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(-) Description

Authors :  A. W. Oliver, L. H. Pearl
Date :  15 Oct 08  (Deposition) - 28 Jul 09  (Release) - 27 Oct 09  (Revision)
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Fanconi Anemia, Homologous Recomination, Polymorphism, Phosphoprotein, Beta-Propeller, Wd40, Fanc-N, Nucleus, Wd Repeat, Coiled Coil, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  A. W. Oliver, S. Swift, C. J. Lord, A. Ashworth, L. H. Pearl
Structural Basis For Recruitment Of Brca2 By Palb2
Embo Rep. V. 10 990 2009
PubMed-ID: 19609323  |  Reference-DOI: 10.1038/EMBOR.2009.126

(-) Compounds

    Expression System Cell LineSF9
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentWD40 DOMAIN, RESIDUES 835-1186
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPALB2, FANCN

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
1AC1SOFTWAREALA A:874 , CYS A:886 , TRP A:906 , SER A:1165 , THR A:1167 , ASP A:1168 , HIS A:1170 , HOH A:3022BINDING SITE FOR RESIDUE GOL A2187
2AC2SOFTWAREVAL A:969 , THR A:1015 , PHE A:1016 , HOH A:3090 , HOH A:3135 , HOH A:3180 , HOH A:3181 , HOH A:3182BINDING SITE FOR RESIDUE GOL A2188
3AC3SOFTWAREGLN A:905 , GLN A:988 , PHE A:1005 , PRO A:1008 , HOH A:3183 , HOH A:3184BINDING SITE FOR RESIDUE GOL A2189
5AC5SOFTWARELYS A:1124 , ASP A:1125 , TRP A:1164 , ASP A:1168 , SER A:1169 , HOH A:3187BINDING SITE FOR RESIDUE GOL A2191

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W18)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
1Ala A:1057 -Ser A:1058
2Ala A:1115 -Gly A:1116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 13)

Asymmetric/Biological Unit (13, 13)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
09UniProtVAR_066380S1075GPALB2_HUMANPolymorphism  ---AS1075G
10UniProtVAR_066381V1105APALB2_HUMANPolymorphism  ---AV1105A
11UniProtVAR_066382Q1114HPALB2_HUMANPolymorphism  ---AQ1114H

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W18)

(-) Exons   (0, 0)

(no "Exon" information available for 2W18)

(-) 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:306
 aligned with PALB2_HUMAN | Q86YC2 from UniProtKB/Swiss-Prot  Length:1186

    Alignment length:333
                                   863       873       883       893       903       913       923       933       943       953       963       973       983       993      1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123      1133      1143      1153      1163      1173      1183   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......eeeeeeeee.----.eeeeeeee..eeeeeee.....eeeeeeee.....eeee.........eeeee....eeeeeee..------..eeeeeeeeeeeeeee...eeeeee......eeeeeee.....eeeeeee......eeeeeeee....eeeeee...eeeeee.....eeeeee...---..eeeeeeee..eeeeeee------------..eeeeeee....eeeeeeee.........eeeeeee..eeeeee....eeeee.....eeeee...--....eeee.....eeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------S----------------------------------------------------A--------------M------W--------------------------V-------------------------------E--------------------------T-----------------A-------------------------------G-----------------------------A--------H----------------------------P--------------------------Y---------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                   863       873    |  883       893       903       913       923       933       943     |   -  |    963       973       983       993      1003      1013      1023      1033      1043      1053   |  1063      1073 |       -    | 1093      1103      1113      1123      1133      1143      1153|  |  1163      1173      1183   
                                                  878  883                                                               949    956                                                                                             1053   |              1075         1088                                                              1154  |                             
                                                                                                                                                                                                                                    1057                                                                                                1157                             

   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 2W18)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W18)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W18)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PALB2_HUMAN | Q86YC2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    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: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:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0031052    chromosome breakage    Regulated cleavage of the developing macronuclear genome at a limited number of chromosome breakage sites (CBS). The macronuclear destined segment (MDS) sequence adjacent to the CBS (or separated from it by a BES) receives a macronuclear telomere following chromosome breakage.
    GO:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
    GO:0048568    embryonic organ development    Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0001833    inner cell mass cell proliferation    The proliferation of cells in the inner cell mass.
    GO:0007498    mesoderm development    The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0036342    post-anal tail morphogenesis    The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance.
    GO:0001756    somitogenesis    The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
    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.


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    Ala A:1057 - Ser A:1058   [ RasMol ]  
    Ala A:1115 - Gly A:1116   [ RasMol ]  

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 Related Entries

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

        PALB2_HUMAN | Q86YC23eu7

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W18)