3W2W - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CMR2DHD-CMR3 SUBCOMPLEX BOUND TO ATP

Authors :   T. Numata, T. Osawa

Date :   06 Dec 12 (Deposition) - 16 Oct 13 (Release) - 16 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Ferredoxin-Like Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Osawa, H. Inanaga, T. Numata
Crystal Structure Of The Cmr2-Cmr3 Subcomplex In The Crispr-Cas Rna Silencing Effector Complex.
J. Mol. Biol. V. 425 3811 2013
PubMed-ID: 23583914 | Reference-DOI: 10.1016/J.JMB.2013.03.042

Molecule 1 - CRISPR SYSTEM CMR SUBUNIT CMR2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 216-871
	Gene	:	CMR2, PF1129
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	186497
	Strain	:	DSM 3638
	Synonym	:	CRISPR-ASSOCIATED PROTEIN CAS10/CMR2, SUBTYPE III-B

Molecule 2 - CRISPR SYSTEM CMR SUBUNIT CMR3
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21-CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CMR3, PF1128
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	186497
	Strain	:	DSM 3638
	Synonym	:	CRISPR TYPE III-B/RAMP MODULE-ASSOCIATED PROTEIN CMR3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	ATP	4	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:448 , CYS A:451 , CYS A:478 , CYS A:481	BINDING SITE FOR RESIDUE ZN A 901
2	AC2	SOFTWARE	LYS A:225 , VAL A:227 , VAL A:229 , GLN A:230 , ILE A:233 , SER A:246 , LEU A:249 , ASN A:300 , ARG A:436 , ASP A:600 , TYR A:669 , ASP A:674 , ATP A:903 , HOH A:1003 , HOH A:1020 , HOH A:1038 , ARG B:262 , MG B:401	BINDING SITE FOR RESIDUE ATP A 902
3	AC3	SOFTWARE	TYR A:271 , LYS A:301 , ASP A:600 , GLY A:601 , ASP A:602 , ASP A:603 , MET A:604 , GLY A:605 , ILE A:608 , HIS A:642 , SER A:646 , LEU A:649 , LYS A:739 , LYS A:744 , ATP A:902 , MG A:904 , HOH A:1044 , LYS B:111	BINDING SITE FOR RESIDUE ATP A 903
4	AC4	SOFTWARE	ASP A:600 , GLY A:601 , ATP A:903 , HOH A:1044	BINDING SITE FOR RESIDUE MG A 904
5	AC5	SOFTWARE	ATP A:902	BINDING SITE FOR RESIDUE MG B 401

Asymmetric Unit

No.	Residues
1	B:54	-	B:183

Asymmetric Unit

No.	Residues
1	Val A:227	-	Pro A:228
2	Tyr A:271	-	Pro A:272

(no "SAP(SNP)/Variant" information available for 3W2W)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GGDEF	PS50887	GGDEF domain profile.	CMR2_PYRFU	592-752	1	A:592-752

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GGDEF	PS50887	GGDEF domain profile.	CMR2_PYRFU	592-752	1	A:592-752

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GGDEF	PS50887	GGDEF domain profile.	CMR2_PYRFU	592-752	2	A:592-752

(no "Exon" information available for 3W2W)

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:618
 aligned with CMR2_PYRFU | Q8U1S6 from UniProtKB/Swiss-Prot  Length:871

    Alignment length:656
                                   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865      
           CMR2_PYRFU   216 VKDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSLSEKEDIYQVTENAGLSDEDVKKWLKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQLKGWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESGLSKKLKNKKEIDEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMGKVISGEVLGEISTRIHPNIRDYVEIPEAKYYSTPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKSFENGSLLPGWKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLLEEKGGVGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHIRGRNKEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee.....hhhhhhhh.....hhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.hhhhhhhhhhhheeeeeeee...eeehhhhhhhh...hhhhhhhhhhhhhhh...eee...hhhhhhhhhhhhhhhhhhhhhh.........................hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee.hhhhhhhhhhhhh-----------.hhhhhhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhhhhh----------------------.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeee..hhhhhhhhhhhhhhhhh.---......eeeeeeeee...hhhhhhhhhhhhhhhhhhhh.....eeeeee.....eeeeee.hhhhhhhhhhhhhhhhhh.--.hhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGDEF  PDB: A:592-752 UniProt: 592-752                                                                                                                           ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w2w A 216 VKDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSLSEKEDIYQVTENAGLSDEDVKKWLKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQLKGWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESG-----------DEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMGKVISGEVL----------------------YSTPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKSFE---LLPGWKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLLEE--GVGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHIRGRNKEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP 871
                                   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555 |       -   |   575       585       595       605       | -         -         -|      645       655       665       675       685       695    |  705       715       725       735       745       755       765       775       | -|      795       805       815       825       835       845       855       865      
                                                                                                                                                                                                                                                                                                                                                                               557         569                                         613                    636                                                             700 704                                                                            783  |                                                                                     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    786

