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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN - MOUSE POLYMERASE IOTA UBIQUITIN BINDING MOTIF FUSION PROTEIN
 
Authors :  N. Suzuki, S. Wakatsuki, M. Kawasaki
Date :  10 May 10  (Deposition) - 29 Sep 10  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Ubm, Ubiquitin-Binding Motif, Gfp, Fusion, Fluorescent Protein, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Suzuki, M. Hiraki, Y. Yamada, N. Matsugaki, N. Igarashi, R. Kato, I. Dikic, D. Drew, S. Iwata, S. Wakatsuki, M. Kawasaki
Crystallization Of Small Proteins Assisted By Green Fluorescent Protein
Acta Crystallogr. , Sect. D V. 66 1059 2010
PubMed-ID: 20944239  |  Reference-DOI: 10.1107/S0907444910032944

(-) Compounds

Molecule 1 - YEAST ENHANCED GREEN FLUORESCENT PROTEIN,DNA POLYMERASE IOTA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRECIDUES 1-230 FOR YEAST ENHANCED GREEN FLUORESCENT PROTEIN,UBIQUITIN BINDING MOTIF FUSION PROTEIN FOR DNA POLYMERASE IOTA
    Organism CommonJELLYFISH, MOUSE
    Organism ScientificAEQUOREA VICTORIA, MUS MUSCULUS
    Organism Taxid6100, 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CR21Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:149 , TYR A:151 , GLY A:174 , HOH A:299 , HOH A:426BINDING SITE FOR RESIDUE SO4 A 283

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AI4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_POLI_MOUSE_003 *Q334KPOLI_MOUSE  ---  ---AT49K
2UniProtVAR_POLI_MOUSE_005 *Y518SPOLI_MOUSE  ---  ---AY143S
3UniProtVAR_POLI_MOUSE_006 *N524YPOLI_MOUSE  ---  ---AN149Y
4UniProtVAR_POLI_MOUSE_007 *A569EPOLI_MOUSE  ---  ---AI167E
5UniProtVAR_POLI_MOUSE_008 *E574DPOLI_MOUSE  ---  ---AE172D
6UniProtVAR_POLI_MOUSE_009 *Q606RPOLI_MOUSE  ---  ---AP187R
   * ID not provided by source

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AI4)

(-) Exons   (0, 0)

(no "Exon" information available for 3AI4)

(-) 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:257
 aligned with POLI_MOUSE | Q6R3M4 from UniProtKB/Swiss-Prot  Length:717

    Alignment length:440
                                   276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706
           POLI_MOUSE   267 KTLEKELGIAIAQRIQQLSFGEDKSPVTPSGPPQSFSEEDTFKKCSSEVEAKAKIEELLSSLLTRVCQDGRKPHTVRLVIRRYSDKHCNRESRQCPIPSHVIQKLGTGNHDSMPPLIDILMKLFRNMVNVKMPFHLTLMSVCFCNLKALSSAKKGPMDCYLTSLSTPAYTDKRAFKVKDTHTEDSHKEKEANWDCLPSRRIESTGTGESPLDATCFPKEKDTSDLPLQALPEGVDQEVFKQLPADIQEEILYGKSRENLKGKGSLSCPLHASRGVLSFFSTKQMQASRLSPRDTALPSKRVSAASPCEPGTSGLSPGSTSHPSCGKDCSYYIDSQLKDEQTSQGPTESQGCQFSSTNPAVSGFHSFPNLQTEQLFSTHRTVDSHKQTATASHQGLESHQGLESRELDSAEEKLPFPPDIDPQVFYELPEEVQKELMAEWE 706
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.eeeeeeeeeeee..eeeeeee----------------eeeee....eee---eeeee......---------------------.hhhhhh...-.---------------------------------hhhhh..hhhhhhhh-----hhhhh....eeeeeeeee....eeeeeeeeeee..eeee-eeeeeee.-------------------------------..................eeee-----------------eeeehhhheeeee----------eeeeee.....eeee-----------------eeeeeeee...........eeeeeeeeee-------------------........eeeeeeeeeee...---------........hhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------K---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S-----Y--------------------------------------------E----D-------------------------------R---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ai4 A   1 MSKGEELFTGVVPILVELDGDVNGHKFSVSG----------------EGEGDATYGKLT---LKFICTTGKLP---------------------VPWPTLVTTF-g---------------------------------VQCFARYPDHMKQHD-----FFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVN-RIELKGID-------------------------------FKEDGNILGHKLEYNYNSHNVY-----------------IMADKQKNGIKVN----------FKIRHNIEDGSVQLA-----------------DHYQQNTPIGDGPVLLPDNHYLSTQSALS-------------------KDPNEKRDHMVLLEFVTAAGIT---------KLPFPPDIDPQVFYELPEEVQKELMAEWE 271
                                    10        20        30|        -       |34        |-  |     51  |      -         -    |   60   | |   -         -         -        68        78   |    83        93       103       113       122      |  -         -         -       131       141       151         -       154       164         -|      174    |    -         -  |    187       197       207|        -         -|      218       228 |       - |     251       261       271
                                                         31               32         43  44        54                    55       64 |                                68            82    83                                   121 |    129                             130                  151               152         164        165           179               180                         208                 209                  230       243                            
                                                                                                                                    66-CR2                                                                                       122                                                                                                                                                                                                                                                

   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 3AI4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AI4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AI4)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (POLI_MOUSE | Q6R3M4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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:0071494    cellular response to UV-C    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 UV-C radiation stimulus. UV-C radiation (UV-C light) spans the wavelengths 100 to 280 nm.
    GO:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    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: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
        POLI_MOUSE | Q6R3M42kwu 2kwv

(-) Related Entries Specified in the PDB File

3ai5 CRYSTAL STRUCTURE OF YEAST ENHANCED GREEN FLUORESCENT PROTEIN UBIQUITIN FUSION PROTEIN