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Title :   CRYSTAL STRUCTURE OF THE AUTOPROTEOLYTIC DOMAIN FROM THE NUCLEAR PORE COMPLEX COMPONENT NUP145 FROM SACCHAROMYCES CEREVISIAE IN THE HEXAGONAL, P61 SPACE GROUP

Authors :   P. Sampathkumar, S. A. Ozyurt, J. Do, K. Bain, M. Dickey, T. Gheyi, A. Sal S. J. Kim, J. Phillips, U. Pieper, J. Fernandez-Martinez, J. D. Franke S. Atwell, D. A. Thompson, J. S. Emtage, S. Wasserman, M. Rout, J. M. Sau S. K. Burley, New York Sgx Research Center For Structural Geno (Nysgxrc)

Date :   26 Oct 09 (Deposition) - 22 Dec 09 (Release) - 10 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Nuclear Pore Complex, Nup145, Nup145-N, Yeast, Autoproteolysis, Protein Maturation, Post-Translational Modification, Structural Genomics, Psi-2, Protein Structure Initiative, Nysgxrc, Rna-Binding, New York Sgx Research Center For Structural Genomics, Protein Transport, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Sampathkumar, S. A. Ozyurt, J. Do, K. T. Bain, M. Dickey, L. A. Rodgers, T. Gheyi, A. Sali, S. J. Kim, J. Phillips, U. Pieper, J. Fernandez-Martinez, J. D. Franke, A. Martel, H. Tsuruta, S. Atwell D. A. Thompson, J. S. Emtage, S. R. Wasserman, M. P. Rout, J. M. Sauder, S. K. Burley
Structures Of The Autoproteolytic Domain From The Saccharomyces Cerevisiae Nuclear Pore Complex Component, Nup145.
Proteins V. 78 1992 2010
PubMed-ID: 20310066 | Reference-DOI: 10.1002/PROT.22707

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 30)

Sites (22, 22)

Asymmetric Unit (22, 22)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:120 , TRP A:462 , CYS A:463 , SER A:466 , PRO A:467 , PHE B:570	BINDING SITE FOR RESIDUE EDO A 2
02	AC2	SOFTWARE	SER A:482 , ASN A:483 , GLN A:497 , HIS A:498 , ASP A:499 , ARG B:581	BINDING SITE FOR RESIDUE EDO A 3
03	AC3	SOFTWARE	ARG A:489 , GLY A:490 , GLU A:551 , HOH A:615 , PHE B:594	BINDING SITE FOR RESIDUE EDO A 4
04	AC4	SOFTWARE	HOH A:32 , HIS A:498 , ASP A:499	BINDING SITE FOR RESIDUE EDO A 5
05	AC5	SOFTWARE	ASP A:577 , TYR A:588 , TYR A:591 , VAL B:485 , HOH B:619	BINDING SITE FOR RESIDUE EDO A 7
06	AC6	SOFTWARE	HOH A:102 , PHE A:594 , GLY A:595 , ARG B:489	BINDING SITE FOR RESIDUE EDO A 16
07	AC7	SOFTWARE	VAL A:485 , ASP B:577 , TYR B:591	BINDING SITE FOR RESIDUE EDO B 1
08	AC8	SOFTWARE	PHE A:570 , TRP B:462 , CYS B:463 , SER B:466 , PRO B:467	BINDING SITE FOR RESIDUE EDO B 6
09	AC9	SOFTWARE	HOH B:128 , GLN B:497 , PRO B:545 , LYS B:601 , ASN B:603	BINDING SITE FOR RESIDUE EDO B 8
10	BC1	SOFTWARE	HOH B:56 , HOH B:158 , ALA B:480 , VAL B:481 , SER B:482 , ASP B:499	BINDING SITE FOR RESIDUE EDO B 9
11	BC2	SOFTWARE	PHE A:594 , HOH B:25 , ARG B:488 , ARG B:489 , GLY B:490 , GLU B:551	BINDING SITE FOR RESIDUE EDO B 10
12	BC3	SOFTWARE	EDO B:22 , HOH B:161 , ASP B:501 , LEU B:502 , THR B:503 , ALA B:504 , PHE B:505 , TYR B:529 , GLY B:541	BINDING SITE FOR RESIDUE EDO B 11
13	BC4	SOFTWARE	EDO B:13 , HOH B:100 , GLU B:471 , THR B:506 , SER B:508 , PHE B:509	BINDING SITE FOR RESIDUE EDO B 12
14	BC5	SOFTWARE	EDO B:12 , PRO B:467 , GLU B:471 , SER B:508 , PHE B:509 , ARG B:510	BINDING SITE FOR RESIDUE EDO B 13
15	BC6	SOFTWARE	SER A:482 , HOH B:136 , HIS B:540	BINDING SITE FOR RESIDUE EDO B 14
16	BC7	SOFTWARE	GLU B:572 , VAL B:575 , PHE B:576	BINDING SITE FOR RESIDUE EDO B 15
17	BC8	SOFTWARE	EDO B:18 , HOH B:153 , SER B:582	BINDING SITE FOR RESIDUE EDO B 17
18	BC9	SOFTWARE	EDO B:17 , EDO B:19 , HOH B:128 , HOH B:150 , HIS B:498 , VAL B:575 , ARG B:578 , LYS B:579	BINDING SITE FOR RESIDUE EDO B 18
19	CC1	SOFTWARE	EDO B:18 , EDO B:20 , HOH B:150 , HIS B:498 , ILE B:538 , GLY B:539 , VAL B:544 , PRO B:545 , ARG B:578 , HOH B:614	BINDING SITE FOR RESIDUE EDO B 19
20	CC2	SOFTWARE	EDO B:19 , EDO B:21 , HOH B:150 , HIS B:498 , ASP B:499 , GLY B:539 , ARG B:578	BINDING SITE FOR RESIDUE EDO B 20
21	CC3	SOFTWARE	EDO B:20 , HOH B:101 , HOH B:111 , ALA B:479 , ASP B:499 , VAL B:500 , ASP B:501 , GLY B:539 , GLY B:541	BINDING SITE FOR RESIDUE EDO B 21
22	CC4	SOFTWARE	EDO B:11 , HOH B:107 , ASP B:501 , THR B:503 , PRO B:536	BINDING SITE FOR RESIDUE EDO B 22

