Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL AND ENERGETIC ANALYSIS OF RNA RECOGNITION BY A UNIVERSALLY CONSERVED PROTEIN FROM THE SIGNAL RECOGNITION PARTICLE
 
Authors :  R. T. Batey, M. B. Sagar, J. A. Doudna
Date :  13 Dec 00  (Deposition) - 03 Jan 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Double Helix, Tetraloop, Internal Loop, Signal Recognition Particle, Srp, Ribonucleoprotein, Signaling Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Batey, M. B. Sagar, J. A. Doudna
Structural And Energetic Analysis Of Rna Recognition By A Universally Conserved Protein From The Signal Recognition Particle.
J. Mol. Biol. V. 307 229 2001
PubMed-ID: 11243816  |  Reference-DOI: 10.1006/JMBI.2000.4454
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 4.5S RNA DOMAIN IV
    Chains: B
    Engineered: YES
    Fragment: RESIDUES 32-74
    Synthetic: YES
 
Molecule 2 - SIGNAL RECOGNITION PARTICLE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEXFFHM8
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C TERMINAL DOMAIN (RESIDUES 328-432)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FIFTY-FOUR HOMOLOG, FFH-M DOMAIN, P48

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CCC1Mod. NucleotideCYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2K3Ligand/IonPOTASSIUM ION
3MG4Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH B:9011 , HOH B:9015 , HOH B:9025 , HOH B:9028 , HOH B:9038 , HOH B:9180BINDING SITE FOR RESIDUE MG B 1801
2AC2SOFTWAREC B:141 , HOH B:9040 , HOH B:9062 , HOH B:9164 , HOH B:9181 , HOH B:9282 , HOH B:9283BINDING SITE FOR RESIDUE MG B 1802
3AC3SOFTWAREG B:149 , K B:4003 , HOH B:9073 , HOH B:9106 , HOH B:9129 , HOH B:9199BINDING SITE FOR RESIDUE MG B 1803
4AC4SOFTWAREHOH B:9046 , HOH B:9058 , HOH B:9285 , HOH B:9286 , HOH B:9287BINDING SITE FOR RESIDUE MG B 1804
5AC5SOFTWAREU B:146 , C B:147 , A B:164 , G B:165 , HOH B:9006 , HOH B:9024BINDING SITE FOR RESIDUE K B 4001
6AC6SOFTWAREU B:135 , G B:136 , U B:137 , HOH B:9033 , HOH B:9049 , HOH B:9189 , HOH B:9196 , HOH B:9244BINDING SITE FOR RESIDUE K B 4002
7AC7SOFTWAREA B:148 , G B:149 , G B:150 , G B:162 , MG B:1803 , HOH B:9106 , HOH B:9199BINDING SITE FOR RESIDUE K B 4003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1HQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 1HQ1)

(-) 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:76
 aligned with SRP54_ECO57 | P0AGD9 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:104
                                   337       347       357       367       377       387       397       407       417       427    
          SRP54_ECO57   328 GFDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKMK 431
               SCOP domains d1hq1a_ A: Si                            gnal sequence binding protein Ffh                               SCOP domains
               CATH domains 1hq1A00 A:1-8                            3  [code=1.10.260.30, no name defined]                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.----------------------------...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1hq1 A   1 GFDLNDFLEQLRQ----------------------------DDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFDDMQRMMKKMK  83
                                    10  |      -         -         - |      29        39        49        59        69        79    
                                       13                           21                                                              


Chain A from PDB  Type:PROTEIN  Length:76
 aligned with SRP54_ECOL6 | P0AGD8 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:104
                                   337       347       357       367       377       387       397       407       417       427    
          SRP54_ECOL6   328 GFDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKMK 431
               SCOP domains d1hq1a_ A: Si                            gnal sequence binding protein Ffh                               SCOP domains
               CATH domains 1hq1A00 A:1-8                            3  [code=1.10.260.30, no name defined]                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.----------------------------...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1hq1 A   1 GFDLNDFLEQLRQ----------------------------DDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFDDMQRMMKKMK  83
                                    10  |      -         -         - |      29        39        49        59        69        79    
                                       13                           21                                                              


Chain A from PDB  Type:PROTEIN  Length:76
 aligned with SRP54_ECOLI | P0AGD7 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:104
                                   337       347       357       367       377       387       397       407       417       427    
          SRP54_ECOLI   328 GFDLNDFLEQLRQMKNMGGMASLMGKLPGMGQIPDNVKSQMDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKMK 431
               SCOP domains d1hq1a_ A: Si                            gnal sequence binding protein Ffh                               SCOP domains
               CATH domains 1hq1A00 A:1-8                            3  [code=1.10.260.30, no name defined]                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh.----------------------------...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 1hq1 A   1 GFDLNDFLEQLRQ----------------------------DDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGSGMQVQDVNRLLKQFDDMQRMMKKMK  83
                                    10  |      -         -         - |      29        39        49        59        69        79    
                                       13                           21                                                              


Chain B from PDB  Type:RNA  Length:49
                                                                                 
                 1hq1 B 130 GGCUCUGUUUACCAGGUCAGGUCCGAAAGGAAGCAGCCAAGGCAGAGCc 178
                                   139       149       159       169        |
                                                                          178-CCC
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HQ1)

(-) Gene Ontology  (11, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SRP54_ECO57 | P0AGD9)
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: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 A   (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 A   (SRP54_ECOL6 | P0AGD8)
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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CCC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1hq1)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1hq1
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SRP54_ECO57 | P0AGD9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SRP54_ECOL6 | P0AGD8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SRP54_ECOLI | P0AGD7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SRP54_ECO57 | P0AGD9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SRP54_ECOL6 | P0AGD8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SRP54_ECOLI | P0AGD7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SRP54_ECO57 | P0AGD9: 1dul
        SRP54_ECOL6 | P0AGD8: 1dul
        SRP54_ECOLI | P0AGD7: 1dul 2j28 2pxb 2pxd 2pxe 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv 2xkv 2xxa 3lqx 4c7o 5aka 5gad 5gaf 5gag 5gah

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1HQ1)