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(-) Description

Title :  CRYSTAL STRUCTURE OF WILDTYPE MENT IN THE NATIVE CONFORMATION
 
Authors :  J. A. Irving, J. C. Whisstock, A. M. Buckle, S. Mcgowan
Date :  25 May 06  (Deposition) - 18 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease Inhibitor, Serpin, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mcgowan, A. M. Buckle, J. A. Irving, P. C. Ong, T. A. Bashtannyk-Puhalovich, W. T. Kan, K. N. Henderson, Y. A. Bulynko E. Y. Popova, A. I. Smith, S. P. Bottomley, J. Rossjohn, S. A. Grigoryev R. N. Pike, J. C. Whisstock
X-Ray Crystal Structure Of Ment: Evidence For Functional Loop-Sheet Polymers In Chromatin Condensation.
Embo J. V. 25 3144 2006
PubMed-ID: 16810322  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601201

(-) Compounds

Molecule 1 - HETEROCHROMATIN-ASSOCIATED PROTEIN MENT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET3A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MENT-1
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: MENT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2H4R)

(-) Sites  (0, 0)

(no "Site" information available for 2H4R)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:406 -A:407

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H4R)

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSGALT000000209901ENSGALE00000198668chr2:68886128-6888607158SPB10_CHICK-00--
1.3ENSGALT000000209903ENSGALE00000138883chr2:68884812-68884636177SPB10_CHICK1-56561A:1-5656
1.4ENSGALT000000209904ENSGALE00000138892chr2:68884248-6888416584SPB10_CHICK57-84281A:57-637
1.5ENSGALT000000209905ENSGALE00000138886chr2:68883776-68883639138SPB10_CHICK85-130461A:91-13040
1.6ENSGALT000000209906ENSGALE00000138856chr2:68882877-68882760118SPB10_CHICK131-170401A:131-17040
1.7ENSGALT000000209907ENSGALE00000138882chr2:68882389-68882247143SPB10_CHICK170-217481A:170-21748
1.8ENSGALT000000209908ENSGALE00000138871chr2:68881414-68881247168SPB10_CHICK218-273561A:218-27356
1.9bENSGALT000000209909bENSGALE00000138898chr2:68880924-688797341191SPB10_CHICK274-4101371A:274-410 (gaps)137

(-) 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:371
 aligned with SPB10_CHICK | O73790 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:413
                               1                                                                                                                                                                                                                                                                                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407   
          SPB10_CHICK     - ---MEQVSASIGNFTVDLFNKLNETNRDKNIFFSPWSISSALALTYLAAKGSTAREMAEVLHFTEAVRAESSSVARPSRGRPKRRRMDPEHEQAENIHSGFKELLTAFNKPRNNYSLRSANRIYVEKTYALLPTYLQLSKKYYKAEPQKVNFKTAPEQSRKEINTWVEKQTESKIKNLLSSDDVKATTRLILVNAIYFKAEWEVKFQAEKTSIQPFRLSKNKSKPVKMMYMRDTFPVLIMEKMNFKMIELPYVKRELSMFILLPDDIKDGTTGLEQLERELTYERLSEWADSKMMTETLVDLHLPKFSLEDRIDLRDTLRNMGMTTAFTTNADFRGMTDKKDLAISKVIHQSFVAVDEKGTEAAAATAVIISFTTSVINHVLKFKVDHPFHFFIRHNKSKTILFFGRFCCPVE 410
               SCOP domains d2h4ra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2h4rA01 A:-2-198,A:302-355 Antithrombin, subunit I, domain 2                                                                                                                                             2h4rA02 A:199-301,A:361-404 Alpha-1-antitrypsin, domain 1                                              2h4rA01 A:-2-198,A:302-355                            -----2h               4rA02 A:199-301,A:361-404  ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhh..hhhhhhhhhhhh.....---------------------------hhhhhhhhhhhhhhhh......eeeeeeeeeee.....hhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhhh........hhhhh.....eeeeeeeeee.......hhhhheeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee.hhh.eeeeeeee.........hhhhhh..hhhhhhhhhh....eeeeeeeeee.eee..eeehhhhhhhh..hhhhh.................eeeeeeeeee.........---------------.eeee....eeeeeee....eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---Exon 1.3  PDB: A:1-56 UniProt: 1-56                     Exon 1.4  PDB: A:57-63      Exon 1.5  PDB: A:91-130 UniProt: 85-130       Exon 1.6  PDB: A:131-170                -----------------------------------------------Exon 1.8  PDB: A:218-273 UniProt: 218-273               Exon 1.9b  PDB: A:274-410 (gaps) UniProt: 274-410                                                                                         Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:170-217 UniProt: 170-217       ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2h4r A  -2 EISMEQVSASIGNFTVDLFNKLNETNRDKNIFFSPWSISSALALTYLAAKGSTAREMAEVLHFTEA---------------------------AENIHSGFKELLTAFNKPRNNYSLRSANRIYVEKTYALLPTYLQLSKKYYKAEPQKVNFKTAPEQSRKEINTWVEKQTESKIKNLLSSDDVKATTRLILVNAIYFKAEWEVKFQAEKTSIQPFRLSKNKSKPVKMMYMRDTFPVLIMEKMNFKMIELPYVKRELSMFILLPDDIKDGTTGLEQLERELTYERLSEWADSKMMTETLVDLHLPKFSLEDRIDLRDTLRNMGMTTAFTTNADFRGMTDKKDLAISKVIHQSFVAVDEKGTEAAA---------------VLKFKVDHPFHFFIRHNKSKTILFFGRFCCPVE 410
                                     7        17        27        37        47        57     |   -         -         -   |    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357    |    -         -|      387       397       407   
                                                                                            63                          91                                                                                                                                                                                                                                                                            362             378
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H4R)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SPB10_CHICK | O73790)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0031490    chromatin DNA binding    Interacting selectively and non-covalently with DNA that is assembled into chromatin.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0030261    chromosome condensation    The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0043362    nucleate erythrocyte maturation    A developmental process, independent of morphogenetic (shape) change, that is required for a nucleate erythrocyte to attain its fully functional state. A nucleate erythrocyte is an erythrocyte with a nucleus.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        SPB10_CHICK | O73790: 2dut 2h4p 2h4q

(-) Related Entries Specified in the PDB File

2h4p WILDTYPE MENT IN THE CLEAVED CONFORMATION
2h4q A M-LOOP DELETION VARIANT OF MENT IN THE CLEAVED CONFORMATION
2h4s A M-LOOP DELETION VARIANT OF MENT IN THE NATIVE CONFORMATION