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(-) Description

Title :  N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS
 
Authors :  D. M. Freymann, R. M. Stroud, P. Walter
Date :  13 Sep 98  (Deposition) - 30 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ffh, Srp, Gtpase, Signal Recognition Particle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Freymann, R. J. Keenan, R. M. Stroud, P. Walter
Functional Changes In The Structure Of The Srp Gtpase On Binding Gdp And Mg2+Gdp.
Nat. Struct. Biol. V. 6 793 1999
PubMed-ID: 10426959  |  Reference-DOI: 10.1038/11572
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGNAL SEQUENCE RECOGNITION PROTEIN FFH
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3C
    Expression System Strain: BL21 (DE3) PLYSE
    Expression System Taxid: 562
    Fragment: NG GTPASE FRAGMENT
    Gene: FFH
    Organism Scientific: THERMUS AQUATICUS
    Organism Taxid: 271
    Synonym: FFH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1CD6Ligand/IonCADMIUM ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01A1UNKNOWNGLY A:105 , LEU A:106 , GLN A:107 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112GTPASE BINDING SITE MOTIF.
02A2UNKNOWNASP A:135 , THR A:136 , GLN A:137 , ARG A:138 , PRO A:139 , ALA A:140 , ALA A:141GTPASE BINDING SITE MOTIF.
03A3UNKNOWNASP A:187 , THR A:188 , ALA A:189 , GLY A:190 , ARG A:191 , LEU A:192GTPASE BINDING SITE MOTIF.
04A4UNKNOWNTHR A:245 , LYS A:246 , LEU A:247 , ASP A:248GTPASE BINDING SITE MOTIF.
05AC1SOFTWAREGLU A:11 , GLU A:33 , GLU B:46 , ASP B:50BINDING SITE FOR RESIDUE CD A 701
06AC2SOFTWAREGLU A:285BINDING SITE FOR RESIDUE CD A 702
07AC3SOFTWAREHIS A:261BINDING SITE FOR RESIDUE CD A 703
08AC4SOFTWAREGLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , THR A:113 , GLN A:144BINDING SITE FOR RESIDUE SO4 A 750
09AC5SOFTWAREGLU A:46 , ASP A:50 , GLU B:11 , GLU B:33BINDING SITE FOR RESIDUE CD B 701
10AC6SOFTWAREGLU B:285BINDING SITE FOR RESIDUE CD B 702
11AC7SOFTWAREHIS B:261BINDING SITE FOR RESIDUE CD B 703
12AC8SOFTWAREGLY B:108 , SER B:109 , GLY B:110 , LYS B:111 , THR B:112 , THR B:113 , GLN B:144BINDING SITE FOR RESIDUE SO4 B 750
13AC9SOFTWAREGLY A:105 , LEU A:106 , GLY A:190 , ARG A:191 , GLN A:193 , ASP A:195 , MET A:199BINDING SITE FOR RESIDUE EDO A 970
14B1UNKNOWNGLY B:105 , LEU B:106 , GLN B:107 , GLY B:108 , SER B:109 , GLY B:110 , LYS B:111 , THR B:112GTPASE BINDING SITE MOTIF.
15B2UNKNOWNASP B:135 , THR B:136 , GLN B:137 , ARG B:138 , PRO B:139 , ALA B:140 , ALA B:141GTPASE BINDING SITE MOTIF.
16B3UNKNOWNASP B:187 , THR B:188 , ALA B:189 , GLY B:190 , ARG B:191 , LEU B:192GTPASE BINDING SITE MOTIF.
17B4UNKNOWNTHR B:245 , LYS B:246 , LEU B:247 , ASP B:248GTPASE BINDING SITE MOTIF.
18BC1SOFTWAREALA A:133 , ALA A:134 , ASP A:135 , ALA A:141 , ARG A:142 , LEU A:145 , ASP A:187 , THR A:188BINDING SITE FOR RESIDUE EDO A 971
19BC2SOFTWAREGLY B:105 , LEU B:106 , GLY B:190 , ARG B:191 , GLN B:193 , ASP B:195 , MET B:199BINDING SITE FOR RESIDUE EDO B 970
20BC3SOFTWAREALA B:133 , ALA B:134 , ASP B:135 , ALA B:141 , ARG B:142 , LEU B:145 , ASP B:187 , THR B:188BINDING SITE FOR RESIDUE EDO B 971

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NG1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NG1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NG1)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRP54PS00300 SRP54-type proteins GTP-binding domain signature.SRP54_THEAQ266-279
 		  2A:266-279
B:266-279
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRP54PS00300 SRP54-type proteins GTP-binding domain signature.SRP54_THEAQ266-279
 		  1A:266-279
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRP54PS00300 SRP54-type proteins GTP-binding domain signature.SRP54_THEAQ266-279
 		  1-
B:266-279

(-) Exons   (0, 0)

(no "Exon" information available for 3NG1)

(-) Sequences/Alignments

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:294
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:294
                                    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 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 294
               SCOP domains d3ng1a1 A:1-88 Signal sequence recognition protein Ffh                                  d3ng1a2 A:89-294 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                  SCOP domains
               CATH domains -3ng1A01 A:2-90  [code=1.20.120.140, no name defined]                                     3ng1A02 A:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          ------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh............eeeeee......hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhh...eeeee.......eee..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ng1 A   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 294
                                    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:294
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:294
                                    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 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 294
               SCOP domains d3ng1b1 B:1-88 Signal sequence recognition protein Ffh                                  d3ng1b2 B:89-294 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                  SCOP domains
               CATH domains -3ng1B01 B:2-90  [code=1.20.120.140, no name defined]                                     3ng1B02 B:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          ------------- CATH domains
           Pfam domains (1) ----SRP54_N-3ng1B03 B:5-82                                                        ---------------SRP54-3ng1B01 B:98-293                                                                                                                                                                              - Pfam domains (1)
           Pfam domains (2) ----SRP54_N-3ng1B04 B:5-82                                                        ---------------SRP54-3ng1B02 B:98-293                                                                                                                                                                              - Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh............eeeeee......hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhh...eeeee.......eee..hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         --------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ng1 B   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 294
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: SRP54 (20)
(-)
Thermus aquaticus (12)
1aSRP54-3ng1B01B:98-293
1bSRP54-3ng1B02B:98-293
(-)
Clan: no clan defined [family: SRP54_N] (20)

(-) Gene Ontology  (11, 11)

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SRP54_THEAQ | O07347: 1ffh 1jpj 1jpn 1ls1 1ng1 1o87 1okk 1rj9 1ry1 2c03 2c04 2cnw 2ffh 2iy3 2j45 2j46 2j7p 2ng1 2xkv 3zn8

(-) Related Entries Specified in the PDB File

1ffh APO-NG STRUCTURE
1ng1 NG GTPASE WITH BOUND MGGDP
2ng1 NG GTPASE WITH BOUND GDP