniProt: 186-236        ---------------------------------------------Exon 1.15  PDB: A:282-336 UniProt: 282-336             ---------------------------------------------------Exon 1.17                -------------------Exon 1.19  PDB: A:432-472 (gaps)         ------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.6a   --------------------------------------Exon 1.8b  PDB: A:60-104 UniProt: 60-104     ---------------------------------------------------------Exon 1.12  PDB: A:162-186-------------------------------------------------Exon 1.14b  PDB: A:236-281 UniProt: 236-281   ------------------------------------------------------Exon 1.16  PDB: A:336-388 (gaps) UniProt: 336-388    -----------------------Exon 1.18            ---------------------------------------Exon 1.20b  PDB: A:472-497 Transcript 1 (2)
                 1ya0 A   1 MSLQSAQYLRQAEVLKADMTDSKLGPAEVWTSRQALQDLYQKMLVTDLEYALDKKVEQDLWNHAFKNQITTLQGQAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCT-------------------------------QSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALESRDEVKTKWGVSDFIKAFIKFHGHVYLSKSLEKLSPLREKLEEQFKELLFQKAFNSQQLVHVTVINLFQLHHLRDFSNETEQHTYSQDEQLCWTQLLALFMSFLGILCKCPLQN-SQEESYNAYPLPAVKVSMDWLRLRPRVFQEAVVDERQYIWPWLISLLNSFHPHEEDL-SISATPLPEEFELQGFLALRPSFRNLDFSKGH------KEGQQRRIRQQRLISIGKWIADNQPRLIQCENEVGKLLFITEIPELILEDP 497
                                    10        20        30        40        50        60        70        80        90       100       110|        -         -         -  |    150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340        |-|      360       370       380       390       400      |410       420       430       440      |450       460       470       480       490       
                                                                                                                                        111                             143                                                                                                                                                                                                           349 |                                                     407 |                            440    447                                                  
                                                                                                                                                                                                                                                                                                                                                                                        351                                                       409                                                                                        


Chain B from PDB  Type:PROTEIN  Length:464
 aligned with SMG7_HUMAN | Q92540 from UniProtKB/Swiss-Prot  Length:1137

    Alignment length:497
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       
           SMG7_HUMAN     1 MSLQSAQYLRQAEVLKADMTDSKLGPAEVWTSRQALQDLYQKMLVTDLEYALDKKVEQDLWNHAFKNQITTLQGQAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVDLPCRVKSSQLGIISNKQTHTSAIVKPQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALESRDEVKTKWGVSDFIKAFIKFHGHVYLSKSLEKLSPLREKLEEQFKRLLFQKAFNSQQLVHVTVINLFQLHHLRDFSNETEQHTYSQDEQLCWTQLLALFMSFLGILCKCPLQNESQEESYNAYPLPAVKVSMDWLRLRPRVFQEAVVDERQYIWPWLISLLNSFHPHEEDLSSISATPLPEEFELQGFLALRPSFRNLDFSKGHQGITGDKEGQQRRIRQQRLISIGKWIADNQPRLIQCENEVGKLLFITEIPELILEDP 497
               SCOP domains d1ya0b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------                      -----------------------------EST1_DNA_bind-1ya0B01 B:171-431                                                                                                                                                                                                                                      -------        --------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------                      -----------------------------EST1_DNA_bind-1ya0B02 B:171-431                                                                                                                                                                                                                                      -------        --------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------EST1-1ya0B03 B:52-172                                                                                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   --------------------------------------------------------------------------------------        --------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------EST1-1ya0B04 B:52-172                                                                                                    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   --------------------------------------------------------------------------------------        --------------------------------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......----------------------...hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.---.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhh......hhhhhh...hhhhhhhhh......--------....hhhhhhhhhhhhhhhhhhhh....eeee....eeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1e ----------Exon 1.7b  PDB: B:21-60 UniProt: 21-60  --------------------------------------------Exon 1.10c  PDB: B:105-162 (gaps) UniProt: 105-162        -----------------------Exon 1.13b  PDB: B:186-236 UniProt: 186-236        ---------------------------------------------Exon 1.15  PDB: B:282-336 UniProt: 282-336             ---------------------------------------------------Exon 1.17  PDB: B:388-412-------------------Exon 1.19  PDB: B:432-472 (gaps)         ------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.6a   --------------------------------------Exon 1.8b  PDB: B:60-104 UniProt: 60-104     ---------------------------------------------------------Exon 1.12  PDB: B:162-186-------------------------------------------------Exon 1.14b  PDB: B:236-281 UniProt: 236-281   ------------------------------------------------------Exon 1.16  PDB: B:336-388 (gaps) UniProt: 336-388    -----------------------Exon 1.18            ---------------------------------------Exon 1.20b  PDB: B:472-497 Transcript 1 (2)
                 1ya0 B   1 MSLQSAQYLRQAEVLKADMTDSKLGPAEVWTSRQALQDLYQKMLVTDLEYALDKKVEQDLWNHAFKNQITTLQGQAKNRANPNRSEVQANLSLFLEAASGFYTQLLQELCTVFNVDLPC----------------------PQSSSCSYICQHCLVHLGDIARYRNQTSQAESYYRHAAQLVPSNGQPYNQLAILASSKGDHLTTIFYYCRSIAVKFPFPAASTNLQKALSKALESRDEVKTKWGVSDFIKAFIKFHGHVYLSKSLEKLSPLREKLEEQFKELLFQKAFNSQQLVHVTVINLFQLHHLRDFSNETEQHTYSQDEQLCWTQLLALFMSFLGILCKCPLQN---EESYNAYPLPAVKVSMDWLRLRPRVFQEAVVDERQYIWPWLISLLNSFHPHEEDLSSISATPLPEEFELQGFLALRPSFRNLDFSK--------KEGQQRRIRQQRLISIGKWIADNQPRLIQCENEVGKLLFITEIPELILEDP 497
                                    10        20        30        40        50        60        70        80        90       100       110        |-         -         - |     150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340        |-  |    360       370       380       390       400       410       420       430       | -      |450       460       470       480       490       
                                                                                                                                                119                    142                                                                                                                                                                                                            349 353                                                                                  438      447
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YA0)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: TPR (230)
(-)
Clan: no clan defined [family: EST1] (1)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SMG7_HUMAN | Q92540)
molecular function
    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.
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.
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:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    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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