2B9E - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   HUMAN NSUN5 PROTEIN

Authors :   J. R. Min, H. Wu, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)

Date :   11 Oct 05 (Deposition) - 18 Oct 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym./Biol. Unit : A

Keywords :   Methytransferase, Nol1/Nop2/Sun Domain Family, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Min, H. Wu, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
The Crystal Structure Of Human Nsun5 Protein In Complex With S-Adenosyl-L-Methionine
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - NOL1/NOP2/SUN DOMAIN FAMILY, MEMBER 5 ISOFORM 2
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28A-LIC
	Expression System Strain	:	BL21 (DE3) CODON PLUS RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:233 , CYS A:234 , ALA A:235 , ALA A:236 , PRO A:237 , GLY A:238 , ASN A:239 , LYS A:240 , ASP A:258 , LEU A:259 , ASP A:260 , ARG A:263 , GLU A:284 , ASP A:285 , PHE A:286 , ASP A:305 , SER A:307 , PHE A:337 , HOH A:1210 , HOH A:1361 , HOH A:1376 , HOH A:1413 , HOH A:1442	BINDING SITE FOR RESIDUE SAM A 1201

(no "SS Bond" information available for 2B9E)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:236	-	Pro A:237

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_051889	P	183	S	NSUN5_HUMAN	Polymorphism	34913552	A	P	183	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2B9E)

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1d	ENST00000252594	1d	ENSE00001927422	chr7:72722803-72722695	109	NSUN5_HUMAN	1-31	31	0	-	-
1.2a	ENST00000252594	2a	ENSE00001600228	chr7:72722550-72722428	123	NSUN5_HUMAN	32-72	41	0	-	-
1.2c	ENST00000252594	2c	ENSE00000689434	chr7:72721754-72721580	175	NSUN5_HUMAN	73-131	59	0	-	-
1.3	ENST00000252594	3	ENSE00001091263	chr7:72721499-72721391	109	NSUN5_HUMAN	131-167	37	1	A:133-167	35
1.4	ENST00000252594	4	ENSE00001667139	chr7:72719094-72718956	139	NSUN5_HUMAN	167-213	47	1	A:167-213	47
1.5	ENST00000252594	5	ENSE00001740465	chr7:72718859-72718744	116	NSUN5_HUMAN	214-252	39	1	A:214-252	39
1.6c	ENST00000252594	6c	ENSE00001664098	chr7:72718405-72718227	179	NSUN5_HUMAN	252-312	61	1	A:252-310	59
1.7b	ENST00000252594	7b	ENSE00001650095	chr7:72718033-72717823	211	NSUN5_HUMAN	312-382	71	1	A:329-382	54
1.8b	ENST00000252594	8b	ENSE00001318064	chr7:72717737-72717227	511	NSUN5_HUMAN	382-429	48	1	A:382-425	44

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:275
 aligned with NSUN5_HUMAN | Q96P11 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:293
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422   
          NSUN5_HUMAN   133 QLPRFVRVNTLKTCSDDVVDYFKRQGFSYQGRASSLDDLRALKGKHFLLDPLMPELLVFPAQTDLHEHPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGKIFAFDLDAKRLASMATLLARAGVSCCELAEEDFLAVSPSDPRYHEVHYILLDPSCSGSGMPSRQLEEPGAGTPSPVRLHALAGFQQRALCHALTFPSLQRLVYSTCSLCQEENEDVVRDALQQNPGAFRLAPALPAWPHRGLSTFPGAEHCLRASPETTLSSGFFVAVIERV 425
               SCOP domains d2b9ea1 A:133-425 NOL1R                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhh..eeeee..hhhhhhh....eeee......eeee........hhhhhh..eee..hhhhhhhhhhh.....eeee.....hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhh....eeeee.hhhhh...hhhhh.eeeeee......------------------.hhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhhh.....eee................hhhhheeehhhhhh...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------S-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:133-167           ----------------------------------------------Exon 1.5  PDB: A:214-252               -----------------------------------------------------------Exon 1.7b  PDB: A:329-382 UniProt: 312-382 [INCOMPLETE]                ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.4  PDB: A:167-213 UniProt: 167-213      --------------------------------------Exon 1.6c  PDB: A:252-310 UniProt: 252-312 [INCOMPLETE]      ---------------------------------------------------------------------Exon 1.8b  PDB: A:382-425 UniProt: 382-429   Transcript 1 (2)
                 2b9e A 133 QLPRFVRVNTLKTCSDDVVDYFKRQGFSYQGRASSLDDLRALKGKHFLLDPLMPELLVFPAQTDLHEHPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGKIFAFDLDAKRLASMATLLARAGVSCCELAEEDFLAVSPSDPRYHEVHYILLDPSCSG------------------VRLHALAGFQQRALCHALTFPSLQRLVYSTCSLCQEENEDVVRDALQQNPGAFRLAPALPAWPHRGLSTFPGAEHCLRASPETTLSSGFFVAVIERV 425
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       | -         -      |332       342       352       362       372       382       392       402       412       422   
                                                                                                                                                                                                           310                329

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

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

Family: NOL1/NOP2/sun (4)

Protein domain: NOL1R (1)

Human (Homo sapiens) [TaxId: 9606] (1)

d2b9ea1

A:133-425

(no "CATH Domain" information available for 2B9E)

(no "Pfam Domain" information available for 2B9E)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NSUN5_HUMAN | Q96P11)

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.
cellular component
	GO:0005730	nucleolus	A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:236 - Pro A:237	[ RasMol ]

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	2b9e
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Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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Exons (6, 6)

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