1RJ9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF THE HETERODIMER OF THE CONSERVED GTPASE DOMAINS OF THE SIGNAL RECOGNITION PARTICLE (FFH) AND ITS RECEPTOR (FTSY)

Authors :   P. F. Egea, S. O. Shan, J. Napetschnig, D. F. Savage, P. Walter, R. M. Stro

Date :   18 Nov 03 (Deposition) - 27 Jan 04 (Release) - 09 Jun 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Srp-Gtpase Domain, Heterodimer, Nucleotide Twinning, Protein-Protein Complex, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. F. Egea, S. O. Shan, J. Napetschnig, D. F. Savage, P. Walter, R. M. Stroud
Substrate Twinning Activates The Signal Recognition Particle And Its Receptor
Nature V. 427 215 2004
PubMed-ID: 14724630 | Reference-DOI: 10.1038/NATURE02250

Molecule 1 - SIGNAL RECOGNITION PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28B
	Expression System Strain	:	BL21(DE3) ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Synonym	:	FTSY

Molecule 2 - SIGNAL RECOGNITION PARTICLE PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28B
	Expression System Strain	:	BL21(DE3) ROSETTA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NG DOMAIN (RESIDUES 1-300)
	Gene	:	FFH
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Synonym	:	FIFTY-FOUR HOMOLOG, FFH

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GCP	2	Ligand/Ion	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:116 , GCP A:500 , HOH A:701 , HOH A:702 , HOH A:703	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	THR B:112 , GCP B:600 , HOH B:704 , HOH B:705 , HOH B:706	BINDING SITE FOR RESIDUE MG B 601
3	AC3	SOFTWARE	ASN A:111 , GLY A:112 , VAL A:113 , GLY A:114 , LYS A:115 , THR A:116 , THR A:117 , LYS A:121 , ASP A:139 , ARG A:142 , GLN A:148 , GLY A:194 , LYS A:256 , ASP A:258 , GLY A:281 , VAL A:282 , GLY A:283 , GLU A:284 , MG A:501 , HOH A:702 , HOH A:713 , HOH A:722 , HOH A:749 , GLN B:107 , ARG B:138 , GCP B:600 , HOH B:718	BINDING SITE FOR RESIDUE GCP A 500
4	AC4	SOFTWARE	ASN A:111 , ARG A:142 , LEU A:196 , GCP A:500 , GLN B:107 , GLY B:108 , SER B:109 , GLY B:110 , LYS B:111 , THR B:112 , THR B:113 , LYS B:117 , ASP B:135 , ARG B:138 , GLN B:144 , GLY B:190 , LYS B:246 , ASP B:248 , GLY B:271 , VAL B:272 , SER B:273 , GLU B:274 , MG B:601 , HOH B:705 , HOH B:707 , HOH B:718 , HOH B:719 , HOH B:727 , HOH B:760	BINDING SITE FOR RESIDUE GCP B 600

(no "SS Bond" information available for 1RJ9)

Asymmetric/Biological Unit

No.	Residues
1	Glu A:220	-	Pro A:221

(no "SAP(SNP)/Variant" information available for 1RJ9)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	SRP54_THEAQ	266-279	1	B:266-279
1	SRP54	PS00300	SRP54-type proteins GTP-binding domain signature.	FTSY_THEAQ	276-289	1	A:276-289

(no "Exon" information available for 1RJ9)

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:277
 aligned with FTSY_THEAQ | P83749 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:277
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       
           FTSY_THEAQ    27 NLEEVLEELEMALLAADVGLSATEEILQEVRASGRKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEALLE 303
               SCOP domains d1rj9a1 A:27-95 Signal recognition particle receptor, FtsY           d1rj9a2 A:96-303 GTPase domain of the signal recognition particle receptor FtsY                                                                                                                                  SCOP domains
               CATH domains 1rj9A01 A:27-95,A:292-303  [code=1.20.120.140, no name defined]      1rj9A02 A:96-291 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               1rj9A01      CATH domains
               Pfam domains SRP54_N-1rj9A02 A:27-77                            ------------------------SRP54-1rj9A01 A:102-303                                                                                                                                                                                    Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhh......hhhhhhhhh...............eeeee.....hhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhh..ee......hhhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhh..eeeee.......eee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         -------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rj9 A  27 NLEEVLEELEMALLAADVGLSATEEILQEVRASGRKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDSAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEALLE 303
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:282
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293  
          SRP54_THEAQ    14 GRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 295
               SCOP domains d1rj9b1 B:14-88 Signal sequence recognition protein Ffh                    d1rj9b2 B:89-295 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                   SCOP domains
               CATH domains 1rj9B01 B:14-90  [code=1.20.120.140, no name defined]                        1rj9B02 B:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          -------------- CATH domains
               Pfam domains SRP54_N-1rj9B02 B:14-82                                              ---------------SRP54-1rj9B01 B:98-293                                                                                                                                                                              -- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...........eeeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhh..eeeee........hhhhhhhhhhh..eeeee.......eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rj9 B  14 GRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 295
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Thermus aquaticus. Organism_taxid: 271. (14)

1a	1rj9B02	B:91-281
1b	1rj9A02	A:96-291

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.140, no name defined] (15)

Thermus aquaticus. Organism_taxid: 271. (6)

2a	1rj9B01	B:14-90
2b	1rj9A01	A:27-95,A:292-303

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: SRP54 (20)

Thermus aquaticus (12)

1a	SRP54-1rj9A01	A:102-303
1b	SRP54-1rj9B01	B:98-293

Clan: no clan defined [family: SRP54_N] (20)

Family: SRP54_N (20)

Thermus aquaticus (12)

2a	SRP54_N-1rj9A02	A:27-77
2b	SRP54_N-1rj9B02	B:14-82

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FTSY_THEAQ | P83749)

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: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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0031226	intrinsic component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
	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.

Chain B (SRP54_THEAQ | O07347)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:220 - Pro A:221	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (4, 4)

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