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

(-) Description

Title :  CRYSTAL STRUCTURE OF SGF29 IN COMPLEX WITH H3R2ME2SK4ME3
 
Authors :  C. B. Bian, C. Xu, C. Bountra, C. H. Arrowsmith, J. Weigelt, A. M. Edwards A. Bochkarev, J. Min
Date :  31 Mar 10  (Deposition) - 28 Apr 10  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.28
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics Consortium, Sgc, Nucleus, Transcription, Transcription Regulation, Chromosomal Protein, Dna-Binding, Nucleosome Core (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bian, C. Xu, J. Ruan, K. K. Lee, T. L. Burke, W. Tempel, D. Barsyte, J. Li, M. Wu, B. O. Zhou, B. E. Fleharty, A. Paulson, A. Allali-Hassani, J. Q. Zhou, G. Mer, P. A. Grant, J. L. Workman, J. Zang, J. Min
Sgf29 Binds Histone H3K4Me2/3 And Is Required For Saga Complex Recruitment And Histone H3 Acetylation.
Embo J. V. 30 2829 2011
PubMed-ID: 21685874  |  Reference-DOI: 10.1038/EMBOJ.2011.193

(-) Compounds

Molecule 1 - SAGA-ASSOCIATED FACTOR 29 HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21(DE3)-V2R-PRARE2
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 115-293
    Gene: CCDC101, SGF29
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: COILED-COIL DOMAIN-CONTAINING PROTEIN 101
 
Molecule 2 - HISTONE H3
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUES 2-14
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Other Details: H3R2ME2SK4ME3 14MER
    Synonym: H3R2ME2SK4ME3 14MER
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
12MR2Mod. Amino AcidN3, N4-DIMETHYLARGININE
2M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
3MSE4Mod. Amino AcidSELENOMETHIONINE
4SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:96 , SER A:206 , ARG A:208 , ARG A:209BINDING SITE FOR RESIDUE SO4 A 500
2AC2SOFTWAREHOH B:47 , SER B:206 , ARG B:208 , ARG B:209 , HOH B:304 , HOH B:358 , HOH B:416BINDING SITE FOR RESIDUE SO4 B 500
3AC3SOFTWAREARG A:115 , ALA C:1 , 2MR C:2 , HOH C:61 , HOH C:362BINDING SITE FOR RESIDUE SO4 C 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MEU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MEU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MEU)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SGF29_CPS51518 SGF29 C-terminal domain profile.SGF29_HUMAN152-293
 		  2A:152-288
B:152-291

(-) Exons   (0, 0)

(no "Exon" information available for 3MEU)

(-) 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:175
 aligned with SGF29_HUMAN | Q96ES7 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:175
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
          SGF29_HUMAN   114 MRRGVLMTLLQQSAMTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVACK 288
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..............................eeeeeee.....eeeeeeeeeeee....eeeeee........eeee...eee..........hhhhh.....eeeee.....eeeeeeeee........eeeee............eeehhh.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------SGF29_C  PDB: A:152-288 UniProt: 152-293                                                                                                  PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3meu A 114 GRRGVLmTLLQQSAmTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVACK 288
                                  |123    |  133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283     
                                  |     128-MSE                                                                                                                                                            
                                120-MSE                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:176
 aligned with SGF29_HUMAN | Q96ES7 from UniProtKB/Swiss-Prot  Length:293

    Alignment length:176
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285      
          SGF29_HUMAN   116 RGVLMTLLQQSAMTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVACKEPK 291
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------DUF1325-3meuB01 B:157-289                                                                                                            -- Pfam domains (1)
           Pfam domains (2) -----------------------------------------DUF1325-3meuB02 B:157-289                                                                                                            -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh..............................eeeeeee.....eeeeeeeeeeee....eeeeee.......eeeee...eee..........hhhhh.....eeeee.....eeeeeeeee........eeeee............eeehhh.eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------SGF29_C  PDB: B:152-291 UniProt: 152-293                                                                                                     PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3meu B 116 RGVLmTLLQQSAmTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILAEVVSYSHATNKYEVDDIDEEGKERHTLSRRRVIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDDYSVLFEDTSYADGYSPPLNVAQRYVVACKEPK 291
                                |  125  |    135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285      
                              120-MSE 128-MSE                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:5
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:5
         Q92133_XENLA     2 ARTKQ   6
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 3meu C   1 ArTkQ   5
                             | | 
                             | | 
                             2-2MR
                               4-M3L


Chain D from PDB  Type:PROTEIN  Length:4
 aligned with Q92133_XENLA | Q92133 from UniProtKB/TrEMBL  Length:136

    Alignment length:4
         Q92133_XENLA     2 ARTK   5
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 3meu D   1 ArTk   4
                             | |
                             | |
                             2-2MR
                               4-M3L
   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 3MEU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MEU)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Tudor (88)

(-) Gene Ontology  (15, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SGF29_HUMAN | Q96ES7)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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).
biological process
    GO:0071169    establishment of protein localization to chromatin    The directed movement of a protein to a part of a chromosome that is organized into chromatin.
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005671    Ada2/Gcn5/Ada3 transcription activator complex    A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
    GO:0070461    SAGA-type complex    A histone acetyltransferase complex that acetylates nucleosomal H3 and H2B and is required for the expression of a subset of Pol II-transcribed genes. The budding yeast complex includes the acetyltransferase Gcn5p, several proteins of the Spt and Ada families, and several TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain C,D   (Q92133_XENLA | Q92133)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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
    2MR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    M3L  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3meu)
 

(-) 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
  3meu
    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
  Q92133_XENLA | Q92133
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  SGF29_HUMAN | Q96ES7
    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
  Q92133_XENLA | Q92133
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  SGF29_HUMAN | Q96ES7
    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
        Q92133_XENLA | Q92133: 2hue 3gv6
        SGF29_HUMAN | Q96ES7: 3lx7 3me9 3mea 3met 3mev 3mew 5c0m
UniProtKB/TrEMBL
        Q92133_XENLA | Q92133: 2l11 2l12 2l1b 3gl6 3h91 3me9 3mea 3met 3mev 3o7a 4hsu 4qeo

(-) Related Entries Specified in the PDB File

3me9 3mea 3met 3mev 3mew