3R9W - JenaLib

Title :   CRYSTAL STRUCTURE OF ERA IN COMPLEX WITH MGGDPNP AND NUCLEOTIDES 1506-1542 OF 16S RIBOSOMAL RNA

Authors :   C. Tu, X. Ji

Date :   26 Mar 11 (Deposition) - 22 Jun 11 (Release) - 06 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Gtpase, Kh Domain, Ribosome, Biogenesis, Gtp, 16S Ribosomal Rna, Gtp Hydrolysis, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Tu, X. Zhou, S. G. Tarasov, J. E. Tropea, B. P. Austin, D. S. Waugh, D. L. Court, X. Ji
The Era Gtpase Recognizes The Gaucaccucc Sequence And Binds Helix 45 Near The 3' End Of 16S Rrna.
Proc. Natl. Acad. Sci. Usa V. 108 10156 2011
PubMed-ID: 21646538 | Reference-DOI: 10.1073/PNAS.1017679108
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:17 , THR A:38 , GNP A:402 , HOH A:611 , HOH A:632	BINDING SITE FOR RESIDUE MG A 401
02	AC2	SOFTWARE	PRO A:12 , ASN A:13 , VAL A:14 , GLY A:15 , LYS A:16 , SER A:17 , THR A:18 , ILE A:31 , SER A:32 , PRO A:33 , GLY A:36 , THR A:37 , THR A:38 , GLY A:61 , ASN A:123 , LYS A:124 , ASP A:126 , SER A:155 , ALA A:156 , LEU A:157 , MG A:401 , HOH A:606 , HOH A:611 , HOH A:617 , HOH A:624 , HOH A:625 , HOH A:632 , HOH A:671	BINDING SITE FOR RESIDUE GNP A 402
03	AC3	SOFTWARE	LYS A:245 , TRP A:280 , C B:1533	BINDING SITE FOR RESIDUE ACT A 502
04	AC4	SOFTWARE	GLU A:208 , C B:1506 , A B:1507 , G B:1530 , A B:1531	BINDING SITE FOR RESIDUE ACT A 503
05	AC5	SOFTWARE	ALA A:95	BINDING SITE FOR RESIDUE ACT A 505
06	AC6	SOFTWARE	GLU A:64	BINDING SITE FOR RESIDUE ACT A 506
07	AC7	SOFTWARE	ARG A:295	BINDING SITE FOR RESIDUE MRD A 507
08	AC8	SOFTWARE	HIS A:142 , THR A:149 , G B:1516	BINDING SITE FOR RESIDUE MRD A 508
09	AC9	SOFTWARE	G B:1511 , U B:1512 , U B:1522 , G B:1523	BINDING SITE FOR RESIDUE CA B 501
10	BC1	SOFTWARE	A B:1531 , U B:1532	BINDING SITE FOR RESIDUE ACT B 504

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_ERA	PS51713	Era-type guanine nucleotide-binding (G) domain profile.	ERA_AQUAE	2-175	1	A:2-175
2	KH_TYPE_2	PS50823	Type-2 KH domain profile.	ERA_AQUAE	206-285	1	A:206-285

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_ERA	PS51713	Era-type guanine nucleotide-binding (G) domain profile.	ERA_AQUAE	2-175	1	A:2-175
2	KH_TYPE_2	PS50823	Type-2 KH domain profile.	ERA_AQUAE	206-285	1	A:206-285

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_ERA	PS51713	Era-type guanine nucleotide-binding (G) domain profile.	ERA_AQUAE	2-175	2	A:2-175
2	KH_TYPE_2	PS50823	Type-2 KH domain profile.	ERA_AQUAE	206-285	2	A:206-285

Exons (0, 0)

Sequences/Alignments

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:302
 aligned with ERA_AQUAE | O67800 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:302
                             1                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299  
           ERA_AQUAE      - -MKVGYVAIVGKPNVGKSTLLNNLLGTKVSIISPKAGTTRMRVLGVKNIPNEAQIIFLDTPGIYEPKKSDVLGHSMVEIAKQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPLNKPVIVVINKIDKIGPAKNVLPLIDEIHKKHPELTEIVPISALKGANLDELVKTILKYLPEGEPLFPEDMITDLPLRLLAAEIVREKAMMLTREEVPTSIAVKINEIKPGDANPNMLVIKGEIIVDRENLKPIIIGKKGQRLKEIGKRARQELELILGRPVYLELWVKVVPDWRRRPEYVRLFGYAL  301
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----MMR_HSR1-3r9wA02 A:5-124                                                                                                ------------------------------------------------------------------------------------KH_2-3r9wA01 A:209-288                                                          ------------- Pfam domains
         Sec.struct. author ..eeeeeeee.....hhhhhhhhhhh................eeeeeee...eeeeeee..........hhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeehhhhh.hhhhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh...hhhhhheeeeeeeee.......eeeeeeeee...hhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeeeeeeee..hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --G_ERA  PDB: A:2-175 UniProt: 2-175                                                                                                                                            ------------------------------KH_TYPE_2  PDB: A:206-285 UniProt: 206-285                                      ---------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3r9w A    0 HMKVGYVAIVGKPNVGKSTLLNNLLGTKVSIISPKAGTTRMRVLGVKNIPNEAQIIFLDTPGIYEPKKSDVLGHSMVEIAKQSLEEADVILFMIDATEGWRPRDEEIYQNFIKPLNKPVIVVINKIDKIGPAKNVLPLIDEIHKKHPELTEIVPISALKGANLDELVKTILKYLPEGEPLFPEDMITDLPLRLLAAEIVREKAMMLTREEVPTSIAVKINEIKPGDANPNMLVIKGEIIVDRENLKPIIIGKKGQRLKEIGKRARQELELILGRPVYLELWVKVVPDWRRRPEYVRLFGYAL  301
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299

Chain B from PDB  Type:RNA  Length:34
                                                                   
                3r9w B 1506 CAACCGUAGGGGAACCUGCGGUUGGAUCACCUCC 1539
                                  1515      1525      1535

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (12, 12)

Asymmetric Unit(hide GO term definitions)

Chain A (ERA_AQUAE | O67800)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	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.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0070181	small ribosomal subunit rRNA binding	Interacting selectively and non-covalently with the small ribosomal subunit RNA (SSU rRNA), a constituent of the small ribosomal subunit. In S. cerevisiae, this is the 18S rRNA.
biological process
	GO:0042274	ribosomal small subunit biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
	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: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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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