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(-) Description

Title :  HUMAN NUCLEOPLASMIN (NPM2): A HISTONE CHAPERONE IN OOCYTES AND EARLY EMBRYOS
 
Authors :  O. Platonova, J. F. Head, C. W. Akey
Date :  23 Jul 11  (Deposition) - 21 Sep 11  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,C,D,E  (1x)
Biol. Unit 2:  F,G,H,I,J  (1x)
Keywords :  Beta-Barrel Jelly Roll Topology, Histone Chaperone, H2A-H2B Dimer And H3-H4 Tetramer, Oocytes And Early Embryos, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. Platonova, I. V. Akey, J. F. Head, C. W. Akey
Crystal Structure And Function Of Human Nucleoplasmin (Npm2): A Histone Chaperone In Oocytes And Embryos.
Biochemistry V. 50 8078 2011
PubMed-ID: 21863821  |  Reference-DOI: 10.1021/BI2006652

(-) Compounds

Molecule 1 - NUCLEOPLASMIN-2
    ChainsB, E, D, A, C, H, I, J, F, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePET23
    FragmentNPM2 OLIGOMERISATION DOMAIN (UNP RESIDUES 14-122)
    GeneNPM2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit ABCDEFGHIJ
Biological Unit 1 (1x)ABCDE     
Biological Unit 2 (1x)     FGHIJ

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3T30)

(-) Sites  (0, 0)

(no "Site" information available for 3T30)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T30)

(-) Cis Peptide Bonds  (24, 24)

Asymmetric Unit
No.Residues
1Pro B:66 -Pro B:67
2Pro B:100 -Pro B:101
3Gly B:111 -Pro B:112
4Pro E:100 -Pro E:101
5Gly E:111 -Pro E:112
6Pro D:100 -Pro D:101
7Gly D:111 -Pro D:112
8Pro A:100 -Pro A:101
9Gly A:111 -Pro A:112
10Pro C:100 -Pro C:101
11Gly C:111 -Pro C:112
12Pro H:66 -Pro H:67
13Pro H:100 -Pro H:101
14Gly H:111 -Pro H:112
15Pro I:66 -Pro I:67
16Pro I:100 -Pro I:101
17Gly I:111 -Pro I:112
18Pro J:66 -Pro J:67
19Pro J:100 -Pro J:101
20Gly J:111 -Pro J:112
21Pro F:100 -Pro F:101
22Gly F:111 -Pro F:112
23Pro G:100 -Pro G:101
24Gly G:111 -Pro G:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3T30)

(-) Exons   (0, 0)

(no "Exon" information available for 3T30)

(-) 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:93
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:105
                                    25        35        45        55        65        75        85        95       105       115     
           NPM2_HUMAN    16 TVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
               SCOP domains d3t30a_ A: automate       d matches                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeee..-------.eeeeeeeee........eeeeee....-----...eeeeee......eeeeeeeee...eeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3t30 A  16 TVLWGCELSQERRTWTFRP-------CRLLLHTICLGEKAKEEMHRVEILPPAN-----MQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
                                    25        |-      | 45        55        65   |    75        85        95       105       115     
                                             34      42                         69    75                                             

Chain B from PDB  Type:PROTEIN  Length:92
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
           NPM2_HUMAN    15 TTVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
               SCOP domains d3t30b_ B: automate       d matches                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeee.-------..eeeeeeeee........eeeeee..--------..eeeeee......eeeeeeeee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3t30 B  15 TTVLWGCELSQERRTWTFR-------SCRLLLHTICLGEKAKEEMHRVEILPP--------QPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
                                    24        |-      | 44        54        64  |      - |      84        94       104       114       
                                             33      41                        67       76                                             

Chain C from PDB  Type:PROTEIN  Length:95
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
           NPM2_HUMAN    15 TTVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
               SCOP domains d3t30c_ C: automated      matches                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeee..-----...eeeeeeeee........eeeeee..-------...eeeeee......eeeeeeeee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3t30 C  15 TTVLWGCELSQERRTWTFRP-----QSCRLLLHTICLGEKAKEEMHRVEILPP-------MQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
                                    24        34     |  44        54        64  |      -|       84        94       104       114       
                                              34    40                         67      75                                              

Chain D from PDB  Type:PROTEIN  Length:90
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
           NPM2_HUMAN    15 TTVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
               SCOP domains d3t30d_ D: automated        matches                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeee..-------.eeeeeeeee........eeeeee.----------.eeeeee......eeeeeeeee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3t30 D  15 TTVLWGCELSQERRTWTFRP-------CRLLLHTICLGEKAKEEMHRVEILP----------PVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
                                    24        34       |44        54        64 |       -  |     84        94       104       114       
                                              34      42                      66         77                                            

