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 :  STRUCTURE OF MRNA STEM-LOOP, HUMAN STEM-LOOP BINDING PROTEIN AND 3'HEXO TERNARY COMPLEX
 
Authors :  D. Tan, L. Tong
Date :  17 Jun 13  (Deposition) - 10 Jul 13  (Release) - 10 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Rna-Rna Binding Protein-Hydrolase Complex, Histone Mrna 3'-End Processing, Histone Mrna Translation, Microrna Homeostasis, 5. 8S Rrna 3 -End Maturation, Zfp100, Lsm11, Nucleus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Tan, W. F. Marzluff, Z. Dominski, L. Tong
Structure Of Histone Mrna Stem-Loop, Human Stem-Loop Bindin Protein, And 3'Hexo Ternary Complex.
Science V. 339 318 2013
PubMed-ID: 23329046  |  Reference-DOI: 10.1126/SCIENCE.1228705

(-) Compounds

Molecule 1 - HISTONE MRNA STEM-LOOP
    Chains: A, D
    Engineered: YES
    Other Details: SYNTHESIZED BY IDT
    Synthetic: YES
 
Molecule 2 - 3'-5' EXORIBONUCLEASE 1
    Chains: B, E
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-24D
    Expression System Strain: BL21 (DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SAP DOMAIN AND NUCLEASE DOMAIN, UNP RESIDUES 55-349
    Gene: 3'EXO, ERI1, THEX1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 3'-5' EXONUCLEASE ERI1, ERI-1 HOMOLOG, HISTONE MRNA 3'-END- SPECIFIC EXORIBONUCLEASE, HISTONE MRNA 3'-EXONUCLEASE 1, PROTEIN 3'HEXO, HEXO
 
Molecule 3 - HISTONE RNA HAIRPIN-BINDING PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: BL21 (DE3) STAR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RNA-BINDING DOMAIN, UNP RESIDUES 125-223
    Gene: HBP, SLBP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE STEM-LOOP-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): ABC  
Biological Unit 2 (1x):    DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric Unit (1, 20)
No.NameCountTypeFull Name
1MSE20Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4L8R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L8R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4L8R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L8R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L8R)

(-) Exons   (0, 0)

(no "Exon" information available for 4L8R)

(-) 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:RNA  Length:26
                                                          
                 4l8r A   1 CCAAAGGCUCUUUUCAGAGCCACCCA  26
                                    10        20      


Chain B from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh......eeee...ee.............eeeeeeeeee.....eeeeeeee.........hhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhhh...hhhh.eeeehhhhhhhhhh...hhhhhhhh..........hhhhhhhhhhhhhhhhhhh.......eee....eee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4l8r B  63 DPVYKEIAITNGCINRmSKEELRAKLSEFKLETRGVKDVLKKRLKNYYKKQKLmDSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWmKLKELGTKYKYSLLTDGSWDmSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVQTKLTImLEKLGmDYDGRPHCGLDDSKNIARIAVRmLQDGCELRINEKmHAGQLmSVSSSLPIEGTPPPQmPHFR 348
                                    72      | 82        92       102       112   ||  129       139       149       159       169       179       189       199       209    |  219       229     | 239       249       259       269||     282   |   292       302      |312       322     | 332       342 |    
                                           79-MSE                              116-MSE                                                                                    214-MSE              235-MSE                            270|     |     |                    309-MSE      322-MSE |             344-MSE
                                                                                124                                                                                                                                                274     |     |                                       328-MSE                
                                                                                                                                                                                                                                         280-MSE |                                                              
                                                                                                                                                                                                                                               286-MSE                                                          


Chain C from PDB  Type:PROTEIN  Length:67
                                                                                                   
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 4l8r C 127 DFETDESVLMRRQKQINYGKNTIAYDRYIKEVPGIHPKTPNKFKKYSRRSWDQQIKLWKVALHFWDP 199
                                   136       146       156 ||    172       182       192       
                                                         158|                                  
                                                          165                                  


Chain D from PDB  Type:DNA/RNA  Length:19
                                                   
                 4l8r D   8 CUCUUUUCAGAGCCACCCA  26
                                    17         


Chain E from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeeee..ee.............eeeeeeeeee.....eeeeeeee.........hhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhhh....hhhh.eeeehhhhhhhhhh.hhhhhhhhh.........hhhhhhhhhhhhhhhhhhh.......eeee..eeee..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l8r E  64 PVYKEIAITNGCINRmSKEELRAKLSEFKLETRGVKDVLKKRLKNYYKKQKLmSYYDYICIIDFEATCEEGNPPEFVHEIIEFPVVLLNTHTLEIEDTFQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWmKLKELGTKYKYSLLTDGSWDmSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKTKLTImLEKLGmDYDGRPHCGLDDSKNIARIAVRmLQDGCELRINEKmHAGQLmSVSSSLPIEGTPPPQmPHFRKL 350
                                    73     |  83        93       103       113  ||   131       141       151       161       171       181       191       201       211  |    221       231   |   241       251       261       276   |   286       296       306  |    316     | 326 |     336       346    
                                          79-MSE                              116-MSE                                                                                   214-MSE              235-MSE                           269|    |     |                    309-MSE      322-MSE |             344-MSE  
                                                                               125                                                                                                                                              275    |     |                                       328-MSE                  
                                                                                                                                                                                                                                     280-MSE |                                                                
                                                                                                                                                                                                                                           286-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 4L8R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L8R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L8R)

(-) Gene Ontology  (32, 37)

Asymmetric Unit(hide GO term definitions)

 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 4l8r)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4l8r)
 
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
  4l8r
    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
  ERI1_HUMAN | Q8IV48
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  SLBP_HUMAN | Q14493
    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)
  3.1.-.-
    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
  ERI1_HUMAN | Q8IV48
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SLBP_HUMAN | Q14493
    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
        ERI1_HUMAN | Q8IV48: 1w0h 1zbh 1zbu 4qoz
        SLBP_HUMAN | Q14493: 2kjm 4qoz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4L8R)