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (1, 2)

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:142
 aligned with NU145_YEAST | P49687 from UniProtKB/Swiss-Prot  Length:1317

    Alignment length:148
                                   468       478       488       498       508       518       528       538       548       558       568       578       588       598        
          NU145_YEAST   459 FGYWCSPSPEQLERLSLKQLAAVSNFVIGRRGYGCITFQHDVDLTAFTKSFREELFGKIVIFRSSKTVEVYPDEATKPMIGHGLNVPAIITLENVYPVDKKTKKPMKDTTKFAEFQVFDRKLRSMREMNYISYNPFGGTWTFKVNHFS 606
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhh..hhhhhh.....eeee...eeeee.....hhhhh.hhhhhhh...eeee...eeee..hhhhh..........eeeee......------......hhhhhhhhhhhhhhh...eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE NUP_C  PDB: - UniProt: 458-605                                                                                                                     - PROSITE
               Transcript 1 Exon 1.1  PDB: A:459-606 (gaps) UniProt: 1-1317 [INCOMPLETE]                                                                                         Transcript 1
                 3kes A 459 FGYWCSPSPEQLERLSLKQLAAVSNFVIGRRGYGCITFQHDVDLTAFTKSFREELFGKIVIFRSSKTVEVYPDEATKPmIGHGLNVPAIITLENVYPV------PmKDTTKFAEFQVFDRKLRSmREmNYISYNPFGGTWTFKVNHFE 606
                                   468       478       488       498       508       518       528       538       548       | -    || 568       578    |  588       598        
                                                                                                        537-MSE            556    563|                583-MSE                   
                                                                                                                                   564-MSE               586-MSE

Chain B from PDB  Type:PROTEIN  Length:153
 aligned with NU145_YEAST | P49687 from UniProtKB/Swiss-Prot  Length:1317

