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(-) Description

Title :  ATOMIC MODEL OF THE SRP-FTSY EARLY CONFORMATION
 
Authors :  L. F. Estrozi, D. Boehringer, S. -O. Shan, N. Ban, C. Schaffitzel
Date :  13 Jul 10  (Deposition) - 15 Dec 10  (Release) - 20 Mar 13  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  13.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. F. Estrozi, D. Boehringer, S. -O. Shan, N. Ban, C. Schaffitzel
Cryo-Em Structure Of The E. Coli Translating Ribosome In Complex With Srp And Its Receptor.
Nat. Struct. Mol. Biol. V. 18 88 2011
PubMed-ID: 21151118  |  Reference-DOI: 10.1038/NSMB.1952

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE PROTEIN
    Chains: A
    EC Number: 3.6.5.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: NG DOMAIN, RESIDUES 1-294
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FIFTY-FOUR HOMOLOG
 
Molecule 2 - 4.5S RNA
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: ONLY THE PART OF THE 4.5S RNA THAT IS VISIBLE IN THE EM RECONSTRUCTION IS INCLUDED
 
Molecule 3 - SIGNAL RECOGNITION PARTICLE PROTEIN
    Chains: C
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: M DOMAIN, RESIDUES 329-430
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: ONLY THE PART OF THE M DOMAIN THAT IS VISIBLE IN THE EM RECONSTRUCTION IS INCLUDED
    Synonym: FIFTY-FOUR HOMOLOG, P48
 
Molecule 4 - CELL DIVISION PROTEIN FTSY
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2XKV)

(-) Sites  (0, 0)

(no "Site" information available for 2XKV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu D:220 -Pro D:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRP54PS00300 SRP54-type proteins GTP-binding domain signature.SRP54_THEAQ266-279  1A:266-279
FTSY_THEAQ276-289  1D:276-289

(-) Exons   (0, 0)

(no "Exon" information available for 2XKV)

(-) Sequences/Alignments

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:291
 aligned with SRP54_THEAQ | O07347 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:291
                                    13        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     4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 294
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -SRP54_N-2xkvA02 A:5-82                                                        ---------------SRP54-2xkvA01 A:98-293                                                                                                                                                                              - Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...........eeeeeee....hhhhhh.hhhhhh......eeeee.........hhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhh....eeeee..........hhhhhhhhh..eeeee.......eee....hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         --------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xkv A   4 QLSARLQEAIGRLRGRGRITEEDLKATLREIRRALMDADVNLEVARDFVERVREEALGKQVLESLTPAEVILATVYEALKEALGGEARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTAGRLQIDEPLMGELARLKEVLGPDEVLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSARHVTGKPIYFAGVSEKPEGLEPFYPERLAGRILGM 294
                                    13        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 


Chain B from PDB  Type:RNA  Length:96
                                                                                                                                
                 2xkv B   6 CUCUGUUGGUUCUCUGUGCUCUGUGCUCUGUUUACCAGGUCAGGUCCGAAAGGAAGCAGCCAAGGCAGAGACGCAGAGCAGGCAGAUGUAGCUGGC 101
                                    15        25        35        45        55        65        75        85        95      


Chain C from PDB  Type:PROTEIN  Length:44
 aligned with SRP54_ECOLI | P0AGD7 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:44
                                   380       390       400       410    
          SRP54_ECOLI   371 KVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVN 414
               SCOP domains -------------------------------------------- SCOP domains
               CATH domains -------------------------------------------- CATH domains
               Pfam domains SRP_SPB-2xkvC01 C:23-66                      Pfam domains
         Sec.struct. author hhhhhhhhhhhh.hhhhhhhhhhh...hhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------- PROSITE
                 Transcript -------------------------------------------- Transcript
                 2xkv C  23 KVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGSGMQVQDVN  66
                                    32        42        52        62    


