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 :  ARCHITECTURE AND DNA RECOGNITION ELEMENTS OF THE FANCONI ANEMIA FANCM-FAAP24 COMPLEX
 
Authors :  R. Coulthard, A. Deans, P. Swuec, M. Bowles, A. Purkiss, A. Costa, S. Wes N. Mcdonald
Date :  15 Jul 13  (Deposition) - 28 Aug 13  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,H,I
Keywords :  Hydrolase-Dna Complex, Dna Binding, Pseudo-Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Coulthard, A. J. Deans, P. Swuec, M. Bowles, A. Costa, S. C. West, N. Q. Mcdonald
Architecture And Dna Recognition Elements Of The Fanconi Anemia Fancm-Faap24 Complex.
Structure V. 21 1648 2013
PubMed-ID: 23932590  |  Reference-DOI: 10.1016/J.STR.2013.07.006

(-) Compounds

Molecule 1 - FANCONI ANEMIA GROUP M PROTEIN
    ChainsA
    EC Number3.6.4.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-KG
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantFB810
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTEIN FACM, ATP-DEPENDENT RNA HELICASE FANCM, FANCONI ANE MIA-ASSOCIATED POLYPEPTIDE OF 250 KDA, FAAP250, PROTEIN HEF ORTHOL OG, FANCM
 
Molecule 2 - FANCONI ANEMIA-ASSOCIATED PROTEIN OF 24 KDA
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-KG
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantFB810
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymFAAP24
 
Molecule 3 - 5'-D(*TP*CP*AP*GP*CP*AP*TP*CP*AP*TP*CP)-3'
    ChainsH
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 4 - 5'-D(*GP*AP*TP*GP*AP*TP*GP*CP*TP*GP*CP)-3'
    ChainsI
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABHI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:1854 , GLU A:1864 , ARG A:1865 , HOH A:3017BINDING SITE FOR RESIDUE CA A 2050
2AC2SOFTWAREGLU B:43 , ASP B:44 , HOH B:2009BINDING SITE FOR RESIDUE CA B 1215
3AC3SOFTWAREGLN B:164 , VAL B:169 , HOH B:2031 , HOH B:2032 , DT I:7BINDING SITE FOR RESIDUE CA B 1216
4AC4SOFTWAREGLU B:196 , VAL B:199 , DA H:11BINDING SITE FOR RESIDUE CA B 1217

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BXO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050989S126FFAP24_HUMANPolymorphism36017455BS126F
2UniProtVAR_029828S158LFAP24_HUMANPolymorphism2304103BS158L
3UniProtVAR_029829I192TFAP24_HUMANPolymorphism3816032BI192T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BXO)

(-) 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:202
 aligned with FANCM_HUMAN | Q8IYD8 from UniProtKB/Swiss-Prot  Length:2048

    Alignment length:218
                                  1827      1837      1847      1857      1867      1877      1887      1897      1907      1917      1927      1937      1947      1957      1967      1977      1987      1997      2007      2017      2027        
         FANCM_HUMAN   1818 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDREKTGDTSRMFRRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNVGIHVPTVVNSNKSEALQFYLSIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQVTHQKAEEIYRYIHYVFDIQML 2035
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhh....eeeee......ee....eeeeeeehhhhhh..hhhhhhhhhhhhhh...eeeeeee...----------..hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.......------hhhhhhhhhh....hhhhhhhhhhhh.hhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4bxo A 1818 TCILVGGHEITSGLEVISSLRAIHGLQVEVCPLNGCDYIVSNRMVVERRSQSEMLNSVNKNKFIEQIQHLQSMFERICVIVEKDR----------RRTKSYDSLLTTLIGAGIRILFSSCQEETADLLKELSLVEQRKNVGIHVP------KSEALQFYLSIPNISYITALNMCHQFSSVKRMANSSLQEISMYAQVTHQKAEEIYRYIHYVFDIQML 2035
                                  1827      1837      1847      1857      1867      1877      1887      1897    |    -     |1917      1927      1937      1947      1957    |    - |    1977      1987      1997      2007      2017      2027        
                                                                                                             1902       1913                                             1962   1969                                                                  

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with FAP24_HUMAN | Q9BTP7 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:203
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         FAP24_HUMAN     12 VHVPLGHIVANEKWRGSQLAQEMQGKIKLIFEDGLTPDFYLSNRCCILYVTEADLVAGNGYRKRLVRVRNSNNLKGIVVVEKTRMSEQYFPALQKFTVLDLGMVLLPVASQMEASCLVIQLVQEQTKEPSKNPLLGKKRALLLSEPSLLRTVQQIPGVGKVKAPLLLQKFPSIQQLSNASIGELEQVVGQAVAQQIHAFFTQP  214
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.hhh.hhhhhhhhh..eeeee......ee....eeeeeehhhhhhhh..hhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhhh...-------.hhhhhhhhhh.......hhhhhhhhhh.hhhhhhh.hhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------F-------------------------------L---------------------------------T---------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4bxo B   12 VHVPLGHIVANEKWRGSQLAEEMQGKIKLIFEDGLTPDFYLSNRCCILYVTEADLVAGNGYRKRLVRVRNSNNLKGIVVVEKTRMSEQYFPALQKFTVLDLGMVLLPVASQMEASCLVIQLVQEQTKEPSKNPLL-------LSEPSLLRTVQQIPGVGKVKAPLLLQKFPSIQQLSNASIGELEQVVGQAVAQQIHAFFTQP  214
                                    21        31        41        51        61        71        81        91       101       111       121       131       141    |    -  |    161       171       181       191       201       211   
                                                                                                                                                                146     154                                                            

Chain H from PDB  Type:DNA  Length:11
                                            
                4bxo H    1 GATGATGCTGA   11
                                    10 

Chain I from PDB  Type:DNA  Length:11
                                            
                4bxo I    1 TCAGCATCATC   11
                                    10 

   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 4BXO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain B   (FAP24_HUMAN | Q9BTP7)
molecular function
    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: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: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.
cellular component
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4bxo)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4bxo
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FANCM_HUMAN | Q8IYD8
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  FAP24_HUMAN | Q9BTP7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.4.13
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  FANCM_HUMAN | Q8IYD8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  FAP24_HUMAN | Q9BTP7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FANCM_HUMAN | Q8IYD84day 4drb 4e45 4m6w
        FAP24_HUMAN | Q9BTP72lyh 2m9m 2m9n 4m6w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4BXO)