2C03 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   GDP COMPLEX OF SRP GTPASE FFH NG DOMAIN

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

Date :   25 Aug 05 (Deposition) - 13 Feb 07 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.24

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

Keywords :   Ffh, Gmppnp, Gtp-Binding, Ng Domain, Rna-Binding, Signaling Protein, Srp54 Nucleotide-Binding, Signal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   U. D. Ramirez, P. J. Focia, D. M. Freymann
Nucleotide-Binding Flexibility In Ultrahigh- Resolution Structures Of The Srp Gtpase Ffh
Acta Crystallogr. , Sect. D V. 64 1043 2008
PubMed-ID: 18931411 | Reference-DOI: 10.1107/S090744490802444X

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	NG, 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 (3, 19)

No.	Name	Count	Type	Full Name
1	DIO	14	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	DIO	7	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	DIO	7	Ligand/Ion	1,4-DIETHYLENE DIOXIDE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:106 , GLN A:107 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , THR A:113 , GLN A:144 , LYS A:246 , ASP A:248 , GLY A:271 , VAL A:272 , SER A:273 , GLU A:274 , HOH A:2271 , HOH A:2273 , HOH A:2275 , HOH A:2288 , HOH A:2289 , HOH A:2291 , HOH A:2292 , HOH A:2293 , GLN B:3	BINDING SITE FOR RESIDUE GDP A1296
02	AC2	SOFTWARE	LYS A:62 , SER A:67 , VAL A:73 , HOH A:2295	BINDING SITE FOR RESIDUE EDO A1297
03	AC3	SOFTWARE	GLY A:105 , ALA A:189 , ARG A:191 , GLN A:193 , ASP A:195 , LEU A:198 , MET A:199 , PHE A:233 , HOH A:2204 , HOH A:2205	BINDING SITE FOR RESIDUE DIO A1298
04	AC4	SOFTWARE	LEU A:148 , LYS A:151 , HOH A:2149 , GLN B:3 , SER B:6	BINDING SITE FOR RESIDUE DIO A1299
05	AC5	SOFTWARE	GLN A:4 , ASP A:250 , HOH A:2003 , ARG B:128 , ALA B:180	BINDING SITE FOR RESIDUE DIO A1300
06	AC6	SOFTWARE	MET A:221 , ASP A:250 , LEU B:178 , ALA B:180	BINDING SITE FOR RESIDUE DIO A1301
07	AC7	SOFTWARE	LEU A:38 , VAL A:47 , PHE A:51 , LEU A:82 , ALA A:85 , LEU A:257 , SER A:258	BINDING SITE FOR RESIDUE DIO A1302
08	AC8	SOFTWARE	LYS A:117 , LEU A:148 , GLU A:274 , PRO A:276	BINDING SITE FOR RESIDUE DIO A1303
09	AC9	SOFTWARE	ALA A:270 , GLU A:280 , PRO A:281 , TYR A:283	BINDING SITE FOR RESIDUE DIO A1304
10	BC1	SOFTWARE	GLN B:107 , GLY B:108 , SER B:109 , GLY B:110 , THR B:112 , THR B:113 , LYS B:117 , GLN B:144 , LYS B:246 , ASP B:248 , GLY B:271 , VAL B:272 , SER B:273 , GLU B:274 , HOH B:2138 , HOH B:2140 , HOH B:2306 , HOH B:2328 , HOH B:2330 , HOH B:2332 , HOH B:2333 , HOH B:2334 , HOH B:2335 , HOH B:2338	BINDING SITE FOR RESIDUE GDP B1297
11	BC2	SOFTWARE	GLU B:84 , GLY B:87 , GLY B:88 , GLY B:210 , PRO B:211 , ASP B:212 , ARG B:260 , HIS B:261 , HOH B:2110 , HOH B:2253 , HOH B:2254	BINDING SITE FOR RESIDUE EDO B1298
12	BC3	SOFTWARE	LYS B:151 , ARG B:191 , LEU B:192 , GLN B:193 , HOH B:2339 , HOH B:2340	BINDING SITE FOR RESIDUE EDO B1299
13	BC4	SOFTWARE	GLU B:280 , PRO B:281 , PHE B:282 , TYR B:283	BINDING SITE FOR RESIDUE DIO B1300
14	BC5	SOFTWARE	GLN B:107 , ALA B:141 , HOH B:2330 , HOH B:2341	BINDING SITE FOR RESIDUE DIO B1301
15	BC6	SOFTWARE	ARG B:49 , ASP B:50 , ARG B:204	BINDING SITE FOR RESIDUE DIO B1302
16	BC7	SOFTWARE	VAL B:47 , PHE B:51 , HIS B:261	BINDING SITE FOR RESIDUE DIO B1303
17	BC8	SOFTWARE	GLY B:105 , ALA B:189 , GLY B:190 , ARG B:191 , GLN B:193 , ASP B:195 , PHE B:233 , HOH B:2230	BINDING SITE FOR RESIDUE DIO B1304
18	BC9	SOFTWARE	ASP B:234 , GLU B:235 , LYS B:236 , VAL B:237 , GLY B:238 , VAL B:262 , THR B:263 , HOH B:2342	BINDING SITE FOR RESIDUE DIO B1305
19	CC1	SOFTWARE	ARG B:56 , GLU B:57 , ARG B:170	BINDING SITE FOR RESIDUE DIO B1306

(no "SS Bond" information available for 2C03)

(no "Cis Peptide Bond" information available for 2C03)

(no "SAP(SNP)/Variant" information available for 2C03)

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 2C03)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:295
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:295
                                    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 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 295
               SCOP domains d2c03a1 A:1-88 automated matches                                                        d2c03a2 A:89-295 automated matches                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh............eeeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c03 A   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMG 295
                                    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 d2c03b1 B:1-88 automated matches                                                        d2c03b2 B:89-297 automated matches                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.............eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c03 B   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVTRDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGDV 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 '\|'

(no "CATH Domain" information available for 2C03)

(no "Pfam Domain" information available for 2C03)

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.

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(no "Cis Peptide Bonds" information available for 2c03)

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	2c03
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1ffh	N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN 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 RECOGNITION PROTEIN 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 GTPASE DOMAINS OF THE SIGNAL RECOGNITION PARTICLE (FFH) AND ITS RECEPTOR (FTSY)
1ry1	STRUCTURE OF THE SIGNAL RECOGNITION PARTICLE INTERACTING WITH THE ELONGATION-ARRESTED RIBOSOME
2bqs	WATER STRUCTURE OF T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION
2bqt	WATER STRUCTURE OF T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION
2c04	GMPPCP COMPLEX OF SRP GTPASE FFH NG DOMAIN AT ULTRA-HIGH RESOLUTION
2ffh	THE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUS AQUATICUS
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

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Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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PROSITE Motifs (1, 2)

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SCOP Domains (2, 4)

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Gene Ontology (11, 11)

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