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 :  CRYSTAL STRUCTURE OF TOPBP1 BRCT7/8-BACH1 PEPTIDE COMPLEX
 
Authors :  C. C. Leung, J. N. Glover
Date :  22 Jul 10  (Deposition) - 01 Dec 10  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Brct Domain-Phosphopeptide Complex, Dna Binding Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. C. Leung, Z. Gong, J. Chen, J. N. Glover
Molecular Basis Of Bach1/Fancj Recognition By Topbp1 In Dna Replication Checkpoint Control
J. Biol. Chem. V. 286 4292 2011
PubMed-ID: 21127055  |  Reference-DOI: 10.1074/JBC.M110.189555

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE 2-BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX
    Expression System StrainBL21 GOLD
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentBRCT7 AND BRCT8, UNP RESIDUES 1264-1493
    GeneKIAA0259, TOPBP1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDNA TOPOISOMERASE II-BINDING PROTEIN 1, DNA TOPOISOMERASE II-BETA-BINDING PROTEIN 1, TOPBP1
 
Molecule 2 - PEPTIDE OF FANCONI ANEMIA GROUP J PROTEIN
    ChainsB
    EngineeredYES
    FragmentUNP RESIDUES 1129-1138
    Other DetailsSYNTHETIC
    SynonymPROTEIN FANCJ, ATP-DEPENDENT RNA HELICASE BRIP1, BRCA1- INTERACTING PROTEIN C-TERMINAL HELICASE 1, BRCA1-INTERACTING PROTEIN 1, BRCA1-ASSOCIATED C-TERMINAL HELICASE 1
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:94 , LEU A:1275 , ASN A:1276 , GLU A:1279 , HIS A:1311 , ARG A:1331BINDING SITE FOR RESIDUE FMT A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AL3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3AL3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AL3)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002590081ENSE00001350462chr17:59940755-59940645111FANCJ_HUMAN-00--
1.2ENST000002590082ENSE00001243809chr17:59938930-59938808123FANCJ_HUMAN1-31310--
1.3ENST000002590083ENSE00000925250chr17:59937268-59937157112FANCJ_HUMAN32-69380--
1.4ENST000002590084ENSE00000925249chr17:59934592-59934419174FANCJ_HUMAN69-127590--
1.5ENST000002590085ENSE00000925248chr17:59926617-59926490128FANCJ_HUMAN127-169430--
1.6ENST000002590086ENSE00000925247chr17:59924581-59924462120FANCJ_HUMAN170-209400--
1.7ENST000002590087ENSE00000925246chr17:59886118-59885828291FANCJ_HUMAN210-306970--
1.8ENST000002590088ENSE00000925245chr17:59878835-59878614222FANCJ_HUMAN307-380740--
1.9ENST000002590089ENSE00000925244chr17:59876660-59876461200FANCJ_HUMAN381-447670--
1.10ENST0000025900810ENSE00000925243chr17:59871090-59870958133FANCJ_HUMAN447-491450--
1.11ENST0000025900811ENSE00000925242chr17:59861785-59861631155FANCJ_HUMAN492-543520--
1.12ENST0000025900812ENSE00000925241chr17:59858366-59858201166FANCJ_HUMAN543-598560--
1.13ENST0000025900813ENSE00000925240chr17:59857762-59857622141FANCJ_HUMAN599-645470--
1.14ENST0000025900814ENSE00000925239chr17:59853923-59853762162FANCJ_HUMAN646-699540--
1.15ENST0000025900815ENSE00000925238chr17:59821952-59821793160FANCJ_HUMAN700-753540--
1.16ENST0000025900816ENSE00000925237chr17:59820495-59820374122FANCJ_HUMAN753-793410--
1.17ENST0000025900817ENSE00000925236chr17:59793424-59793312113FANCJ_HUMAN794-831380--
1.18ENST0000025900818ENSE00000925235chr17:59770873-5977079183FANCJ_HUMAN831-859290--
1.19aENST0000025900819aENSE00000925234chr17:59763526-59763197330FANCJ_HUMAN859-9691110--
1.20ENST0000025900820ENSE00001132193chr17:59761501-597599851517FANCJ_HUMAN969-12492811B:1129-113810

