1DUL | PR0021 - JenaLib

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Asym./Biol. Unit - sites (Jmol Viewer)

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

Authors :   R. T. Batey, R. P. Rambo, L. Lucast, B. Rha, J. Doudna

Date :   17 Jan 00 (Deposition) - 28 Feb 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Protein-Rna Complex, Double Helix, Tetraloop, Internal Loop, Signal Recognition Particle, Srp, Ribonucleoprotein, Signaling Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. T. Batey, R. P. Rambo, L. Lucast, B. Rha, J. A. Doudna
Crystal Structure Of The Ribonucleoprotein Core Of The Signal Recognition Particle.
Science V. 287 1232 2000
PubMed-ID: 10678824 | Reference-DOI: 10.1126/SCIENCE.287.5456.1232
(for further references see the PDB file header)

Molecule 1 - 4.5 S RNA DOMAIN IV
	Chains	:	B
	Engineered	:	YES
	Fragment	:	4.5S RNA FRAGMENT (RESIDUES 32-74)
	Mutation	:	YES
	Synthetic	:	YES

Molecule 2 - SIGNAL RECOGNITION PARTICLE PROTEIN (FIFTY-FOUR HOMOLOG)
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	C TERMINAL DOMAIN (RESIDUES 328-432)
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	FFH-M DOMAIN, P48

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 16)

No.	Name	Count	Type	Full Name
1	CCC	1	Mod. Nucleotide	CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2	K	3	Ligand/Ion	POTASSIUM ION
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	U B:146 , C B:147 , A B:164 , G B:165 , HOH B:816 , HOH B:842	BINDING SITE FOR RESIDUE K B 701
2	AC2	SOFTWARE	U B:135 , G B:136 , U B:137 , HOH B:833 , HOH B:855 , HOH B:893 , HOH B:908 , HOH B:1028	BINDING SITE FOR RESIDUE K B 702
3	AC3	SOFTWARE	GLY A:57 , G B:149 , G B:150 , G B:162 , C B:163	BINDING SITE FOR RESIDUE K B 703
4	AC4	SOFTWARE	HOH B:810 , HOH B:820 , HOH B:826 , HOH B:832 , HOH B:881 , HOH B:882	BINDING SITE FOR RESIDUE MG B 801
5	AC5	SOFTWARE	C B:141 , HOH B:817 , HOH B:845 , HOH B:883 , HOH B:884 , HOH B:885	BINDING SITE FOR RESIDUE MG B 802
6	AC6	SOFTWARE	G B:149 , HOH B:806 , HOH B:886 , HOH B:887 , HOH B:888 , HOH B:889	BINDING SITE FOR RESIDUE MG B 803
7	AC7	SOFTWARE	HOH B:835 , HOH B:865 , HOH B:870 , HOH B:890 , HOH B:891 , HOH B:892	BINDING SITE FOR RESIDUE MG B 804

(no "SS Bond" information available for 1DUL)

(no "Cis Peptide Bond" information available for 1DUL)

(no "SAP(SNP)/Variant" information available for 1DUL)

(no "PROSITE Motif" information available for 1DUL)

(no "Exon" information available for 1DUL)

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
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Chain A from PDB  Type:PROTEIN  Length:69
 aligned with SRP54_ECO57 | P0AGD9 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:102
                                   338       348       358       368       378       388       398       408       418       428  
          SRP54_ECO57   329 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKM 430
               SCOP domains d1dula_ A                                 : Signal sequence binding protein Ffh                        SCOP domains
               CATH domains 1dulA00 A                                 :1-81  [code=1.10.260.30, no name defined]                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh---------------------------------hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1dul 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 A from PDB  Type:PROTEIN  Length:69
 aligned with SRP54_ECOL6 | P0AGD8 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:102
                                   338       348       358       368       378       388       398       408       418       428  
          SRP54_ECOL6   329 FDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKM 430
               SCOP domains d1dula_ A                                 : Signal sequence binding protein Ffh                        SCOP domains
               CATH domains 1dulA00 A                                 :1-81  [code=1.10.260.30, no name defined]                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh---------------------------------hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1dul 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 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 d1dula_ A                                 : Signal sequence binding protein Ffh                        SCOP domains
               CATH domains 1dulA00 A                                 :1-81  [code=1.10.260.30, no name defined]                 - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh---------------------------------hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1dul 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
                                                                                 
                 1dul B 130 GGCUCUGUUUACCAGGUCAGGUCCGAAAGGAAGCAGCCAAGGCAGAGCc 178
                                   139       149       159       169        |
                                                                          178-CCC

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: All alpha proteins (14657)

Fold: Signal peptide-binding domain (20)

Superfamily: Signal peptide-binding domain (20)

Family: Signal peptide-binding domain (20)

Protein domain: Signal sequence binding protein Ffh (17)

Escherichia coli [TaxId: 562] (14)

d1dula_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: 434 Repressor (Amino-terminal Domain) (116)

Homologous Superfamily: [code=1.10.260.30, no name defined] (16)

[unclassified] (3)

1dulA00

A:1-81

(no "Pfam Domain" information available for 1DUL)

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.

Chain A (SRP54_ECO57 | P0AGD9)

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: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.

Chain A (SRP54_ECOL6 | P0AGD8)

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: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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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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