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Title :   CRYSTAL STRUCTURE OF A SUBSTRATE-BOUND GAR1-MINUS H/ACA RNP FROM PYROCOCCUS FURIOSUS

Authors :   K. Ye

Date :   03 May 09 (Deposition) - 23 Jun 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

Chains :   Asym./Biol. Unit : A,C,D,E,F

Keywords :   H/Aca, Guide Rna, Rna-Protein Complex, Pseudouridine Synthase, Isomerase, Trna Processing, Ribonucleoprotein, Ribosome Biogenesis, Rrna Processing, Ribosomal Protein, Rna-Binding, Isomerase- Biosynthetic Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Duan, L. Li, J. Lu, W. Wang, K. Ye
Structural Mechanism Of Substrate Rna Recruitment In H/Aca Rna-Guided Pseudouridine Synthase.
Mol. Cell V. 34 427 2009
PubMed-ID: 19481523 | Reference-DOI: 10.1016/J.MOLCEL.2009.05.005

Molecule 1 - PROBABLE TRNA PSEUDOURIDINE SYNTHASE B
	Chains	:	A
	EC Number	:	5.4.99.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TRUB, PF1785
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261
	Synonym	:	CBF5, TRNA PSEUDOURIDINE 55 SYNTHASE, PSI55 SYNTHASE, TRNA- URIDINE ISOMERASE, TRNA PSEUDOURIDYLATE SYNTHASE

Molecule 2 - RIBOSOME BIOGENESIS PROTEIN NOP10
	Chains	:	C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PF1141
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

Molecule 3 - 50S RIBOSOMAL PROTEIN L7AE
	Chains	:	D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RPL7AE, PF1367
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

Molecule 4 - H/ACA RNA
	Chains	:	E
	Engineered	:	YES
	Other Details	:	RNA WAS PREPARED BY IN VITRO TRANSCRIPTION
	Synthetic	:	YES

*Molecule 5 - 5'-R(APUPAPAPUPUP(FHU)PGPAPCPUPCPAPA)-3'*
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 12)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	FHU	1	Mod. Nucleotide	(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5'-MONOPHOSPHATE
3	MG	5	Ligand/Ion	MAGNESIUM ION
4	PG4	1	Ligand/Ion	TETRAETHYLENE GLYCOL
5	PGE	2	Ligand/Ion	TRIETHYLENE GLYCOL
6	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:44 , TRP A:230 , LYS A:231 , GLY A:234 , ARG D:46 , HOH D:521 , G E:21 , G E:22	BINDING SITE FOR RESIDUE PGE A 401
02	AC2	SOFTWARE	VAL A:21 , TRP A:257 , LYS A:279 , LEU A:295 , ASP A:297 , PRO C:21	BINDING SITE FOR RESIDUE PGE A 402
03	AC3	SOFTWARE	GLU A:134	BINDING SITE FOR RESIDUE EDO A 403
04	AC4	SOFTWARE	CYS C:8 , CYS C:11 , CYS C:20 , CYS C:23	BINDING SITE FOR RESIDUE ZN C 201
05	AC5	SOFTWARE	ARG C:34 , GLU D:62 , HIS D:66	BINDING SITE FOR RESIDUE PG4 C 401
06	AC6	SOFTWARE	GLY D:106 , LYS D:107	BINDING SITE FOR RESIDUE EDO D 401
07	AC7	SOFTWARE	HOH E:401 , HOH E:402 , HOH E:403 , HOH E:404 , HOH E:405 , HOH E:406	BINDING SITE FOR RESIDUE MG E 200
08	AC8	SOFTWARE	ASP D:110 , GLU D:113 , HOH E:411 , HOH E:412 , HOH E:413 , HOH E:414	BINDING SITE FOR RESIDUE MG E 201
09	AC9	SOFTWARE	GLU C:43 , C E:37 , HOH E:421 , HOH E:422 , HOH E:423 , HOH E:424	BINDING SITE FOR RESIDUE MG E 202
10	BC1	SOFTWARE	HOH E:431 , HOH E:432 , HOH E:433	BINDING SITE FOR RESIDUE MG E 203
11	BC2	SOFTWARE	HOH E:441 , HOH E:442 , HOH E:443 , HOH E:444	BINDING SITE FOR RESIDUE MG E 204

