2PXF - JenaLib

Title :   VARIANT 5 OF RIBONUCLEOPROTEIN CORE OF THE E. COLI SIGNAL RECOGNITION PARTICLE

Authors :   A. Y. Keel, R. P. Rambo, R. T. Batey, J. S. Kieft

Date :   14 May 07 (Deposition) - 07 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Gu Pair, Hexamine, Rna Phasing, Rna, Cation Binding, Signaling Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Y. Keel, R. P. Rambo, R. T. Batey, J. S. Kieft
A General Strategy To Solve The Phase Problem In Rna Crystallography.
Structure V. 15 761 2007
PubMed-ID: 17637337 | Reference-DOI: 10.1016/J.STR.2007.06.003
(for further references see the PDB file header)

Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(PLYSS)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C TERMINAL DOMAIN (RESIDUES 328-432)
	Gene	:	FFH
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	FIFTY-FOUR HOMOLOG, P48

Molecule 2 - 4.5 S RNA
	Chains	:	B
	Engineered	:	YES
	Fragment	:	DOMAIN IV
	Mutation	:	YES
	Other Details	:	SYNTHETIC
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 15)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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

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Chain A from PDB  Type:PROTEIN  Length:69
 aligned with SRP54_ECOLI | P0AGD7 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:102
                                   338       348       358       368       378       388       398       408       418       428  
          SRP54_ECOLI   329 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKM 430
               SCOP domains d2pxfa_ A                                 : Signal sequence binding protein Ffh                        SCOP domains
               CATH domains 2pxfA00 A                                 :1-81  [code=1.10.260.30, no name defined]                 - CATH domains
               Pfam domains SRP_SPB-2                                 pxfA01 A:1-79                                            --- Pfam domains
         Sec.struct. author .hhhhhhhh---------------------------------.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2pxf A   1 FDLNDFLEQ---------------------------------KVLVRmEAIINSmTmKERAKPEIIKGSRKRRIAAGSGmQVQDVNRLLKQFDDmQRmmKKm  82
                                    |-         -         -         -  |    |30    | | 40        50        60        70    |  |80 |
                                    9                                23    |     35-MSE                   60-MSE         75-MSE  |
                                                                          28-MSE   37-MSE                                   78-MSE
                                                                                                                             79-MSE
                                                                                                                                82-MSE

Chain B from PDB  Type:RNA  Length:49
                                                                                 
                 2pxf B 130 GGGGGUGUUUACCAGGUCAGGUCCGAAAGGAAGCAGCCAAGGCACUUCC 178
                                   139       149       159       169

Legend:		→ Mismatch	(orange background)
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	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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (SRP54_ECOLI | P0AGD7)

molecular function
	GO:0008312	7S RNA binding	Interacting selectively and non-covalently with 7S RNA, the RNA component of the signal recognition particle (SRP).
	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.
biological process
	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	The targeting of proteins to a membrane that occurs during translation and is dependent upon two key components, the signal-recognition particle (SRP) and the SRP receptor. SRP is a cytosolic particle that transiently binds to the endoplasmic reticulum (ER) signal sequence in a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
	GO:0006612	protein targeting to membrane	The process of directing proteins towards a membrane, usually using signals contained within the protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0048500	signal recognition particle	A complex of protein and RNA which facilitates translocation of proteins across membranes.

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