2NNW - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   ALTERNATIVE CONFORMATIONS OF NOP56/58-FIBRILLARIN COMPLEX AND IMPLICATION FOR INDUCED-FIT ASSENLY OF BOX C/D RNPS

Authors :   S. Oruganti, Y. Zhang, R. Terns, M. P. Terns, H. Li

Date :   24 Oct 06 (Deposition) - 21 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Box C/D, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Oruganti, Y. Zhang, H. Li, H. Robinson, M. P. Terns, R. M. Terns, W. Yang, H. Li
Alternative Conformations Of The Archaeal Nop56/58-Fibrillarin Complex Imply Flexibility In Box C/D Rnps.
J. Mol. Biol. V. 371 1141 2007
PubMed-ID: 17617422 | Reference-DOI: 10.1016/J.JMB.2007.06.029

Molecule 1 - NOP5/NOP56 RELATED PROTEIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

Molecule 2 - FIBRILLARIN-LIKE RRNA/TRNA 2'-O-METHYLTRANSFERASE
	Chains	:	B, D
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	FLPA
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (2x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2NNW)

(no "Site" information available for 2NNW)

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

Asymmetric Unit

No.	Residues
1	Phe A:88	-	Pro A:89
2	Glu B:213	-	Pro B:214
3	Phe C:88	-	Pro C:89
4	Glu D:213	-	Pro D:214

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIBRILLARIN	PS00566	Fibrillarin signature.	FLPA_PYRFU	99-113	2	B:99-113 D:99-113

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIBRILLARIN	PS00566	Fibrillarin signature.	FLPA_PYRFU	99-113	2	B:99-113 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FIBRILLARIN	PS00566	Fibrillarin signature.	FLPA_PYRFU	99-113	2	- D:99-113

(no "Exon" information available for 2NNW)

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:350
 aligned with Q8U4M1_PYRFU | Q8U4M1 from UniProtKB/TrEMBL  Length:402

    Alignment length:363
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363   
         Q8U4M1_PYRFU     4 FISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYDEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRIQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTVGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLRTGAKPPKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEARIREIK 366
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeee..........ee...hhhhhhhhhh....hhhhhhhhhhhhh.....eee.hhhhhhhhhh....eee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhh.hhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....-------------...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nnw A   8 FISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYDEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRIQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTVGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAE-------------PKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEARIREIK 369
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287        |-         -  |    316       326       336       346       356       366   
                                                                                                                                                                                                                                                                                                                          296           309

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with FLPA_PYRFU | Q8U4M2 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           FLPA_PYRFU     1 MVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGAAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEERRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKSRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP 227
               SCOP domains d2nnwb_ B: Fibrillarin homologue                                                                                                                                                                                                    SCOP domains
               CATH domains 2nnwB01 B:1-51 Phosphorylase Kinase; domain 1      2nnwB02 B:52-227 Vaccinia Virus protein VP39                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeeee.....eeeeee...........eeee....eeee.....hhhhhhhhh...........eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh..eeeee....hhhhhh.....eeeeee.....hhhhhhhhhhhhheeeeeeeeeeeehhhhh...hhhhhhhhhhhhhhh.....eeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------FIBRILLARIN    ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nnw B   1 MVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGAAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEERRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKSRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:PROTEIN  Length:350
 aligned with Q8U4M1_PYRFU | Q8U4M1 from UniProtKB/TrEMBL  Length:402

    Alignment length:363
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363   
         Q8U4M1_PYRFU     4 FISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYDEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRIQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTVGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLRTGAKPPKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEARIREIK 366
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------NOSIC-2nnwC01 C:134-186                              ----------------------------------------Nop-2nnwC03 C:227-369                                                                                                                            Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------NOSIC-2nnwC02 C:134-186                              ----------------------------------------Nop-2nnwC04 C:227-369                                                                                                                            Pfam domains (2)
         Sec.struct. author .eee...eeeee.....eeeeee...hhhhhhhhhh....hhhhhhhhhhhhhh....eee.hhhhhhhhhh....eee...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...-------------...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nnw C   8 FISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYDEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRIQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTVGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAE-------------PKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEARIREIK 369
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287        |-         -  |    316       326       336       346       356       366   
                                                                                                                                                                                                                                                                                                                          296           309

Chain D from PDB  Type:PROTEIN  Length:227
 aligned with FLPA_PYRFU | Q8U4M2 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           FLPA_PYRFU     1 MVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGAAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEERRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKSRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP 227
               SCOP domains d2nnwd_ D: Fibrillarin homologue                                                                                                                                                                                                    SCOP domains
               CATH domains 2nnwD01 D:1-51 Phosphorylase Kinase; domain 1      2nnwD02 D:52-227 Vaccinia Virus protein VP39                                                                                                                                     CATH domains
           Pfam domains (1) ---Fibrillarin-2nnwD01 D:4-227                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) ---Fibrillarin-2nnwD02 D:4-227                                                                                                                                                                                                      Pfam domains (2)
         Sec.struct. author ..eeee.....eeeee.....eeeeee............eee....eeee.....hhhhhhhhh...........eeeee....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeeee....hhhhhhhhh..eeeeee.....hhhhhhhhhhhhheeeeeeeeeeeehhhhh...hhhhhhhhhhhhhhh.....eeee.......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------FIBRILLARIN    ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nnw D   1 MVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGAAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEERRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKSRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: S-adenosyl-L-methionine-dependent methyltransferases (533)

Superfamily: S-adenosyl-L-methionine-dependent methyltransferases (533)

Family: Fibrillarin homologue (7)

Protein domain: Fibrillarin homologue (7)

Pyrococcus furiosus [TaxId: 2261] (3)

1a	d2nnwb_	B:
1b	d2nnwd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phosphorylase Kinase; domain 1 (1392)

Homologous Superfamily: Phosphorylase Kinase; domain 1 (1392)

Pyrococcus furiosus. Organism_taxid: 2261. (1)

1a	2nnwB01	B:1-51
1b	2nnwD01	D:1-51

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Pyrococcus furiosus. Organism_taxid: 2261. (6)

2a	2nnwB02	B:52-227
2b	2nnwD02	D:52-227

Asymmetric Unit(hide GO term definitions)

Chain A,C (Q8U4M1_PYRFU | Q8U4M1)


GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.

Chain B,D (FLPA_PYRFU | Q8U4M2)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2nnw)

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

	Cis Peptide Bonds
		Glu B:213 - Pro B:214	[ RasMol ]
		Glu D:213 - Pro D:214	[ RasMol ]
		Phe A:88 - Pro A:89	[ RasMol ]
		Phe C:88 - Pro C:89	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
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	2nnw
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	FLPA_PYRFU \| Q8U4M2
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	Q8U4M1_PYRFU \| Q8U4M1
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	2.1.1.-
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	FLPA_PYRFU \| Q8U4M2
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	Q8U4M1_PYRFU \| Q8U4M1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	FLPA_PYRFU \| Q8U4M2	:	1pry 3nmu 3nvk 3nvm 4by9
UniProtKB/TrEMBL
	Q8U4M1_PYRFU \| Q8U4M1	:	3nmu 3nvi 3nvk 3nvm 4by9

(no "Related Entries Specified in the PDB File" available for 2NNW)

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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PROSITE Motifs (1, 2)

Exons (0, 0)

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Gene Ontology (9, 9)

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