2CA6 - JenaLib

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Title :   MIRAS STRUCTURE DETERMINATION FROM HEMIHEDRALLY TWINNED CRYSTALS

Authors :   R. C. Hillig, L. Renault

Date :   17 Dec 05 (Deposition) - 11 Jan 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

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

Reference :   R. C. Hillig, L. Renault
Detecting And Overcoming Hemihedral Twinning During The Mir Structure Determination Of Rna1P.
Acta Crystallogr. , Sect. D V. 62 750 2006
PubMed-ID: 16790931 | Reference-DOI: 10.1107/S0907444906016222
(for further references see the PDB file header)

Molecule 1 - RAN GTPASE-ACTIVATING PROTEIN 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector	:	PET3D
	Organism Common	:	FISSION YEAST
	Organism Scientific	:	SCHIZOSACCHAROMYCES POMBE
	Organism Taxid	:	4896
	Other Details	:	C-TERMINI OF BOTH COPIES OF RNA1P (RESIDUES 345-386) ARE DISORDERED AND WERE OMITTED FROM THE MODEL
	Synonym	:	RNA1P, PROTEIN RNA1

		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, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:162 , LYS B:219 , HOH B:2120	BINDING SITE FOR RESIDUE SO4 B1345
2	AC2	SOFTWARE	ARG B:162 , HOH B:2062 , HOH B:2121 , HOH B:2122	BINDING SITE FOR RESIDUE SO4 B1346
3	AC3	SOFTWARE	ARG B:50 , ARG B:84 , LEU B:85 , HOH B:2017 , HOH B:2124	BINDING SITE FOR RESIDUE SO4 B1347
4	AC4	SOFTWARE	LYS A:35 , TYR B:128 , LYS B:193 , HOH B:2125	BINDING SITE FOR RESIDUE SO4 B1348

(no "SS Bond" information available for 2CA6)

(no "Cis Peptide Bond" information available for 2CA6)

(no "SAP(SNP)/Variant" information available for 2CA6)

(no "PROSITE Motif" information available for 2CA6)

(no "Exon" information available for 2CA6)

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:344
 aligned with RNA1_SCHPO | P41391 from UniProtKB/Swiss-Prot  Length:386

    Alignment length: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    
           RNA1_SCHPO     2 SRFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDMEE 345
               SCOP domains d2ca6a_ A: Rna1p (RanGAP1), N-terminal domain                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2ca6A00 A:2-345 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......ee....hhhhhh.hhhhhhh....eee....eehhhhhhhhhhh........eee........hhhhhhhhhhhhhhhhh......eee.........hhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhh.......eee......hhhhhhhhhhhhhhhh....eee.........hhhhhhhhhhhhhhh..ee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ca6 A   2 ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDMEE 345
                                    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:344
 aligned with RNA1_SCHPO | P41391 from UniProtKB/Swiss-Prot  Length:386

    Alignment length: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    
           RNA1_SCHPO     2 SRFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDMEE 345
               SCOP domains d2ca6b_ B: Rna1p (RanGAP1), N-terminal domain                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2ca6B00 B:2-345 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee......ee......................eee....eehhhhhhhhhhhhhhh....eee........hhhhhhhhhhhhhhhhh......eee......hhhhhhhhhhhhh......eee.....hhhhhhhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhh....eee......hhhhhhhhhhhhh........eee......hhhhhhhhhhhhhhhh....eee..........hhhhhhhhhhhhhh..ee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ca6 B   2 ARFSIEGKSLKLDAITTEDEKSVFAVLLEDDSVKEIVLSGNTIGTEAARWLSENIASKKDLEIAEFSDIFTGRVKDEIPEALRLLLQALLKCPKLHTVRLSDNAFGPTAQEPLIDFLSKHTPLEHLYLHNNGLGPQAGAKIARALQELAVNKKAKNAPPLRSIICGRNRLENGSMKEWAKTFQSHRLLHTVKMVQNGIRPEGIEHLLLEGLAYCQELKVLDLQDNTFTHLGSSALAIALKSWPNLRELGLNDCLLSARGAAAVVDAFSKLENIGLQTLRLQYNEIELDAVRTLKTVIDEKMPDLLFLELNGNRFSEEDDVVDEIREVFSTRGRGELDELDDMEE 345
                                    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 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	2ca6A00	A:2-345
1b	2ca6B00	B:2-345

(no "Pfam Domain" information available for 2CA6)

Asymmetric 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.

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

1k5d	CRYSTAL STRUCTURE OF RAN-GPPNHP-RANBP1- RANGAP COMPLEX
1k5g	CRYSTAL STRUCTURE OF RAN-GDP-ALFX-RANBP1- RANGAP COMPLEX
1yrg	THE CRYSTAL STRUCTURE OF RNA1P: A NEW FOLD FOR A GTPASE-ACTIVATING PROTEIN

Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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