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(-) Description

Title :  SIGNAL RECOGNITION PARTICLE RECEPTOR BETA-SUBUNIT IN NUCLEOTIDE-FREE DIMERIZED FORM
 
Authors :  D. Schmidt, T. U. Schwartz
Date :  19 Mar 06  (Deposition) - 18 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Transport, G Protein, Signal Recognition Particle, Proline Isomerization, Circular Permutation, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. U. Schwartz, D. Schmidt, S. G. Brohawn, G. Blobel
Homodimerization Of The G Protein Sr{Beta} In The Nucleotide-Free State Involves Proline Cis/Trans Isomerization In The Switch Ii Region.
Proc. Natl. Acad. Sci. Usa V. 103 6823 2006
PubMed-ID: 16627619  |  Reference-DOI: 10.1073/PNAS.0602083103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE RECEPTOR BETA SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SRP102
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SR-BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:46 , GLN A:47 , ASN A:48 , SER A:49 , GLY A:50 , LYS A:51 , THR A:52 , HOH A:497 , HOH B:490BINDING SITE FOR RESIDUE SO4 A 401
2AC2SOFTWAREHOH A:416 , PRO B:46 , GLN B:47 , ASN B:48 , SER B:49 , GLY B:50 , LYS B:51 , THR B:52 , HOH B:487BINDING SITE FOR RESIDUE SO4 B 402
3AC3SOFTWARETYR A:37 , GLN A:38 , ARG A:105BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWARELYS A:97 , LEU A:98 , SER A:99 , ILE A:138 , HOH A:498 , HOH A:501 , ARG B:95BINDING SITE FOR RESIDUE SO4 A 404
5AC5SOFTWARETYR B:37 , GLN B:38 , ALA B:76 , ARG B:105 , HOH B:486 , HOH B:493BINDING SITE FOR RESIDUE SO4 B 405
6AC6SOFTWAREARG A:95 , LYS B:97 , LEU B:98 , SER B:99 , ILE B:138 , HOH B:485BINDING SITE FOR RESIDUE SO4 B 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:88 -Pro A:89
2Phe B:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GED)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YKL154W1YKL154W.1XI:161606-162340735SRPB_YEAST1-2442442A:211-182 (gaps)
B:212-182 (gaps)		182
182

(-) 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:170
 aligned with SRPB_YEAST | P36057 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:183
                             1                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   
           SRPB_YEAST     - -MLSNTLIIACLLVIGTTIALIAVQKASSKTGIKQKSYQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADYDGSGVTLVDFPGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERR 182
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...eeeee.......hhhhhhhhhhhh-....eeeee.....hhhhhhhhhhhh...------------........eeee........hhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 -Exon 1.1  PDB: A:211-182 (gaps) UniProt: 1-244 [INCOMPLETE]                                                                                                                            Transcript 1
                 2ged A 210 DGFKFANLEASVVAFEGSINKRKISQWREWIDEKL-SYQPSIIIAGPQNSGKTSLLTLLTTDSVR------------DYDGSGVTLVDFPGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERR 182
                                   219       229       239    | | 39        49        59    |    -       |79        89        99       109       119       129       139       149       159       169       179   
                                                            244 |                          64           77                                                                                                         
                                                               36                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with SRPB_YEAST | P36057 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
           SRPB_YEAST     2 LSNTLIIACLLVIGTTIALIAVQKASSKTGIKQKSYQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADYDGSGVTLVDFPGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERR 182
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eeeee.......hh--hhhhhhhhhh...eeeee.....hhhhhhhhhh----------------.........eeee....ee..hhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:212-182 (gaps) UniProt: 1-244 [INCOMPLETE]                                                                                                                           Transcript 1
                 2ged B 212 FKFANLEASVVAFEGSINKRKIS--QWREWIDEKLYQPSIIIAGPQNSGKTSLLTLLT----------------ADYDGSGVTLVDFPGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERR 182
                                   221       231  |  | 239    ||  41        51       | -         -    |   81        91       101       111       121       131       141       151       161       171       181 
                                                234  |      244|                    59               76                                                                                                          
                                                   235        37
   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 2GED)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SRPB_YEAST | P36057)
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).
    GO:0005047    signal recognition particle binding    Interacting selectively and non-covalently with the signal recognition particle.
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:0045047    protein targeting to ER    The process of directing proteins towards the endoplasmic reticulum (ER) using signals contained within the protein. One common mechanism uses a 16- to 30-residue signal sequence, typically located at the N-terminus of the protein and containing positively charged amino acids followed by a continuous stretch of hydrophobic residues, which directs the ribosome to the ER membrane and initiates transport of the growing polypeptide across the ER membrane.
cellular component
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0030176    integral component of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005785    signal recognition particle receptor complex    A transmembrane heterodimeric protein located in the membrane of the rough endoplasmic reticulum. Both subunits contain GTPase domains with which signal recognition particle interacts. In the presence of GTP and SRP receptor, SRP is released from the ribosome-nascent chain complex.

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 Related Entries

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        SRPB_YEAST | P36057: 1nrj

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