1YRG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN

Authors :   R. C. Hillig, L. Renault, I. R. Vetter, T. Drell, A. Wittinghofer, J. Becker

Date :   29 Mar 99 (Deposition) - 29 Mar 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.66

Chains :   Asym./Biol. Unit : A,B

Keywords :   Gtpase-Activating Protein, Gap, Rna1P, Rangap, Lrr, Leucine- Rich Repeat Protein, Twinning, Hemihedral Twinning, Merohedral Twinning, Merohedry, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. C. Hillig, L. Renault, I. R. Vetter, T. Drell 4Th. , A. Wittinghofer, J. Becker
The Crystal Structure Of Rna1P: A New Fold For A Gtpase-Activating Protein.
Mol. Cell V. 3 781 1999
PubMed-ID: 10394366 | Reference-DOI: 10.1016/S1097-2765(01)80010-1
(for further references see the PDB file header)

Molecule 1 - GTPASE-ACTIVATING PROTEIN RNA1_SCHPO
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET3D
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Other Details	:	SELENOMETHIONINE MUTANT EXPRESSED IN E.COLI B834
	Synonym	:	RNA1P

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1YRG)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	HG1	AUTHOR	CYS A:93	COMMON HG-SITE IN ETHYLMERCURY(II)-CHLORIDE AND MERCURY(II)ACETATE (FRACT. COORD. AS REFINED BY MLPHARE): -0.109 -0.369 0.000 -0.353 -0.355 -0.150
2	HG2	AUTHOR	ALA A:2	ADDITIONAL HG-SITE IN MERCURY(II)ACETATE (FRACT. COORD. AS REFINED BY MLPHARE): -0.179 -0.112 -0.019 - 0.310 -0.156 -0.130
3	HG3	AUTHOR	CYS B:93	NULL
4	HG4	AUTHOR	ALA B:2	NULL

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

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

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

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

(no "Exon" information available for 1YRG)

Asymmetric/Biological 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:343
 aligned with RNA1_SCHPO | P41391 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:343
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
           RNA1_SCHPO     2 SRFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDME 344
               SCOP domains d1yrga_ A: Rna1p (RanGAP1), N-terminal domain                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1yrgA00 A:2-344 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee............hhhhh...hhhhh.....eee.......hhhhhhhhhhh.......eee.........hhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhh......eee........hhhhhhhhhhhh.....eee.......hhhhhhhhhh.hhh.....eee......hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.......eee.......hhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yrg A   2 ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDME 344
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341

Chain B from PDB  Type:PROTEIN  Length:343
 aligned with RNA1_SCHPO | P41391 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:343
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341   
           RNA1_SCHPO     2 SRFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDME 344
               SCOP domains d1yrgb_ B: Rna1p (RanGAP1), N-terminal domain                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1yrgB00 B:2-344 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_6-1yrgB01 B:215-238 ---------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LRR_6-1yrgB02 B:215-238 ---------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eee..............hhh...hhhhh.....eee.......hhhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhhh......eee........hhhhhhhhhhhh.....eee.......hhhhhhhhhh.hhh.....eee......hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.......eee.......hhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yrg B   2 ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDME 344
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (112)

Superfamily: RNI-like (17)

Family: Rna1p (RanGAP1), N-terminal domain (4)

Protein domain: Rna1p (RanGAP1), N-terminal domain (4)

Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896] (4)

1a	d1yrga_	A:
1b	d1yrgb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Horseshoe (92)

Topology: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (73)

Homologous Superfamily: Ribonuclease Inhibitor (73)

Fission yeast (Schizosaccharomyces pombe) (2)

1a	1yrgA00	A:2-344
1b	1yrgB00	B:2-344

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: LRR (77)

Family: LRR_6 (24)

Schizosaccharomyces pombe (strain ATCC 38366 / 972) (Fission yeast) (3)

1a	LRR_6-1yrgB01	B:215-238
1b	LRR_6-1yrgB02	B:215-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RNA1_SCHPO | P41391)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
biological process
	GO:0030702	chromatin silencing at centromere	Repression of transcription of centromeric DNA by altering the structure of chromatin.
	GO:0051383	kinetochore organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the kinetochore, a multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
	GO:0000070	mitotic sister chromatid segregation	The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
	GO:0006913	nucleocytoplasmic transport	The directed movement of molecules between the nucleus and the cytoplasm.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0046827	positive regulation of protein export from nucleus	Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
	GO:0043087	regulation of GTPase activity	Any process that modulates the rate of GTP hydrolysis by a GTPase.
cellular component
	GO:0000775	chromosome, centromeric region	The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
	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:0031965	nuclear membrane	Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
	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.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1yrg)

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		HG2	[ RasMol ]	+environment [ RasMol ]
		HG3	[ RasMol ]	+environment [ RasMol ]
		HG4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yrg)

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	1yrg
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	RNA1_SCHPO \| P41391
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	RNA1_SCHPO \| P41391
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	RNA1_SCHPO \| P41391	:	1k5d 1k5g 2ca6

(no "Related Entries Specified in the PDB File" available for 1YRG)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

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