2XLJ - JenaLib

Title :   CRYSTAL STRUCTURE OF THE CSY4-CRRNA COMPLEX, HEXAGONAL FORM

Authors :   R. E. Haurwitz, M. Jinek, B. Wiedenheft, K. Zhou, J. A. Doudna

Date :   20 Jul 10 (Deposition) - 22 Sep 10 (Release) - 29 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Hydrolase-Rna Complex, Endoribonuclease, Crispr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. E. Haurwitz, M. Jinek, B. Wiedenheft, K. Zhou, J. A. Doudna
Sequence- And Structure-Specific Rna Processing By A Crispr Endonuclease.
Science V. 329 1355 2010
PubMed-ID: 20829488 | Reference-DOI: 10.1126/SCIENCE.1192272

Compounds

Molecule 1 - CSY4 ENDORIBONUCLEASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHMGWA
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	ROSETTA 2 (DE3)
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208963
	Strain	:	UCBPP-PA14

*Molecule 2 - 5'-R(CPUPGPCPCPGPUPAPUPAPGPGPCPADGC)-3'*
	Chains	:	B
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208963
	Other Details	:	2-DEOXY MODIFICATION AT G20
	Strain	:	UCBPP-PA14
	Synonym	:	PA14 CRRNA HAIRPIN
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:178
 aligned with CAS6_PSEAB | Q02MM2 from UniProtKB/Swiss-Prot  Length:187

    Alignment length:188
                             1                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179        
           CAS6_PSEAB     - -MDHYLDIRLRPDPEFPPAQLMSVLFGKLHQALVAQGGDRIGVSFPDLDESRSRLGERLRIHASADDLRALLARPWLEGLRDHLQFGEPAVVPHPTPYRQVSRVQAKSNPERLRRRLMRRHDLSEEEARKRIPDTVARALDLPFVTLRSQSTGQHFRLFIRHGPLQVTAEEGGFTCYGLSKGGFVPWF 187
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhhhhhhhh....eee.............eeeeeehhhhhhhhh...........eee...ee......ee.eeee....hhhhhhhhhhhh..--hhhhhhh--------....eeeee......eeeeeeee......................ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xlj A   0 TMDHYLDIRLRPDPEFPPAQLMCVLFGKLHQALVAQGGDRIGVSFPDLDESRSRLGERLRIHASADDLRALLARPWLEGLRDHLQFGEPAVVPHPTPYRQVSRVQAKSNPERLRRRLMRRHD--EEEARKR--------LDLPFVTLRSQSTGQHFRLFIRHGPLQVTAEEGGFTCYGLSKGGFVPWF 187
                                     9        19        29        39        49        59        69        79        89        99       109       119 |  |  129|      139       149       159       169       179        
                                                                                                                                                   121  |   130      139                                                
                                                                                                                                                      124

Chain B from PDB  Type:DNA/RNA  Length:16
                                                
                 2xlj B   6 CUGCCGUAUAGGCAGC  21
                                    15

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 (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CAS6_PSEAB | Q02MM2)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0043571	maintenance of CRISPR repeat elements	Any process involved in sustaining CRISPR repeat clusters, including capture of new spacer elements, expansion or contraction of clusters, propagation of the leader sequence and repeat clusters within a genome, transfer of repeat clusters and CRISPR-associated (cas) genes to new genomes, transcription of the CRISPR repeat arrays into RNA and processing, and interaction of CRISPR/cas loci with the host genome. CRISPR (clustered regularly interspaced short palindromic repeat) elements are a family of sequence elements containing multiple direct repeats of 24-48 bp with weak dyad symmetry which are separated by regularly sized nonrepetitive spacer sequences.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2xlj)

	Sites
(no "Sites" information available for 2xlj)

	Cis Peptide Bonds
		His A:93 - Pro A:94	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2xlj
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CAS6_PSEAB \| Q02MM2
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description