(no "SS Bond" information available for 3HAX)

Asymmetric/Biological Unit

No.	Residues
1	Asp D:59	-	Pro D:60

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L7AE	PS01082	Ribosomal protein L7Ae signature.	RL7A_PYRFU	70-87	1	D:71-88
2	PUA	PS50890	PUA domain profile.	TRUB_PYRFU	250-325	1	A:253-328

(no "Exon" information available for 3HAX)

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:329
 aligned with TRUB_PYRFU | Q7LWY0 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:329
                                    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       297       307       317       327         
           TRUB_PYRFU     8 RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLWEK 336
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.............hhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhh...eee........eeeeeeee.hhhhhhhhh....eeeeeeeee....hhhhhhhhhhh..eeeee............eeeeeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee.....eehhhhhhhhhhhhh...hhhhhhhhee.hhhhh...eeeehhhhhhhhhh...ee...eeeee.......eeeeee....eeeeeee..hhhhhhhh...eeeeeeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: A:253-328 UniProt: 250-325                                        ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hax A  11 RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKLWEK 339
                                    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       330

Chain C from PDB  Type:PROTEIN  Length:53
 aligned with NOP10_PYRFU | Q8U1R4 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:53
                                    12        22        32        42        52   
          NOP10_PYRFU     3 FRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI  55
               SCOP domains d3haxc_ C: Ribosome biogenesis protein Nop10          SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......ee............ee...........hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                 3hax C   3 FRIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI  55
                                    12        22        32        42        52

Chain D from PDB  Type:PROTEIN  Length:121
 aligned with RL7A_PYRFU | Q8U160 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:121
                                    12        22        32        42        52        62        72        82        92       102       112       122 
           RL7A_PYRFU     3 KPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELMK 123
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3haxD00 D:4-124  [code=3.30.1330.30, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhheeeehhhhhhhhhhh....eeeee....hhhhh.hhhhhhhhhh..eeee.hhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------RIBOSOMAL_L7AE    ------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hax D   4 KPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKELMK 124
                                    13        23        33        43        53        63        73        83        93       103       113       123

Chain E from PDB  Type:DNA/RNA  Length:60
                                                                                            
                 3hax E   1 GGGUCCGCCUUGAGUGCCCGGGUGAGAGCAUGAUCCCGGGUAAUUAUGGCGGACCCACAG  61
                                    10        20     || 31        41        51        61
                                                    26|                                 
                                                     28

Chain F from PDB  Type:RNA  Length:14
                                              
                 3hax F   1 AUAAUUuGACUCAA  14
                                  | 10    
                                  7-FHU

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: Small proteins (3458)

Fold: Rubredoxin-like (572)

Superfamily: Nop10-like SnoRNP (19)

Family: Nucleolar RNA-binding protein Nop10-like (19)

Protein domain: Ribosome biogenesis protein Nop10 (12)

Pyrococcus furiosus [TaxId: 2261] (10)

d3haxc_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.30, no name defined] (102)

Pyrococcus furiosus. Organism_taxid: 2261. (1)

3haxD00

D:4-124

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TRUB_PYRFU | Q7LWY0)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0009982	pseudouridine synthase activity	Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
biological process
	GO:0009451	RNA modification	The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
	GO:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0001522	pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
	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.
	GO:0031119	tRNA pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

Chain C (NOP10_PYRFU | Q8U1R4)

molecular function
	GO:0030515	snoRNA binding	Interacting selectively and non-covalently with small nucleolar RNA.
biological process
	GO:0001522	pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.
	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:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.

Chain D (RL7A_PYRFU | Q8U160)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0004526	ribonuclease P activity	Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	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:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
	GO:0001682	tRNA 5'-leader removal	Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P.
	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.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp D:59 - Pro D:60	[ RasMol ]

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	3hax
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	5.4.99.-
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 12)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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