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(-) Description

Title :  CRYSTAL STRUCTURE OF XENOPUS LAEVIS REPLICATION INITIATION FACTOR MCM10 INTERNAL DOMAIN
 
Authors :  E. M. Warren, B. F. Eichman
Date :  27 Aug 08  (Deposition) - 09 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Ob-Fold, Zinc Finger, Ccch, Dna Replication, Metal-Binding, Nucleus, Zinc-Finger, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Warren, S. Vaithiyalingam, J. Haworth, B. Greer, A. K. Bielinsky W. J. Chazin, B. F. Eichman
Structural Basis For Dna Binding By Replication Initiator Mcm10.
Structure V. 16 1892 2008
PubMed-ID: 19081065  |  Reference-DOI: 10.1016/J.STR.2008.10.005

(-) Compounds

Molecule 1 - PROTEIN MCM10 HOMOLOG
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 230-427
    Gene: MCM10
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:381 , CYS A:391 , CYS A:403 , HIS A:406BINDING SITE FOR RESIDUE ZN A 500
2AC2SOFTWARECYS B:381 , CYS B:391 , CYS B:403 , HIS B:406BINDING SITE FOR RESIDUE ZN B 501
3AC3SOFTWARECYS C:381 , CYS C:391 , CYS C:403 , HIS C:406BINDING SITE FOR RESIDUE ZN C 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr B:356 -Asp B:357
2Pro C:231 -Val C:232
3Thr C:296 -Pro C:297

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3EBE)

(-) Sequences/Alignments

Asymmetric 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:172
 aligned with MCM10_XENLA | Q5EAW4 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:179
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404         
          MCM10_XENLA   235 QYHVEKFSGLRIRKPRVSSSEMERKMNGRKLIRLAQLQNKIATEKLEEEDWVTFGVIVKKITPQSSNNGKTFSIWRLNDLKDLDKYISLFLFGDVHKEHWKTDQGTVIGLLNANPMKPKEGTDEVCLSVDNPQKVLLMGDAVDLGTCKARKKNGDPCTQMVNLNDCEYCQYHVQAQYKK 413
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee....hhhhhhhhhh..ee.hhhhhhhhhhh.......eeeeeeeeeee..-------..eeeeee........eeeeehhhhhhhhh.....eeeeee..ee.........eeee..hhh.eeeeeee..eee.............eee......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebe A 235 QYHVEKFSGLRIRKPRVSSSEMERKMNGRKLIRLAQLQNKIATEKLEEEDWVTFGVIVKKITP-------TFSIWRLNDLKDLDKYISLFLFGDVHKEHWKTDQGTVIGLLNANPMKPKEGTDEVCLSVDNPQKVLLMGDAVDLGTCKARKKNGDPCTQMVNLNDCEYCQYHVQAQYKK 413
                                   244       254       264       274       284       294  |      -|      314       324       334       344       354       364       374       384       394       404         
                                                                                        297     305                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with MCM10_XENLA | Q5EAW4 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:174
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404    
          MCM10_XENLA   235 QYHVEKFSGLRIRKPRVSSSEMERKMNGRKLIRLAQLQNKIATEKLEEEDWVTFGVIVKKITPQSSNNGKTFSIWRLNDLKDLDKYISLFLFGDVHKEHWKTDQGTVIGLLNANPMKPKEGTDEVCLSVDNPQKVLLMGDAVDLGTCKARKKNGDPCTQMVNLNDCEYCQYHVQ 408
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee....eeee....hhhhhhhhhh..ee.hhhhhhhhhhh.......eeeeeeeeeee.--------..eeeeee.......eeeeeehhhhhhhhh.....eeeeee..ee.........eeeee.hhh.eeeeeee..eee.............eee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ebe B 235 QYHVEKFSGLRIRKPRVSSSEMERKMNGRKLIRLAQLQNKIATEKLEEEDWVTFGVIVKKIT--------TFSIWRLNDLKDLDKYISLFLFGDVHKEHWKTDQGTVIGLLNANPMKPKEGTDEVCLSVDNPQKVLLMGDAVDLGTCKARKKNGDPCTQMVNLNDCEYCQYHVQ 408
                                   244       254       264       274       284       294 |       -|      314       324       334       344       354       364       374       384       394       404    
                                                                                       296      305                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:177
 aligned with MCM10_XENLA | Q5EAW4 from UniProtKB/Swiss-Prot  Length:860

    Alignment length:189
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410         
          MCM10_XENLA   231 PVGQQYHVEKFSGLRIRKPRVSSSEMERKMNGRKLIRLAQLQNKIATEKLEEEDWVTFGVIVKKITPQSSNNGKTFSIWRLNDLKDLDKYISLFLFGDVHKEHWKTDQGTVIGLLNANPMKPKEGTDEVCLSVDNPQKVLLMGDAVDLGTCKARKKNGDPCTQMVNLNDCEYCQYHVQAQYKKVSSKRA 419
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee....hhhhhhhhhh..ee.hhhhhhhhhhh.......eeeeeeeeeee..--------.eeeeee........eeeeehhhhhhhhh.....eeeeee..ee.----....eeeee.hhh.eeeeeee..eee.............eee.........hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ebe C 231 PVGQQYHVEKFSGLRIRKPRVSSSEMERKMNGRKLIRLAQLQNKIATEKLEEEDWVTFGVIVKKITP--------FSIWRLNDLKDLDKYISLFLFGDVHKEHWKTDQGTVIGLLNANPM----GTDEVCLSVDNPQKVLLMGDAVDLGTCKARKKNGDPCTQMVNLNDCEYCQYHVQAQYKKVSSKRA 419
                                   240       250       260       270       280       290      |  -     | 310       320       330       340       350    |  360       370       380       390       400       410         
                                                                                            297      306                                         350  355
   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 3EBE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (MCM10_XENLA | Q5EAW4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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.
cellular component
    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
        MCM10_XENLA | Q5EAW4: 2kwq 3h15 4jbz

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