Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  NOE-BASED 3D STRUCTURE OF THE CYLR2 HOMODIMER AT 270K (-3 CELSIUS DEGREES)
 
Authors :  M. Jaremko, L. Jaremko, H. Kim, M. Cho, C. D. Schwieters, K. Giller, S. Be M. Zweckstetter
Date :  19 Sep 12  (Deposition) - 20 Feb 13  (Release) - 03 Apr 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
NMR Structure *:  A,B  (1x)
Keywords :  Homodimer, Cylr2, Dna Binding Protein, Noe-Based Structure, Protein Folding, Cold Denaturation, Cytolysin Repressor 2, Helix-Turn-Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Jaremko, L. Jaremko, H. Y. Kim, M. K. Cho, C. D. Schwieters, K. Giller S. Becker, M. Zweckstetter
Cold Denaturation Of A Protein Dimer Monitored At Atomic Resolution.
Nat. Chem. Biol. V. 9 264 2013
PubMed-ID: 23396077  |  Reference-DOI: 10.1038/NCHEMBIO.1181

(-) Compounds

Molecule 1 - CYLR2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CYLR2
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Synonym: PUTATIVE TRANSCRIPTION REGULATOR

 Structural Features

(-) Chains, Units

  12
NMR Structure (20x): AB
NMR Structure * (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2LYK)

(-) Sites  (0, 0)

(no "Site" information available for 2LYK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LYK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2LYK)

(-) Sequences/Alignments

NMR Structure
   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:66
 aligned with Q8VL32_ENTFL | Q8VL32 from UniProtKB/TrEMBL  Length:66

    Alignment length:66
                                    10        20        30        40        50        60      
         Q8VL32_ENTFL     1 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE  66
               SCOP domains d2lyka_ A: Putative transcription regulator CylR2                  SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhh..hhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhh.hhhhheee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 2lyk A   1 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE  66
                                    10        20        30        40        50        60      


Chain B from PDB  Type:PROTEIN  Length:66
 aligned with Q8VL32_ENTFL | Q8VL32 from UniProtKB/TrEMBL  Length:66

    Alignment length:66
                                    10        20        30        40        50        60      
         Q8VL32_ENTFL     1 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE  66
               SCOP domains d2lykb_ B: Putative transcription regulator CylR2                  SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeehhhhhhhhhh.hhhhhhhhh..hhhhhhhhh......hhhhhhhhhhhhh.hhhhheee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 2lyk B  67 MIINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQWQPE 132
                                    76        86        96       106       116       126
   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, 2)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

NMR Structure(hide GO term definitions)
Chain A,B   (Q8VL32_ENTFL | Q8VL32)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

 Visualization

(-) Interactive Views

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 2lyk)
 
  Sites
(no "Sites" information available for 2lyk)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2lyk)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2lyk
    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
  Q8VL32_ENTFL | Q8VL32
    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
  Q8VL32_ENTFL | Q8VL32
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8VL32_ENTFL | Q8VL32: 1utx 2gzu 2lyj 2lyl 2lyp 2lyq 2lyr 2lys 2xi8 2xiu 2xj3

(-) Related Entries Specified in the PDB File

1utx X-RAY STRUCTURE OF THE SAME PROTEIN AT 1.9 A RESOLUTION
2gzu STRUCTURE OF THE SAME PROTEIN USING INTERMONOMER DISTANCES FROM PARAMAGNETIC RELAXATION ENHANCEMENT AND NMR DIPOLAR COUPLINGS
2lyj
2lyl
2lyp
2lyq
2lyr
2lys RELATED ID: 17893 RELATED DB: BMRB
2xi8 X-RAY STRUCTURE OF THE SAME PROTEIN AT 1.21 A RESOLUTION
2xiu X-RAY STRUCTURE OF MTSL-TAGGED CYLR2
2xj3 X-RAY STRUCTURE OF T55C MUTANT OF CYLR2