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(-) Description

Title :  SIGNAL RECOGNITION PARTICLE RECEPTOR BETA-SUBUNIT IN COMPLEX WITH THE SRX DOMAIN FROM THE ALPHA-SUBUNIT
 
Authors :  T. Schwartz
Date :  24 Jan 03  (Deposition) - 25 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Signal Recognition Particle, Transmembrane, Receptor, Endoplasmic Reticulum, Gtp-Binding, Gtpase-Effector Complex, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Schwartz, G. Blobel
Structural Basis For The Function Of The Beta Subunit Of The Eukaryotic Signal Recognition Particle Receptor
Cell(Cambridge, Mass. ) V. 112 793 2003
PubMed-ID: 12654246  |  Reference-DOI: 10.1016/S0092-8674(03)00161-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIGNAL RECOGNITION PARTICLE RECEPTOR ALPHA SUBUNIT HOMOLOG
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-158
    Gene: SRP101
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SR-ALPHA, DOCKING PROTEIN ALPHA, DP-ALPHA
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE RECEPTOR BETA SUBUNIT
    Chains: 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
    Fragment: RESIDUES 31-244
    Gene: SRP102
    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  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:52 , SER B:69 , GTP B:1001 , HOH B:3003 , HOH B:3006BINDING SITE FOR RESIDUE MG B 1
2AC2SOFTWAREALA B:215 , LEU B:217 , HOH B:3018 , HOH B:3093 , HOH B:3106 , HOH B:3124BINDING SITE FOR RESIDUE MG B 2
3AC3SOFTWAREMG B:1 , GLN B:47 , ASN B:48 , SER B:49 , GLY B:50 , LYS B:51 , THR B:52 , SER B:53 , THR B:66 , SER B:69 , GLY B:90 , ASN B:154 , LYS B:155 , GLU B:157 , LEU B:158 , SER B:227 , ILE B:228 , ASN B:229 , HOH B:3003 , HOH B:3006 , HOH B:3012 , HOH B:3020 , HOH B:3025 , HOH B:3030 , HOH B:3107 , HOH B:3116 , HOH B:3117BINDING SITE FOR RESIDUE GTP B 1001
4AC4SOFTWAREVAL B:205 , GLU B:218 , LYS B:230 , HOH B:3050 , HOH B:3137BINDING SITE FOR RESIDUE EDO B 3001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NRJ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:82 -Pro A:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NRJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NRJ)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR292C1YDR292C.1IV:1045008-10431431866SRPR_YEAST1-6216211A:1-155 (gaps)155
2.1YKL154W1YKL154W.1XI:161606-162340735SRPB_YEAST1-2442441B:36-244 (gaps)209

(-) 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:147
 aligned with SRPR_YEAST | P32916 from UniProtKB/Swiss-Prot  Length:621

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
           SRPR_YEAST     1 MFDQLAVFTPQGQVLYQYNCLGKKFSEIQINSFISQLITSPVTRKESVANANTDGFDFNLLTINSEHKNSPSFNALFYLNKQPELYFVVTFAEQTLELNQETQQTLALVLKLWNSLHLSESILKNRQGQNEKNKHNYVDILQGIEDDLKKFEQYF 155
               SCOP domains d1nrja_ A: Srx domain of the signal recognition particle recepto        r alpha-subunit                                                                     SCOP domains
               CATH domains 1nrjA00 A:1-155  [code=3.30.450.60, no name defined]                                                                                                        CATH domains
               Pfam domains SRX-1nrjA01 A:1-155                                                                                                                                         Pfam domains
         Sec.struct. author ...eeeee.....eeeeee......hhhhhhhhhhhhhhh..hhh.ee.hhhhh...eeeee..--------.eeeeeee....eeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-155 (gaps) UniProt: 1-621 [INCOMPLETE]                                                                                                   Transcript 1
                 1nrj A   1 MFDQLAVFTPQGQVLYQYNCLGKKFSEIQINSFISQLITSPVTRKESVANANTDGFDFNLLTIN--------FNALFYLNKQPELYFVVTFAEQTLELNQETQQTLALVLKLWNSLHLSESILKNRQGQNEKNKHNYVDILQGIEDDLKKFEQYF 155
                                    10        20        30        40        50        60   |     -  |     80        90       100       110       120       130       140       150     
                                                                                          64       73                                                                                  


Chain B from PDB  Type:PROTEIN  Length:191
 aligned with SRPB_YEAST | P36057 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:209
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235         
           SRPB_YEAST    36 SYQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADYDGSGVTLVDFPGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERRKKSLNEVERKINEEDYAENTLDVLQSTDGFKFANLEASVVAFEGSINKRKISQWREWIDEKL 244
               SCOP domains d1nrjb_ B: Signal recognition particle receptor beta-subunit                                                                                                                                                      SCOP domains
               CATH domains 1nrjB00 B:36-244 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                             CATH domains
               Pfam domains SRPRB-1nrjB01 B:36-221                                                                                                                                                                    ----------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhhh...........eee.hhhhh..eeee...hhhhhhhhhhhhhhhh..eeeeeeeee...............................eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhh--------------....----..hhhhh...eeeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: B:36-244 (gaps) UniProt: 1-244 [INCOMPLETE]                                                                                                                                                        Transcript 2
                 1nrj B  36 SYQPSIIIAGPQNSGKTSLLTLLTTDSVRPTVVSQEPLSAADYDGSGVTLVDFPGHVKLRYKLSDYLKTRAKFVKGLIFMVDSTVDPKKLTTTAEFLVDILSITESSCENGIDILIACNKSELFTARPPSKIKDALESEIQKVIERRKKSLNE--------------LDVL----GFKFANLEASVVAFEGSINKRKISQWREWIDEKL 244
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185  |      -       205|    | 215       225       235         
                                                                                                                                                                                  188            203  |  211                                 
                                                                                                                                                                                                    206
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: SRX] (1)

(-) Gene Ontology  (14, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRPR_YEAST | P32916)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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: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.

Chain 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

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

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        SRPB_YEAST | P36057: 2ged

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