Chain D from PDB  Type:PROTEIN  Length:267
 aligned with FTSY_THEAQ | P83749 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:284
                                    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       300    
           FTSY_THEAQ    21 AIPWGGNLEEVLEELEMALLAADVGLSATEEILQEVRASGRKDLKEAVKEKLVGMLEPDERRATLRKLGFNPQKPKPVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEALLED 304
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains SRP54_N-2xkvD02 D:21-77                                  ------------------------SRP54-2xkvD01 D:102-303                                                                                                                                                                                   - Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.......hhhhhhhhhh.....hhhhhhhhhhhhhhh..-----------------.......eeeeee....hhhhhhhhhhhhh......eeee..........hhhhhhhh.....ee...........hhhhhhhhhh....eeee...............hhhhhhhhh........eeeeee......hhhhhhhhhhhhh...eeee.............hhhhhh...eeeee.......eee...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SRP54         --------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xkv D  21 AIPWGGNLEEVLEELEMALLAADVGLSATEEILQEVRASGRKDLKEAVKEKLVGMLEPD-----------------PVEPKGRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDTFRAAGGTQLSEWGKRLSIPVIQGPEGTDPAALAYDAVQAMKARGYDLLFVDTAGRLHTKHNLMEELKKVKRAIAKADPEEPKEVWLVLDAVTGQNGLEQAKKFHEAVGLTGVIVTKLDGTAKGGVLIPIVRTLKVPIKFVGVGEGPDDLQPFDPEAFVEALLED 304
                                    30        40        50        60        70        |-         -      |100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300    
                                                                                     79                97
   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  (0, 0)

(no "SCOP Domain" information available for 2XKV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: SRP54 (20)
(-)
Thermus aquaticus (12)
1aSRP54-2xkvD01D:102-303
1bSRP54-2xkvA01A:98-293
(-)
Clan: no clan defined [family: SRP54_N] (20)
(-)
Clan: no clan defined [family: SRP_SPB] (20)

(-) Gene Ontology  (15, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain C   (SRP54_ECOLI | P0AGD7)
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.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

Chain D   (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.

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    Glu D:220 - Pro D:221   [ RasMol ]  
 

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  2xkv
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  FTSY_THEAQ | P83749
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  SRP54_ECOLI | P0AGD7
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  SRP54_THEAQ | O07347
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 Related Entries

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

UniProtKB/Swiss-Prot
        FTSY_THEAQ | P83749: 1okk 1rj9 2cnw 2iyl 2j7p 2q9a 2q9b 2q9c
        SRP54_ECOLI | P0AGD7: 1dul 1hq1 2j28 2pxb 2pxd 2pxe 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv 2xxa 3lqx 4c7o 5aka 5gad 5gaf 5gag 5gah
        SRP54_THEAQ | O07347: 1ffh 1jpj 1jpn 1ls1 1ng1 1o87 1okk 1rj9 1ry1 2c03 2c04 2cnw 2ffh 2iy3 2j45 2j46 2j7p 2ng1 3ng1 3zn8

(-) Related Entries Specified in the PDB File

1dul STRUCTURE OF THE RIBONUCLEOPROTEIN CORE OF THE E. COLISIGNAL RECOGNITION PARTICLE
1ffh N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITIONPROTEIN FFH FROM THERMUS AQUATICUS
1hq1 STRUCTURAL AND ENERGETIC ANALYSIS OF RNA RECOGNITION BY AUNIVERSALLY CONSERVED PROTEIN FROM THE SIGNAL RECOGNITIONPARTICLE
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
2iy3
2iyl STRUCTURE OF AN FTSY:GDP COMPLEX
2j28 MODEL OF E. COLI SRP BOUND TO 70S RNCS
2j45 WATER STRUCTURE OF T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION
2j46 WATER STRUCTURE OF T. AQUATICUS FFH NG DOMAIN AT 1.1A RESOLUTION
2j7p GMPPNP-STABILIZED NG DOMAIN COMPLEX OF THE SRP GTPASES FFH AND FTSY
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 RELATED ID: EMD-1762 RELATED DB: EMDB CRYO-EM STRUCTURE OF THE E. COLI TRANSLATING RIBOSOME IN COMPLEX WITH SRP AND ITS RECEPTOR