Chain B from PDB  Type:PROTEIN  Length:308
 aligned with CMR3_PYRFU | Q8U1S7 from UniProtKB/Swiss-Prot  Length:322

    Alignment length:322
                                    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  
           CMR3_PYRFU     1 MIEVTFTPYDVLLFRESRPFDAGSESVARSIIPLPQTVAGAIRTLLFYKGLKNCVGVGEEEPEFTLVGIAIGTEKGRIYPLPFNIIKSEKFYKVVNPGRFLGKLILPPKGKYKSGYVTESILEKYLKGELKEVEENKVIRIEKEKRIGIKLSREKKVVEEGMLYTVEFLRIEKIYAWIEDPGCGIKDILSSYEFLTLGGESRVAFVEVDDKTPDIFNRELGSTKKALFYFSTPTIGKVGEIVQELEKRLNAKIDDYLLVSSRPTAISGWDMHEKKPKGTKFAIPPGSVLFVEFKEEVEVPPYIKLGKLKKLGYGLALGGIWE 322
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..........hhhhhhh.............hhhhhh--.hhhhh..........eeeeeeeee..eeeee....ee..--.eee...eee..eee..........eeehhhhhhhhh....eehhhhh....eeeeeee..----------.eeeeeee...eeeeeee....hhhhhhhh..eee.....eeeeeeee...hhhhh....eeeeeeeee...ee.hhhhhhhhhhhhh...eeeeeee....eee..ee....ee...eeee....eeeeeeeeeee...eee...hhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w2w B   1 MIEVTFTPYDVLLFRESRPFDAGSESVARSIIPLPQTVAGAIRTLL--KGLKNCVGVGEEEPEFTLVGIAIGTEKGRIYPLPFNIIKS--FYKVVNPGRFLGKLILPPKGKYKSGYVTESILEKYLKGELKEVEENKVIRIEKEKRIGIKL----------MLYTVEFLRIEKIYAWIEDPGCGIKDILSSYEFLTLGGESRVAFVEVDDKTPDIFNRELGSTKKALFYFSTPTIGKVGEIVQELEKRLNAKIDDYLLVSSRPTAISGWDMHEKKPKGTKFAIPPGSVLFVEFKEEVEVPPYIKLGKLKKLGYGLALGGIWE 322
                                    10        20        30        40     |  50        60        70        80       | -|      100       110       120       130       140       150|        - |     170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320  
                                                                        46 49                                     88 91                                                         151        162

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 '\|'

(no "SCOP Domain" information available for 3W2W)

(no "CATH Domain" information available for 3W2W)

(no "Pfam Domain" information available for 3W2W)

Asymmetric Unit(hide GO term definitions)

Chain A (CMR2_PYRFU | Q8U1S6)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (CMR3_PYRFU | Q8U1S7)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
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		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Tyr A:271 - Pro A:272	[ RasMol ]
		Val A:227 - Pro A:228	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3w2w
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	CMR2_PYRFU \| Q8U1S6
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	CMR3_PYRFU \| Q8U1S7
		Comparative Protein Structure Models	:	ModBase
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		Protein-protein Interaction	:	DIP
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	CMR2_PYRFU \| Q8U1S6
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	CMR3_PYRFU \| Q8U1S7
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	CMR2_PYRFU \| Q8U1S6	:	3ung 3ur3 3w2v 3x1l 4doz 4h4k 4w8y
	CMR3_PYRFU \| Q8U1S7	:	3w2v 3x1l 4h4k

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 9)

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