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Title :  CRYSTAL STRUCTURE OF THE RMI CORE COMPLEX WITH MM2 PEPTIDE FROM FANCM
 
Authors :  K. A. Hoadley, J. L. Keck
Date :  13 Jan 12  (Deposition) - 14 Mar 12  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ob Fold, Protein Binding-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. A. Hoadley, Y. Xue, C. Ling, M. Takata, W. Wang, J. L. Keck
Defining The Molecular Interface That Connects The Fanconi Anemia Protein Fancm To The Bloom Syndrome Dissolvasome.
Proc. Natl. Acad. Sci. Usa V. 109 4437 2012
PubMed-ID: 22392978  |  Reference-DOI: 10.1073/PNAS.1117279109

(-) Compounds

Molecule 1 - RECQ-MEDIATED GENOME INSTABILITY PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentC-TERMINAL OB DOMAIN (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
 
Molecule 3 - FANCONI ANEMIA GROUP M PROTEIN
    ChainsC
    EC Number3.6.4.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentMM2 PEPTIDE (RESIDUES 1218-1251)
    GeneFANCM, KIAA1596
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN FACM, ATP-DEPENDENT RNA HELICASE FANCM, FANCONI ANEMIA-ASSOCIATED POLYPEPTIDE OF 250 KDA, FAAP250, PROTEIN HEF ORTHOLOG

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4DAY)

(-) Sites  (0, 0)

(no "Site" information available for 4DAY)

(-) SS Bonds  (0, 0)

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

(-) 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 4DAY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DAY)

(-) 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:144
 aligned with RMI1_HUMAN | Q9H9A7 from UniProtKB/Swiss-Prot  Length:625

    Alignment length:144
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621    
          RMI1_HUMAN    482 IAMDLYSPPFVYLSVLMASKPKEVTTVKVKAFIVTLTGNLSSSGGIWSITAKVSDGTAYLDVDFVDEILTSLIGFSVPEMKQSKKDPLQYQKFLEGLQKCQRDLIDLCCLMTISFNPSLSKAMVLALQDVNMEHLENLKKRLNK  625
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhh....eeeeeeeeeeee.....hhhhh....eeee....eeeeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee......eeeeeee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4day A  482 IAMDLYSPPFVYLSVLMASKPKEVTTVKVKAFIVTLTGNLSSSGGIWSITAKVSDGTAYLDVDFVDEILTSLIGFSVPEMKQSKKDPLQYQKFLEGLQKCQRDLIDLCCLMTISFNPSLSKAMVLALQDVNMEHLENLKKRLNK  625
                                   491       501       511       521       531       541       551       561       571       581       591       601       611       621    

Chain B from PDB  Type:PROTEIN  Length:113
 aligned with RMI2_HUMAN | Q96E14 from UniProtKB/Swiss-Prot  Length:147

    Alignment length:135
                                    22        32        42        52        62        72        82        92       102       112       122       132       142     
          RMI2_HUMAN     13 AGVRLPRSPPLKVLAEQLRRDAEGGPGAWRLSRAAAGRGPLDLAAVWMQGRVVMADRGEARLRDPSGDFSVRGLERVPRGRPCLVPGKYVMVMGVVQACSPEPCLQAVKMTDLSDNPIHESMWELEVEDLHRNIP  147
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.hhhhhhhh----------------------.eeeeeeeeeeee..eeeee....eeeeehhhhh...........eeeeeeee.......eeeeeeeee....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4day B   13 AGVRLPRSPPLKVLAEQLRRD----------------------AAVWMQGRVVMADRGEARLRDPSGDFSVRGLERVPRGRPCLVPGKYVMVMGVVQACSPEPCLQAVKMTDLSDNPIHESMWELEVEDLHRNIP  147
                                    22        32|        -         -   |    62        72        82        92       102       112       122       132       142     
                                               33                     56                                                                                           

Chain C from PDB  Type:PROTEIN  Length:12
 aligned with FANCM_HUMAN | Q8IYD8 from UniProtKB/Swiss-Prot  Length:2048

    Alignment length:12
                                  1235  
         FANCM_HUMAN   1226 DLFSVTFDLGFC 1237
               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
                4day C 1226 DLFSVTFDLGFC 1237
                                  1235  

   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 4DAY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 40)

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.

Chain C   (FANCM_HUMAN | Q8IYD8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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:0006259    DNA metabolic process    Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0036297    interstrand cross-link repair    Removal of a DNA interstrand crosslink (a covalent attachment of DNA bases on opposite strands of the DNA) and restoration of the DNA. DNA interstrand crosslinks occur when both strands of duplex DNA are covalently tethered together (e.g. by an exogenous or endogenous agent), thus preventing the strand unwinding necessary for essential DNA functions such as transcription and replication.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0031297    replication fork processing    The process in which a DNA replication fork that has stalled is restored to a functional state and replication is restarted. The stalling may be due to DNA damage, DNA secondary structure, bound proteins, dNTP shortage, or other causes.
    GO:0000712    resolution of meiotic recombination intermediates    The cleavage and rejoining of intermediates, such as Holliday junctions, formed during meiotic recombination to produce two intact molecules in which genetic material has been exchanged.
cellular component
    GO:0071821    FANCM-MHF complex    A protein complex contains the proteins FANCM and MHF, or their orthologs, plays an essential role in DNA remodeling, protects replication forks, and is conserved in eukaryotes.
    GO:0043240    Fanconi anaemia nuclear complex    A protein complex composed of the Fanconi anaemia (FA) proteins including A, C, E, G and F (FANCA-F). Functions in the activation of the downstream protein FANCD2 by monoubiquitylation, and is essential for protection against chromosome breakage.
    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
        FANCM_HUMAN | Q8IYD84bxo 4drb 4e45 4m6w
        RMI1_HUMAN | Q9H9A73mxn 3nbh 3nbi 4cgy 4cht
        RMI2_HUMAN | Q96E143mxn 3nbh

(-) Related Entries Specified in the PDB File

3mxn CRYSTAL STRUCTURE OF THE RMI CORE COMPLEX
3nbh CRYSTAL STRUCTURES OF RMI1 AND RMI2, TWO OB-FOLD REGULATORY SUBUNITS OF THE BLM COMPLEX