2.1ENST000002608101ENSE00001289464chr3:133380737-133380613125TOPB1_HUMAN-00--
2.2ENST000002608102ENSE00000933924chr3:133379978-13337988891TOPB1_HUMAN1-28280--
2.3ENST000002608103ENSE00001018318chr3:133377994-133377860135TOPB1_HUMAN29-73450--
2.4ENST000002608104ENSE00000933926chr3:133376785-133376642144TOPB1_HUMAN74-121480--
2.5aENST000002608105aENSE00000933927chr3:133375701-133375520182TOPB1_HUMAN122-182610--
2.6ENST000002608106ENSE00001078162chr3:133374330-133374134197TOPB1_HUMAN182-248670--
2.7ENST000002608107ENSE00001078164chr3:133372368-133372189180TOPB1_HUMAN248-308610--
2.8aENST000002608108aENSE00001289360chr3:133371473-133371307167TOPB1_HUMAN308-363560--
2.9bENST000002608109bENSE00001289349chr3:133368787-133368624164TOPB1_HUMAN364-418550--
2.9dENST000002608109dENSE00001289339chr3:133368477-133368227251TOPB1_HUMAN418-502850--
2.10cENST0000026081010cENSE00001078161chr3:133363207-133362864344TOPB1_HUMAN502-6161150--
2.11ENST0000026081011ENSE00000933934chr3:133362216-133362044173TOPB1_HUMAN617-674580--
2.12ENST0000026081012ENSE00001078166chr3:133359014-133358803212TOPB1_HUMAN674-745720--
2.13ENST0000026081013ENSE00001150558chr3:133357006-133356720287TOPB1_HUMAN745-840960--
2.14aENST0000026081014aENSE00001150552chr3:133347577-133347404174TOPB1_HUMAN841-898580--
2.15aENST0000026081015aENSE00000933939chr3:133347315-133347206110TOPB1_HUMAN899-935370--
2.16ENST0000026081016ENSE00000933940chr3:133343019-133342896124TOPB1_HUMAN935-976420--
2.17ENST0000026081017ENSE00001078177chr3:133342301-133342155147TOPB1_HUMAN977-1025490--
2.18ENST0000026081018ENSE00001078179chr3:133342037-133341935103TOPB1_HUMAN1026-1060350--
2.19ENST0000026081019ENSE00000933943chr3:133339191-133338999193TOPB1_HUMAN1060-1124650--
2.20aENST0000026081020aENSE00001289481chr3:133337277-133337057221TOPB1_HUMAN1124-1198750--
2.21bENST0000026081021bENSE00000933945chr3:133336170-133336004167TOPB1_HUMAN1198-1253560--
2.22bENST0000026081022bENSE00000933946chr3:133335769-133335658112TOPB1_HUMAN1254-1291381A:1266-129126
2.23ENST0000026081023ENSE00000933947chr3:133331396-133331233164TOPB1_HUMAN1291-1345551A:1291-134555
2.24ENST0000026081024ENSE00000933948chr3:133329985-133329848138TOPB1_HUMAN1346-1391461A:1346-139146
2.25ENST0000026081025ENSE00000933949chr3:133327806-13332771790TOPB1_HUMAN1392-1421301A:1392-142130
2.26ENST0000026081026ENSE00001150487chr3:133327540-133327379162TOPB1_HUMAN1422-1475541A:1422-1475 (gaps)54
2.27ENST0000026081027ENSE00001289455chr3:133320237-133319417821TOPB1_HUMAN1476-1522471A:1476-149116

(-) 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:218
 aligned with TOPB1_HUMAN | Q92547 from UniProtKB/Swiss-Prot  Length:1522

