2J45 - JenaLib

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Title :   WATER STRUCTURE OF T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION

Authors :   D. M. Freymann, U. D. Ramirez

Date :   24 Aug 06 (Deposition) - 30 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.14

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

Keywords :   Ribonucleoprotein, Nucleotide-Binding, Srp, Ffh, Water, Gtpase, Rna-Binding, Gtp-Binding, Signal Recognition Particle, Nucleotide Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. D. Ramirez, D. M. Freymann
Analysis Of Protein Hydration In Ultra-High Resolution Structures Of The Srp Gtpase Ffh
Acta Crystallogr. , Sect. D V. 62 1520 2006
PubMed-ID: 17139088 | Reference-DOI: 10.1107/S0907444906040807
(for further references see the PDB file header)

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	G DOMAIN, RESIDUES 1-296
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271
	Synonym	:	FIFTY-FOUR HOMOLOG

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 9)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MES	3	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MRD	2	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	MRD	1	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:110 , THR A:112 , THR A:113 , MES A:1303 , HOH A:2238 , HOH A:2476	BINDING SITE FOR RESIDUE NA A1299
2	AC2	SOFTWARE	GLU A:46 , GLU A:207 , HOH A:2350 , GLU B:72 , HOH B:2156 , HOH B:2157	BINDING SITE FOR RESIDUE CA A1401
3	AC3	SOFTWARE	HOH A:2456 , HOH A:2459 , GLU B:46 , GLU B:207 , HOH B:2306 , HOH B:2307	BINDING SITE FOR RESIDUE CA B1401
4	AC4	SOFTWARE	LYS A:151 , PRO A:276 , HOH A:2249 , HOH A:2465	BINDING SITE FOR RESIDUE MRD A1300
5	AC5	SOFTWARE	ARG A:146 , VAL A:156 , LEU A:157 , GLU A:158 , HOH A:2467 , HOH A:2468 , HOH A:2469 , HOH A:2470 , HOH A:2471 , HOH A:2472 , ARG B:19	BINDING SITE FOR RESIDUE MES A1302
6	AC6	SOFTWARE	GLN A:107 , GLY A:108 , LYS A:111 , THR A:112 , ALA A:141 , GLN A:144 , GLY A:190 , NA A:1299 , HOH A:2186 , HOH A:2240 , HOH A:2473 , HOH A:2474 , HOH A:2475 , HOH A:2476 , HOH A:2477 , HOH A:2478	BINDING SITE FOR RESIDUE MES A1303
7	AC7	SOFTWARE	LEU B:247 , TYR B:283 , ARG B:286 , LEU B:287 , ARG B:290 , HOH B:2393 , HOH B:2394	BINDING SITE FOR RESIDUE MRD B1298
8	AC8	SOFTWARE	GLN B:107 , GLY B:108 , SER B:109 , GLY B:110 , LYS B:111 , THR B:112 , THR B:113 , GLN B:144 , HOH B:2195 , HOH B:2419	BINDING SITE FOR RESIDUE MES B1299
9	AC9	SOFTWARE	GLU A:285 , HOH A:2448 , ARG B:35 , ARG B:49 , VAL B:52 , HOH B:2128 , HOH B:2420 , HOH B:2422	BINDING SITE FOR RESIDUE EDO B1300

(no "SS Bond" information available for 2J45)

(no "Cis Peptide Bond" information available for 2J45)

(no "SAP(SNP)/Variant" information available for 2J45)

Asymmetric 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	2	A:266-279 B:266-279

Biological Unit 1 (1, 1)

	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	A:266-279 -

Biological Unit 2 (1, 1)

	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

(no "Exon" information available for 2J45)

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:297
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:297
                                    10        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       
          SRP54_THEAQ     1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDV 297
               SCOP domains d2j45a1 A:1-88 Signal sequence recognition protein Ffh                                  d2j45a2 A:89-297 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------2j45A02 A:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          ---------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh............eeeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhh..eeeee...hhh.eee.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j45 A   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDV 297
                                    10        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

Chain B from PDB  Type:PROTEIN  Length:297
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:297
                                    10        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       
          SRP54_THEAQ     1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDV 297
               SCOP domains d2j45b1 B:1-88 Signal sequence recognition protein Ffh                                  d2j45b2 B:89-297 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------2j45B02 B:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          ---------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j45 B   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDV 297
                                    10        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

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: 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	2j45A02	A:91-281
1b	2j45B02	B:91-281

(no "Pfam Domain" information available for 2J45)

Asymmetric Unit(hide GO term definitions)

Chain A,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 Unit
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	2j45
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1ffh	N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITIONPROTEIN FFH FROM THERMUS AQUATICUS
1jpj	GMPPNP COMPLEX OF SRP GTPASE NG DOMAIN
1jpn	GMPPNP COMPLEX OF SRP GTPASE NG DOMAIN
1ls1	T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION
1ng1	N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITIONPROTEIN FFH FROM THERMUS AQUATICUS
1o87	A NEW MGGDP COMPLEX OF THE FFH NG DOMAIN
1okk	A SCARILY SYMMETRIC HOMO-HETERODIMER
1rj9	STRUCTURE OF THE HETERODIMER OF THE CONSERVED GTPASEDOMAINS OF THE SIGNAL RECOGNITION PARTICLE (FFH) AND ITSRECEPTOR ( FTSY)
1ry1	STRUCTURE OF THE SIGNAL RECOGNITION PARTICLE INTERACTINGWITH THE ELONGATION-ARRESTED RIBOSOME
2c03	GDP COMPLEX OF SRP GTPASE FFH NG DOMAIN
2c04	GMPPCP COMPLEX OF SRP GTPASE FFH NG DOMAIN AT ULTRA-HIGH RESOLUTION
2cnw	GDPALF4 COMPLEX OF THE SRP GTPASES FFH AND FTSY
2ffh	THE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUSAQUATICUS
2j46	WATER STRUCTURE OF T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION
2ng1	N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITIONPROTEIN FFH FROM THERMUS AQUATICUS
3ng1	N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITIONPROTEIN FFH FROM THERMUS AQUATICUS

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (9, 9)

SS Bonds (0, 0)

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PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (2, 4)

CATH Domains (1, 2)

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Gene Ontology (11, 11)

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