2EY4 - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A CBF5-NOP10-GAR1 COMPLEX

Authors :   R. Rashid, B. Liang, H. Li, Southeast Collaboratory For Structural (Secsg)

Date :   09 Nov 05 (Deposition) - 24 Jan 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,E  (1x)
Biol. Unit 2: B,D,F  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)

Keywords :   Trimeric Complex, Structural Genomics, Psi, Protein Structure Initiative, Southeast Collaboratory For Structural Genomics, Secsg, Isomerase-Biosynthetic Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Rashid, B. Liang, D. L. Baker, O. A. Youssef, Y. He, K. Phipps, R. M. Terns, M. P. Terns, H. Li
Crystal Structure Of A Cbf5-Nop10-Gar1 Complex And Implications In Rna-Guided Pseudouridylation And Dyskeratosis Congenita.
Mol. Cell V. 21 249 2006
PubMed-ID: 16427014 | Reference-DOI: 10.1016/J.MOLCEL.2005.11.017

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

Molecule 2 - SMALL NUCLEOLAR RNP SIMILAR TO GAR1
	Chains	:	C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	186497
	Strain	:	DSM 3638

Molecule 3 - RIBOSOME BIOGENESIS PROTEIN NOP10
	Chains	:	E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A		C		E
Biological Unit 2 (1x)	:		B		D		F
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)	F (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS E:8 , LYS E:10 , CYS E:11 , CYS E:20 , CYS E:23	BINDING SITE FOR RESIDUE ZN E 201
2	AC2	SOFTWARE	CYS F:8 , CYS F:11 , CYS F:20 , CYS F:23 , GLU F:25	BINDING SITE FOR RESIDUE ZN F 301

(no "SS Bond" information available for 2EY4)

(no "Cis Peptide Bond" information available for 2EY4)

(no "SAP(SNP)/Variant" information available for 2EY4)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUA	PS50890	PUA domain profile.	TRUB_PYRFU	250-325	2	A:253-328 B:253-328

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUA	PS50890	PUA domain profile.	TRUB_PYRFU	250-325	1	A:253-328 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUA	PS50890	PUA domain profile.	TRUB_PYRFU	250-325	1	- B:253-328

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PUA	PS50890	PUA domain profile.	TRUB_PYRFU	250-325	2	A:253-328 B:253-328

(no "Exon" information available for 2EY4)

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

    Alignment length:329
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324         
           TRUB_PYRFU     5 EVRRILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKL 333
               SCOP domains d2ey4a2 A:8-252 Pseudouridine synthase II TruB                                                                                                                                                                                                       d2ey4a1 A:253-336 Pseudouridine synthase II TruB, C-terminal domain                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh...eee.............hhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhhh...eeeeeeeee....hhhhhhhhhhh..eeeee............eeeeeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhh...eeeeeeeeeee..ee......hhhhhhhhhhhhhhhh.hhhhhhh.ee.hhhhh...eeeehhhhhhhhh....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
                 2ey4 A   8 EVRRILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKL 336
                                    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

Chain B from PDB  Type:PROTEIN  Length:326
 aligned with TRUB_PYRFU | Q7LWY0 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:326
                                    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 RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKL 333
               SCOP domains d2ey4b2 B:11-252 Pseudouridine synthase II TruB                                                                                                                                                                                                   d2ey4b1 B:253-336 Pseudouridine synthase II TruB, C-terminal domain                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...eee.............hhhhhhhhhhhhheeeeeee....hhhhhhhhhhhhh....eee........eeeeeeee.hhhhhhhhh....eeeeeeeee....hhhhhhhhhhhh.eeee..............eeeeeeeeeeeee..eeeeeeee....hhhhhhhhhhhhhh..eeeeeeeeeee..ee......hhhhhhhhhhhhhhhh.hhhhhhheee.hhhhh...eeeehhhhhhhhhh...ee...eeeee.......eeeee.....eeeeeee..hhhhhhhh...eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PUA  PDB: B:253-328 UniProt: 250-325                                        -------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ey4 B  11 RILPADIKREVLIKDENAETNPDWGFPPEKRPIEMHIQFGVINLDKPPGPTSHEVVAWIKKILNLEKAGHGGTLDPKVSGVLPVALEKATRVVQALLPAGKEYVALMHLHGDVPEDKIIQVMKEFEGEIIQRPPLRSAVKRRLRTRKVYYIEVLEIEGRDVLFRVGVEAGTYIRSLIHHIGLALGVGAHMSELRRTRSGPFKEDETLITLHDLVDYYYFWKEDGIEEYFRKAIQPMEKAVEHLPKVWIKDSAVAAVTHGADLAVPGIAKLHAGIKRGDLVAIMTLKDELVALGKAMMTSQEMLEKTKGIAVDVEKVFMPRDWYPKL 336
                                    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:73
 aligned with Q8U029_PYRFU | Q8U029 from UniProtKB/TrEMBL  Length:104

