Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  ASSEMBLY CHAPERONE OF RPL4 (ACL4) (RESIDUES 28-338)
 
Authors :  F. M. Huber, A. Hoelz
Date :  11 Mar 15  (Deposition) - 13 May 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribosome Assembly, Chaperone, Nucleocytoplasmic Transport, Tetratricopeptide Repeat, Ribosome Biogenesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Stelter, F. M. Huber, R. Kunze, D. Flemming, A. Hoelz, E. Hurt
Coordinated Ribosomal L4 Protein Assembly Into The Pre-Ribosome Is Regulated By Its Eukaryote-Specific Extension.
Mol. Cell V. 58 854 2015
PubMed-ID: 25936803  |  Reference-DOI: 10.1016/J.MOLCEL.2015.03.029

(-) Compounds

Molecule 1 - ACL4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 27-338
    Gene: CTHT_0010130
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719

 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  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4YNV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YNV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YNV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YNV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YNV)

(-) Exons   (0, 0)

(no "Exon" information available for 4YNV)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ynv A  28 INPKELLDRATTLLEEGDIETAAKVARTAYEHIGENGRHAGAALTLLGQIHVELGDIDAARNYYAAAVKVDEDGSLPEELGGGPEKFLWLAQLSEEGGHDSVAWFERGATVLRAQIQSLmDSLEQRPLSRGQVEAAIADKRRRLAETLCAVVEVYmTDLSWEDDAEQRCEALITEATmIAPEWPETWQTVANVRISQERTEEAREALRRSLGLWTHLPPEDPGVPPFPSRVSLVRLLIEVDmEEEALEVTERLIAEDDLSVEVWYLGGYARYRLGEKEREASG 310
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177     | 187       197       207       217       227       237       247       257       267 |     277       287       297       307   
                                                                                                                                                 147-MSE                             183-MSE               205-MSE                                                         269-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ynv B  28 INPKELLDRATTLLEEGDIETAAKVARTAYEHIGENGRHAGAALTLLGQIHVELGDIDAARNYYAAAVKVDEDGSLPEELGGGPEKFLWLAQLSEEGGHDSVAWFERGATVLRAQIQSLmDSLEQRPLSRGQVEAAIADKRRRLAETLCAVVEVYmTDLSWEDDAEQRCEALITEATmIAPEWPETWQTVANVRISQERTEEAREALRRSLGLWTHLPPEDPGVPPFPSRVSLVRLLIEVDmEEEALEVTERLIAEDDLSVEVWYLGGYARYRLGEKEREASG 310
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177     | 187       197       207       217       227       237       247       257       267 |     277       287       297       307   
                                                                                                                                                 147-MSE                             183-MSE               205-MSE                                                         269-MSE
   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 4YNV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YNV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YNV)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YNV)

 Visualization

(-) Interactive Views

Asymmetric 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4ynv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ynv)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 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
  4ynv
    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
  G0S0I4_CHATD | G0S0I4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  G0S0I4_CHATD | G0S0I4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        G0S0I4_CHATD | G0S0I4: 4ynw 5tqb

(-) Related Entries Specified in the PDB File

4ynw