    Alignment length:226
                                  1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435      1445      1455      1465      1475      1485      
         TOPB1_HUMAN   1266 KQYIFQLSSLNPQERIDYCHLIEKLGGLVIEKQCFDPTCTHIVVGHPLRNEKYLASVAAGKWVLHRSYLEACRTAGHFVQEEDYEWGSSSILDVLTGINVQQRRLALAAMRWRKKIQQRQESGIVEGAFSGWKVILHVDQSREAGFKRLLQSGGAKVLPGHSVPLFKEATHLFSDLNKLKPDDSGVNIAEAAAQNVYCLRTEYIADYLMQESPPHVENYCLPEAIS 1491
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhh...ee...........eeee......hhhhhhhh...eee..hhhhhhhhh......hhh....hhhh.......hhhhhhhhhhhhhhhhhhhhh............eeeee.....hhhhhhhhhh...ee.....hhh.....eeee..--------...hhhhhh...eeee.hhhhhhhh......hhhh..hhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 2 (1) Exon 2.22b [INCOMPLETE]   ------------------------------------------------------Exon 2.24  PDB: A:1346-1391 UniProt: 1346-1391Exon 2.25  PDB: A:1392-1421   Exon 2.26  PDB: A:1422-1475 (gaps) UniProt: 1422-1475 Exon 2.27        Transcript 2 (1)
           Transcript 2 (2) -------------------------Exon 2.23  PDB: A:1291-1345 UniProt: 1291-1345         -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 2 (2)
                3al3 A 1266 KQYIFQLSSLNPQERIDYCHLIEKLGGLVIEKQCFDPTCTHIVVGHPLRNEKYLASVAAGKWVLHRSYLEACRTAGHFVQEEDYEWGSSSILDVLTGINVQQRRLALAAMRWRKKIQQRQESGIVEGAFSGWKVILHVDQSREAGFKRLLQSGGAKVLPGHSVPLFKEATHLFSDL--------GVNIAEAAAQNVYCLRTEYIADYLMQESPPHVENYCLPEAIS 1491
                                  1275      1285      1295      1305      1315      1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      1435     |   -    | 1455      1465      1475      1485      
                                                                                                                                                                                                        1441     1450                                         

Chain B from PDB  Type:PROTEIN  Length:10
 aligned with FANCJ_HUMAN | Q9BX63 from UniProtKB/Swiss-Prot  Length:1249

    Alignment length:10
                                  1138
         FANCJ_HUMAN   1129 SIYFTPELYD 1138
               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 1 Exon 1.20  Transcript 1
                3al3 B 1129 SIYFtPELYD 1138
                                | 1138
                                |     
                             1133-TPO 

   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 3AL3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AL3)

(-) Gene Ontology  (44, 53)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TOPB1_HUMAN | Q92547)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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: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: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: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:0010212    response to ionizing radiation    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 ionizing radiation stimulus. Ionizing radiation is radiation with sufficient energy to remove electrons from atoms and may arise from spontaneous decay of unstable isotopes, resulting in alpha and beta particles and gamma rays. Ionizing radiation also includes X-rays.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0016605    PML body    A class of nuclear body; they react against SP100 auto-antibodies (PML, promyelocytic leukemia); cells typically contain 10-30 PML bodies per nucleus; alterations in the localization of PML bodies occurs after viral infection.
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0001673    male germ cell nucleus    The nucleus of a male germ cell, a reproductive cell in males.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    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.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

Chain B   (FANCJ_HUMAN | Q9BX63)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0016818    hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides    Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0000077    DNA damage checkpoint    A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds.
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    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: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: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:0071295    cellular response to vitamin    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 vitamin stimulus.
    GO:0006302    double-strand break repair    The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TPO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3al3)
 

(-) 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
  3al3
    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
  FANCJ_HUMAN | Q9BX63
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
  TOPB1_HUMAN | Q92547
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  FANCJ_HUMAN | Q9BX63
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  TOPB1_HUMAN | Q92547
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FANCJ_HUMAN | Q9BX631t15 1t29
        TOPB1_HUMAN | Q925471wf6 2xnh 2xnk 3al2 3jve 3olc 3pd7 3uen 3ueo

(-) Related Entries Specified in the PDB File

3al2