Chain E from PDB  Type:PROTEIN  Length:92
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:104
                                    26        36        46        56        66        76        86        96       106       116    
           NPM2_HUMAN    17 VLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
               SCOP domains d3t30e_ E: automat     ed matches                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeee..-----....eeeeeeee........eeeeee...-------..eeeeee......eeeeeeeee...eeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 3t30 E  17 VLWGCELSQERRTWTFRP-----QSCRLLLHTICLGEKAKEEMHRVEILPPA-------QPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
                                    26       | -   |    46        56        66 |      76        86        96       106       116    
                                            34    40                          68      76                                            

Chain F from PDB  Type:PROTEIN  Length:91
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:105
                                    25        35        45        55        65        75        85        95       105       115     
           NPM2_HUMAN    16 TVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
               SCOP domains d3t30f_ F: automated       matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....eeee...------.eeeeeeeee........eeeeee..--------..eeeeee......eeeeeeeee...eeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3t30 F  16 TVLWGCELSQERRTWTFRPQ------CRLLLHTICLGEKAKEEMHRVEILPP--------QPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
                                    25        35      | 45        55        65 |       -|       85        95       105       115     
                                              35     42                       67       76                                            

Chain G from PDB  Type:PROTEIN  Length:94
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
           NPM2_HUMAN    15 TTVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
               SCOP domains d3t30g_ G: automated       matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.....eeee...------.eeeeeeeee........eeeee....------...eeeeee......eeeeeeeee...eeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3t30 G  15 TTVLWGCELSQERRTWTFRPQ------CRLLLHTICLGEKAKEEMHRVEILPPA------MQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
                                    24        34|      |44        54        64   |     -|       84        94       104       114      
                                               35     42                        68     75                                             

Chain H from PDB  Type:PROTEIN  Length:93
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
           NPM2_HUMAN    15 TTVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
               SCOP domains d3t30h_ H: automated       matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeee..------..eeeeeeeee........eeeeee..--------..eeeeee......eeeeeeeee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3t30 H  15 TTVLWGCELSQERRTWTFRP------SCRLLLHTICLGEKAKEEMHRVEILPP--------QPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
                                    24        34      | 44        54        64  |      - |      84        94       104       114       
                                              34     41                        67       76                                             

Chain I from PDB  Type:PROTEIN  Length:92
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
           NPM2_HUMAN    15 TTVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
               SCOP domains d3t30i_ I: automated       matches                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.....eeee..------..eeeeeeeee........eeeeee..---------.eeeeee......eeeeeeeee...eeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 3t30 I  15 TTVLWGCELSQERRTWTFRP------SCRLLLHTICLGEKAKEEMHRVEILPP---------PVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQERY 121
                                    24        34      | 44        54        64  |      -  |     84        94       104       114       
                                              34     41                        67        77                                            

Chain J from PDB  Type:PROTEIN  Length:90
 aligned with NPM2_HUMAN | Q86SE8 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
           NPM2_HUMAN    15 TTVLWGCELSQERRTWTFRPQLEGKQSCRLLLHTICLGEKAKEEMHRVEILPPANQEDKKMQPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
               SCOP domains d3t30j_ J: automat         ed matches                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeehhhh.eeee---------.eeeeeeeee........eeeeee...-------..eeeeee......eeeeeeeee...eeeeeee....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 3t30 J  15 TTVLWGCELSQERRTWTF---------CRLLLHTICLGEKAKEEMHRVEILPPA-------QPVTIASLQASVLPMVSMVGVQLSPPVTFQLRAGSGPVFLSGQER 120
                                    24       | -       |44        54        64   |     - |      84        94       104       114      
                                            32        42                        68      76                                            

   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, 10)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T30)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J   (NPM2_HUMAN | Q86SE8)
molecular function
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0009790    embryo development    The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0009994    oocyte differentiation    The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete.
    GO:0051054    positive regulation of DNA metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA.
    GO:0045740    positive regulation of DNA replication    Any process that activates or increases the frequency, rate or extent of DNA replication.
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0045836    positive regulation of meiotic nuclear division    Any process that activates or increases the frequency, rate or extent of meiosis.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0007096    regulation of exit from mitosis    Any process involved in the progression from anaphase/telophase to G1 that is associated with a conversion from high to low mitotic CDK activity.
    GO:0007338    single fertilization    The union of male and female gametes to form a zygote.
cellular component
    GO:0000789    cytoplasmic chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the cytoplasm.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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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  Cis Peptide Bonds
    Gly A:111 - Pro A:112   [ RasMol ]  
    Gly B:111 - Pro B:112   [ RasMol ]  
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