    Alignment length:177
                                   462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       
          NU145_YEAST   453 HEKSSSFGYWCSPSPEQLERLSLKQLAAVSNFVIGRRGYGCITFQHDVDLTAFTKSFREELFGKIVIFRSSKTVEVYPDEATKPMIGHGLNVPAIITLENVYPVDKKTKKPMKDTTKFAEFQVFDRKLRSMREMNYISYNPFGGTWTFKVNHFSIWGLVNEEDAEIDEDDLSKQEDG 629
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eeee.hhhhhhh.hhhhhh.....eeee...eeeee.....hhhhh.hhhhhhh...eeee...eeee..hhhhh..........eeeee.......--.........hhhhhhhhhhhhhhh...eeeeee....eeeeee...----------------------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----NUP_C  PDB: B:458-605 UniProt: 458-605                                                                                                              ------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: B:453-607 (gaps) UniProt: 1-1317 [INCOMPLETE]                                                                                                                      Transcript 1
                 3kes B 453 HEKSSSFGYWCSPSPEQLERLSLKQLAAVSNFVIGRRGYGCITFQHDVDLTAFTKSFREELFGKIVIFRSSKTVEVYPDEATKPmIGHGLNVPAIITLENVYPVD--TKKPmKDTTKFAEFQVFDRKLRSmREmNYISYNPFGGTWTFKVNHF----------------------EG 607
                                   462       472       482       492       502       512       522       532    |  542       552    |  562 |     572       582|  |   592       602  |      -         -     | 
                                                                                                              537-MSE             557  |   |                583-MSE               605                    606 
                                                                                                                                     560   |                   586-MSE                                       
                                                                                                                                         564-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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (29, 29)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NU145_YEAST | P49687)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008139	nuclear localization sequence binding	Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus.
	GO:0005487	nucleocytoplasmic transporter activity	Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
	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:0017056	structural constituent of nuclear pore	The action of a molecule that contributes to the structural integrity of the nuclear pore complex.
biological process
	GO:0006607	NLS-bearing protein import into nucleus	The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0006302	double-strand break repair	The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
	GO:0051028	mRNA transport	The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0035392	maintenance of chromatin silencing at telomere	The maintenance of chromatin in a transcriptionally silent state such as heterochromatin at the telomere.
	GO:0031081	nuclear pore distribution	Any process that establishes the spatial arrangement of nuclear pores within the nuclear envelope.
	GO:0016973	poly(A)+ mRNA export from nucleus	The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0000973	posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery	The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed.
	GO:0006606	protein import into nucleus	The directed movement of a protein from the cytoplasm to the nucleus.
	GO:0036228	protein localization to nuclear inner membrane	A process in which a protein is transported to, or maintained in, a location within the nuclear inner membrane.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0046822	regulation of nucleocytoplasmic transport	Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm.
	GO:0006409	tRNA export from nucleus	The directed movement of tRNA from the nucleus to the cytoplasm.
	GO:0034398	telomere tethering at nuclear periphery	The process in which a telomere is maintained in a specific location at the nuclear periphery.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0000781	chromosome, telomeric region	The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	GO:0005643	nuclear pore	Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
	GO:0044613	nuclear pore central transport channel	The central substructure of the nuclear pore complex (NPC), through which nucleocytoplasmic transport of RNAs, proteins and small molecules occurs. The central transport channel is filled with FG-nucleoporins, which form a selective barrier and provide a series of binding sites for transporter proteins. Characterized S. cerevisiae FG-nucleoporins include Nup159p, Nup145Np, Nup116p, Nup100p, Nsp1p, Nup57p, Nup49p, Nup42p, Nup53p, Nup59p/Asm4p, Nup60p and Nup1. Characterized vertebrate FG-nucleoporins include Nup214, Nup98, Nup62, Nup54, Nup58/45, NLP1, and Nup153.
	GO:0044614	nuclear pore cytoplasmic filaments	Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
	GO:0031080	nuclear pore outer ring	A subcomplex of the nuclear pore complex (NPC) that forms the outer rings of the core scaffold, a lattice-like structure that gives the NPC its shape and strength. In S. cerevisiae, the two outer rings each contain multiple copies of the following proteins: Nup133p, Nup120p, Nup145Cp, Nup85p, Nup84p, Seh1p, and Sec13p. In vertebrates, the two outer rings each contain multiple copies of the following proteins: Nup133, Nup160, Nup96, Nup75, Nup107, Seh1, Sec13, Nup43, Nup37, and ALADIN. Components are arranged in 8-fold symmetrical 'spokes' around the central transport channel. A single 'spoke', can be isolated and is sometimes referred to as the Nup84 complex (S. cerevisiae) or the Nup107-160 complex (vertebrates).
	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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Description