    Alignment length:73
                                    17        27        37        47        57        67        77   
         Q8U029_PYRFU     8 MKRLGKVLHYAKQGFLIVRTNWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEIYVGEVLYVD  80
               SCOP domains d2ey4c1 C:1-73 Gar1 homolog PF1791                                        SCOP domains
               CATH domains 2ey4C00 C:1-73 Probable tRNA pseudouridine synthase domain                CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...eeeee.........eee.......eeeeeeeee....eeeeee.............ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 2ey4 C   1 MKRLGKVLHYAKQGFLIVRTNWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEIYVGEVLYVD  73
                                    10        20        30        40        50        60        70

Chain D from PDB  Type:PROTEIN  Length:75
 aligned with Q8U029_PYRFU | Q8U029 from UniProtKB/TrEMBL  Length:104

    Alignment length:75
                                    17        27        37        47        57        67        77     
         Q8U029_PYRFU     8 MKRLGKVLHYAKQGFLIVRTNWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEIYVGEVLYVDER  82
               SCOP domains d2ey4d_ D: automated matches                                                SCOP domains
               CATH domains 2ey4D00 D:1-75 Probable tRNA pseudouridine synthase domain                  CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee...eeeee.........eeee....eeeeeeeeeee....eeeeee...hhhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2ey4 D   1 MKRLGKVLHYAKQGFLIVRTNWVPSLNDRVVDKRLQFVGIVKDVFGPVKMPYVAIKPKVSNPEIYVGEVLYVDER  75
                                    10        20        30        40        50        60        70

Chain E from PDB  Type:PROTEIN  Length:52
 aligned with NOP10_PYRFU | Q8U1R4 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:52
                                    13        23        33        43        53  
          NOP10_PYRFU     4 RIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI  55
               SCOP domains d2ey4e1 E:4-55 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
                 2ey4 E   4 RIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI  55
                                    13        23        33        43        53

Chain F from PDB  Type:PROTEIN  Length:52
 aligned with NOP10_PYRFU | Q8U1R4 from UniProtKB/Swiss-Prot  Length:60

    Alignment length:52
                                    13        23        33        43        53  
          NOP10_PYRFU     4 RIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI  55
               SCOP domains d2ey4f_ F: automated matches                         SCOP domains
               CATH domains 2ey4F00 F:4-55 Nop10-like SnoRNP                     CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee............ee...........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                 2ey4 F   4 RIRKCPKCGRYTLKEVCPVCGEKTKVAHPPRFSPEDPYGEYRRRWKREVLGI  55
                                    13        23        33        43        53

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Thrombin, subunit H (1535)

Homologous Superfamily: Probable tRNA pseudouridine synthase domain (3)

Pyrococcus furiosus. Organism_taxid: 2261. (1)

1a	2ey4C00	C:1-73
1b	2ey4D00	D:1-75

Architecture: Single Sheet (341)

Topology: Rubrerythrin, domain 2 (145)

Homologous Superfamily: Nop10-like SnoRNP (3)

Pyrococcus furiosus. Organism_taxid: 2261. (1)

2ey4F00

F:4-55

(no "Pfam Domain" information available for 2EY4)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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,D (Q8U029_PYRFU | Q8U029)

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: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.

Chain E,F (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.

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	2ey4
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	NOP10_PYRFU \| Q8U1R4
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	Q8U029_PYRFU \| Q8U029
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	TRUB_PYRFU \| Q7LWY0
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	5.4.99.-
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UniProtKB/Swiss-Prot
	NOP10_PYRFU \| Q8U1R4	:	2hvy 2rfk 3hax 3hay 3hjw 3hjy 3lwo 3lwp 3lwq 3lwr 3lwv 3mqk
	TRUB_PYRFU \| Q7LWY0	:	2hvy 2rfk 3hax 3hay 3hjw 3hjy 3lwo 3lwp 3lwq 3lwr 3lwv 3mqk
UniProtKB/TrEMBL
	Q8U029_PYRFU \| Q8U029	:	2hvy 2rfk 3hay 3mqk

(no "Related Entries Specified in the PDB File" available for 2EY4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (6, 8)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (12, 15)

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