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(-) Description

Title :  HMGD(M13A)-DNA COMPLEX
 
Authors :  M. E. A. Churchill, J. Klass, D. L. Zoetewey
Date :  22 Jun 10  (Deposition) - 22 Sep 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Keywords :  High Mobility Group, Dna Bending, Non-Sequence-Specific, Hmg Domain, Chromosomal Protein, Dna, Gene Regulation-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Churchill, J. Klass, D. L. Zoetewey
Structural Analysis Of Hmgd-Dna Complexes Reveals Influence Of Intercalation On Sequence Selectivity And Dna Bending.
J. Mol. Biol. V. 403 88 2010
PubMed-ID: 20800069  |  Reference-DOI: 10.1016/J.JMB.2010.08.031

(-) Compounds

Molecule 1 - HIGH MOBILITY GROUP PROTEIN D
    ChainsA, D, G, J, M, P
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-D74-M13A
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET13A
    GeneCG17950, HMGD
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymHMG-D
 
Molecule 2 - DNA 5'-D(*G*GP*CP*GP*AP*TP*AP*TP*CP*GP*C)-3'
    ChainsB, C, E, F, H, I, K, L, N, O
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678910111213141516
Asymmetric/Biological Unit ABCDEFGHIJKLMNOP

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3NM9)

(-) Sites  (0, 0)

(no "Site" information available for 3NM9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NM9)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HMG_BOX_2PS50118 HMG boxes A and B DNA-binding domains profile.HMGD_DROME5-71
 
 
 
 
 
  6A:5-71
D:5-71
G:5-71
J:5-71
M:5-71
P:5-71

(-) Exons   (0, 0)

(no "Exon" information available for 3NM9)

(-) 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:73
 aligned with HMGD_DROME | Q05783 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:73
                                    11        21        31        41        51        61        71   
            HMGD_DROME    2 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
               SCOP domains d3nm9a_ A: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: A:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 A  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71   

Chain B from PDB  Type:DNA  Length:10
                                         
                  3nm9 B  2 GCGATATCGC 11
                                    11

Chain C from PDB  Type:DNA  Length:10
                                         
                  3nm9 C  2 GCGATATCGC 11
                                    11

Chain D from PDB  Type:PROTEIN  Length:73
 aligned with HMGD_DROME | Q05783 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:73
                                    11        21        31        41        51        61        71   
            HMGD_DROME    2 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
               SCOP domains d3nm9d_ D: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: D:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 D  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71   

Chain E from PDB  Type:DNA  Length:10
                                         
                  3nm9 E  2 GCGATATCGC 11
                                    11

Chain F from PDB  Type:DNA  Length:10
                                         
                  3nm9 F  2 GCGATATCGC 11
                                    11

Chain G from PDB  Type:PROTEIN  Length:73
 aligned with HMGD_DROME | Q05783 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:73
                                    11        21        31        41        51        61        71   
            HMGD_DROME    2 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
               SCOP domains d3nm9g_ G: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: G:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 G  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71   

Chain H from PDB  Type:DNA  Length:10
                                         
                  3nm9 H  2 GCGATATCGC 11
                                    11

Chain I from PDB  Type:DNA  Length:10
                                         
                  3nm9 I  2 GCGATATCGC 11
                                    11

Chain J from PDB  Type:PROTEIN  Length:73
 aligned with HMGD_DROME | Q05783 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:73
                                    11        21        31        41        51        61        71   
            HMGD_DROME    2 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
               SCOP domains d3nm9j_ J: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: J:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 J  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71   

Chain K from PDB  Type:DNA  Length:10
                                         
                  3nm9 K  2 GCGATATCGC 11
                                    11

Chain L from PDB  Type:DNA  Length:11
                                          
                  3nm9 L  1 GGCGATATCGC 11
                                    10 

Chain M from PDB  Type:PROTEIN  Length:73
 aligned with HMGD_DROME | Q05783 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:73
                                    11        21        31        41        51        61        71   
            HMGD_DROME    2 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
               SCOP domains d3nm9m_ M: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: M:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 M  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71   

Chain N from PDB  Type:DNA  Length:10
                                         
                  3nm9 N  2 GCGATATCGC 11
                                    11

Chain O from PDB  Type:DNA  Length:10
                                         
                  3nm9 O  2 GCGATATCGC 11
                                    11

Chain P from PDB  Type:PROTEIN  Length:73
 aligned with HMGD_DROME | Q05783 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:73
                                    11        21        31        41        51        61        71   
            HMGD_DROME    2 SDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
               SCOP domains d3nm9p_ P: automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---HMG_box-3nm9P01 P:5-71                                             --- Pfam domains (1)
           Pfam domains (2) ---HMG_box-3nm9P02 P:5-71                                             --- Pfam domains (2)
           Pfam domains (3) ---HMG_box-3nm9P03 P:5-71                                             --- Pfam domains (3)
           Pfam domains (4) ---HMG_box-3nm9P04 P:5-71                                             --- Pfam domains (4)
           Pfam domains (5) ---HMG_box-3nm9P05 P:5-71                                             --- Pfam domains (5)
           Pfam domains (6) ---HMG_box-3nm9P06 P:5-71                                             --- Pfam domains (6)
         Sec.struct. author ........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HMG_BOX_2  PDB: P:5-71 UniProt: 5-71                               --- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                  3nm9 P  2 SDKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSEWEAKAAKAKDDYDRAVKEFEANG 74
                                    11        21        31        41        51        61        71   

   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, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NM9)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: HMG-box (15)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,D,G,J,M,P   (HMGD_DROME | Q05783)
molecular function
    GO:0003680    AT DNA binding    Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA).
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
biological process
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
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:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HMGD_DROME | Q057831e7j 1hma 1qrv

(-) Related Entries Specified in the PDB File

1qrv CRYSTAL STRUCTURE OF THE COMPLEX OF HMG-D AND DNA