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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RMI CORE COMPLEX
 
Authors :  K. A. Hoadley, D. Xu, Y. Xue, K. A. Satyshur, W. Wang, J. L. Keck
Date :  07 May 10  (Deposition) - 15 Sep 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bloom Syndrome, Helicase, Rmi, Topoisomerase, Replication Protein A, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. A. Hoadley, D. Xu, Y. Xue, K. A. Satyshur, W. Wang, J. L. Keck
Structure And Cellular Roles Of The Rmi Core Complex From The Bloom Syndrome Dissolvasome.
Structure V. 18 1149 2010
PubMed-ID: 20826341  |  Reference-DOI: 10.1016/J.STR.2010.06.009

(-) Compounds

Molecule 1 - RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentC-TERMINAL OB DOMAIN (UNP RESIDUES 473-625)
    GeneRMI1, C9ORF76
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBLM-ASSOCIATED PROTEIN OF 75 KDA, BLAP75, FAAP75
 
Molecule 2 - RECQ-MEDIATED GENOME INSTABILITY PROTEIN 2
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneRMI2, C16ORF75
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHRMI2, BLM-ASSOCIATED PROTEIN OF 18 KDA, BLAP18

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:555 , GLU A:560 , MET A:613 , GLU A:617BINDING SITE FOR RESIDUE BEN A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:489 -Pro A:490
2Ser B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MXN)

(-) Exons   (0, 0)

(no "Exon" information available for 3MXN)

(-) 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:151
 aligned with RMI1_HUMAN | Q9H9A7 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:151
                                   484       494       504       514       524       534       544       554       564       574       584       594       604       614       624 
           RMI1_HUMAN   475 ENSINLSIAMDLYSPPFVYLSVLMASKPKEVTTVKVKAFIVTLTGNLSSSGGIWSITAKVSDGTAYLDVDFVDEILTSLIGFSVPEMKQSKKDPLQYQKFLEGLQKCQRDLIDLCCLMTISFNPSLSKAMVLALQDVNMEHLENLKKRLNK 625
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh....hhhhhhhh.....eeeeeeeeeeee.....hhhhh...eeeee....eeeeeehhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhheeeeeeeee....eeeeeeee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mxn A 475 ENSINLSIAMDLYSPPFVYLSVLMASKPKEVTTVKVKAFIVTLTGNLSSSGGIWSITAKVSDGTAYLDVDFVDEILTSLIGFSVPEMKQSKKDPLQYQKFLEGLQKCQRDLIDLCCLMTISFNPSLSKAMVLALQDVNMEHLENLKKRLNK 625
                                   484       494       504       514       524       534       544       554       564       574       584       594       604       614       624 

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with RMI2_HUMAN | Q96E14 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:131
                                    26        36        46        56        66        76        86        96       106       116       126       136       146 
           RMI2_HUMAN    17 LPRSPPLKVLAEQLRRDAEGGPGAWRLSRAAAGRGPLDLAAVWMQGRVVMADRGEARLRDPSGDFSVRGLERVPRGRPCLVPGKYVMVMGVVQACSPEPCLQAVKMTDLSDNPIHESMWELEVEDLHRNIP 147
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.hhhhhhhhee......ee.........ee..eeeeeeeeeeee..eeeeee..eeeeeehhhhh...........eeeeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mxn B  17 LPRSPPLKVLAEQLRRDAEGGPGAWRLSRAAAGRGPLDLAAVWMQGRVVMADRGEARLRDPSGDFSVRGLERVPRGRPCLVPGKYVMVMGVVQACSPEPCLQAVKMTDLSDNPIHESMWELEVEDLHRNIP 147
                                    26        36        46        56        66        76        86        96       106       116       126       136       146 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3MXN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MXN)

(-) Gene Ontology  (15, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RMI1_HUMAN | Q9H9A7)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0000731    DNA synthesis involved in DNA repair    Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0002023    reduction of food intake in response to dietary excess    An eating behavior process whereby detection of a dietary excess results in a decrease in intake of nutrients.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0002021    response to dietary excess    The physiological process in which dietary excess is sensed by the central nervous system, resulting in a reduction in food intake and increased energy expenditure.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0000732    strand displacement    The rejection of the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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 B   (RMI2_HUMAN | Q96E14)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0000731    DNA synthesis involved in DNA repair    Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0000732    strand displacement    The rejection of the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        RMI1_HUMAN | Q9H9A73nbh 3nbi 4cgy 4cht 4day
        RMI2_HUMAN | Q96E143nbh 4day

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MXN)