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(-) Description

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 (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)

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentG DOMAIN, RESIDUES 1-296
    Organism ScientificTHERMUS AQUATICUS
    Organism Taxid271
    SynonymFIFTY-FOUR HOMOLOG

 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  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL4Ligand/IonCHLORIDE ION
3MN2Ligand/IonMANGANESE (II) ION
4MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION
4MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MN-1Ligand/IonMANGANESE (II) ION
4MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:109 , ASP A:219 , HOH A:2137 , HOH A:2248 , HOH A:2252BINDING SITE FOR RESIDUE CL A1299
02AC2SOFTWAREALA 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 ACT A1300
03AC3SOFTWAREGLN B:107 , ARG B:138 , LEU B:192BINDING SITE FOR RESIDUE CL A1301
04AC4SOFTWAREARG A:138 , LEU A:192BINDING SITE FOR RESIDUE CL A1302
05AC5SOFTWAREGLU A:46 , GLU A:207 , HOH A:2310 , HOH A:2311 , HOH A:2312BINDING SITE FOR RESIDUE MN A1400
06AC6SOFTWARELYS B:206 , ARG B:260 , HOH B:2182 , HOH B:2185 , HOH B:2218BINDING SITE FOR RESIDUE CL B1298
07AC7SOFTWAREALA B:133 , ALA B:134 , ASP B:135 , ARG B:142 , LEU B:145 , ASP B:187 , THR B:188BINDING SITE FOR RESIDUE ACT B1302
08AC8SOFTWAREGLU B:46 , GLU B:207 , HOH B:2245 , HOH B:2246 , HOH B:2247BINDING SITE FOR RESIDUE MN B1400
09AC9SOFTWAREALA A:81 , GLU A:84 , ARG A:169 , GLU A:207 , VAL A:208 , HOH A:2305 , HOH A:2306 , HOH A:2307 , HOH A:2308 , HOH A:2309BINDING SITE FOR RESIDUE MRD A1297
10BC1SOFTWAREGLU B:280 , PRO B:281 , TYR B:283 , ARG B:286 , LEU B:287 , ARG B:290 , HOH B:2244BINDING SITE FOR RESIDUE MRD B1299

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J46)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J46)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J46)

(-) 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 2J46)

(-) 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:296
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:296
                                    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 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 296
               SCOP domains d2j46a1 A:1-88 Signal sequence recognition protein Ffh                                  d2j46a2 A:89-296 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------2j46A02 A:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          --------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh............eeeeee.hhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ----------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j46 A   1 MFQQLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGMGD 296
                                    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 d2j46b1 B:1-88 Signal sequence recognition protein Ffh                                  d2j46b2 B:89-297 GTPase domain of the signal sequence recognition protein Ffh                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------2j46B02 B:91-281 P-loop containing nucleotide triphosphate hydrolases                                                                                                                          ---------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh............eeeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhh..eeeee.......eee.hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j46 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J46)

(-) 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 | O073471ffh 1jpj 1jpn 1ls1 1ng1 1o87 1okk 1rj9 1ry1 2c03 2c04 2cnw 2ffh 2iy3 2j45 2j7p 2ng1 2xkv 3ng1 3zn8

(-) Related Entries Specified in the PDB File

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
2j45 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