Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE AND FUNCTION OF XENOPUS NO38-CORE, A HISTONE CHAPERONE IN THE NUCLEOLUS
 
Authors :  V. M. Namboodiri, I. V. Akey, M. S. Schmidt-Zachmann, J. F. Head, C. W. Akey
Date :  30 Aug 04  (Deposition) - 21 Dec 04  (Release) - 24 Feb 09  (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 :  No38, Drosophila Nucleoplasmin-Like Protein (Dnlp), Nucleoplasmin (Np), Histone Binding, X-Ray Crystallography, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Namboodiri, I. V. Akey, M. S. Schmidt-Zachmann, J. F. Head, C. W. Akey
The Structure And Function Of Xenopus No38-Core, A Histone Chaperone In The Nucleolus.
Structure V. 12 2149 2004
PubMed-ID: 15576029  |  Reference-DOI: 10.1016/J.STR.2004.09.017
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOPHOSMIN
    Chains: A, B, C, D, E, F, G, H, I, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PPEP-T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL CORE (RESIDUES 16-124)
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: NPM, NUCLEOLAR PHOSPHOPROTEIN B23, NUMATRIN, NUCLEOLAR PROTEIN NO38

 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 1XB9)

(-) Sites  (0, 0)

(no "Site" information available for 1XB9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XB9)

(-) Cis Peptide Bonds  (20, 20)

Asymmetric Unit
No.Residues
1Pro A:98 -Pro A:99
2Gly A:109 -Pro A:110
3Pro B:98 -Pro B:99
4Gly B:109 -Pro B:110
5Pro C:98 -Pro C:99
6Gly C:109 -Pro C:110
7Pro D:98 -Pro D:99
8Gly D:109 -Pro D:110
9Pro E:98 -Pro E:99
10Gly E:109 -Pro E:110
11Pro F:98 -Pro F:99
12Gly F:109 -Pro F:110
13Pro G:98 -Pro G:99
14Gly G:109 -Pro G:110
15Pro H:98 -Pro H:99
16Gly H:109 -Pro H:110
17Pro I:98 -Pro I:99
18Gly I:109 -Pro I:110
19Pro J:98 -Pro J:99
20Gly J:109 -Pro J:110

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XB9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XB9)

(-) Exons   (0, 0)

(no "Exon" information available for 1XB9)

(-) 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:108
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:108
                                    24        34        44        54        64        74        84        94       104       114        
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVALE 122
               SCOP domains d1xb9a_ A: Nucleophosmin (NO38)                                                                              SCOP domains
               CATH domains 1xb9A00 A:15-122  [code=2.60.120.340, no name defined]                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.....eeee.......eeeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1xb9 A  15 SQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVALE 122
                                    24        34        44        54        64        74        84        94       104       114        


Chain B from PDB  Type:PROTEIN  Length:107
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVAL 121
               SCOP domains d1xb9b_ B: Nucleophosmin (NO38)                                                                             SCOP domains
               CATH domains 1xb9B00 B:15-121  [code=2.60.120.340, no name defined]                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eeee.......eeeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1xb9 B  15 SQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVAL 121
                                    24        34        44        54        64        74        84        94       104       114       


Chain C from PDB  Type:PROTEIN  Length:104
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVA 120
               SCOP domains d1xb9c_ C: Nucleophosmin   (NO38)                                                                          SCOP domains
               CATH domains 1xb9C00 C:15-120  [code=  2.60.120.340, no name defined]                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eeee.....--.eeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1xb9 C  15 SQNFLFGCELKADKKEYSFKVEDD--EHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVA 120
                                    24        34   |  | 44        54        64        74        84        94       104       114      
                                                  38 41                                                                               


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:105
                                    24        34        44        54        64        74        84        94       104       114     
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLV 119
               SCOP domains d1xb9d_ D: Nucleoph osmin (NO38)                                                                          SCOP domains
               CATH domains 1xb9D00 D:15-119  [ code=2.60.120.340, no name defined]                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eee.-........eeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee....eeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1xb9 D  15 SQNFLFGCELKADKKEYSF-VEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLV 119
                                    24        |-|       44        54        64        74        84        94       104       114     
                                             33 |                                                                                    
                                               35                                                                                    


Chain E from PDB  Type:PROTEIN  Length:106
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVA 120
               SCOP domains d1xb9e_ E: Nucleophosmin (NO38)                                                                            SCOP domains
               CATH domains 1xb9E00 E:15-120  [code=2.60.120.340, no name defined]                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eeee.......eeeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1xb9 E  15 SQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVA 120
                                    24        34        44        54        64        74        84        94       104       114      


Chain F from PDB  Type:PROTEIN  Length:105
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:106
                                    24        34        44        54        64        74        84        94       104       114      
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVA 120
               SCOP domains d1xb9f_ F: Nucleophosm in (NO38)                                                                           SCOP domains
               CATH domains 1xb9F00 F:15-120  [cod e=2.60.120.340, no name defined]                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eeee...-.......eeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeee....eeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 1xb9 F  15 SQNFLFGCELKADKKEYSFKVE-DENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVA 120
                                    24        34 | |    44        54        64        74        84        94       104       114      
                                                36 |                                                                                  
                                                  38                                                                                  


Chain G from PDB  Type:PROTEIN  Length:105
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVAL 121
               SCOP domains d1xb9g_ G: Nucleophos  min (NO38)                                                                           SCOP domains
               CATH domains 1xb9G00 G:15-121  [co  de=2.60.120.340, no name defined]                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eeee..--....eeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeee......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1xb9 G  15 SQNFLFGCELKADKKEYSFKV--DENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVAL 121
                                    24        34|  |    44        54        64        74        84        94       104       114       
                                               35 38                                                                                   


Chain H from PDB  Type:PROTEIN  Length:107
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:108
                                    24        34        44        54        64        74        84        94       104       114        
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVALE 122
               SCOP domains d1xb9h_ H: Nucleophosmin  (NO38)                                                                             SCOP domains
               CATH domains 1xb9H00 H:15-122  [code= 2.60.120.340, no name defined]                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.....eeee.....-.eeeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 1xb9 H  15 SQNFLFGCELKADKKEYSFKVEDD-NEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVALE 122
                                    24        34   | |  44        54        64        74        84        94       104       114        
                                                  38 |                                                                                  
                                                    40                                                                                  


Chain I from PDB  Type:PROTEIN  Length:107
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVAL 121
               SCOP domains d1xb9i_ I: Nucleophosmin (NO38)                                                                             SCOP domains
               CATH domains 1xb9I00 I:15-121  [code=2.60.120.340, no name defined]                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eeee.......eeeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1xb9 I  15 SQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVAL 121
                                    24        34        44        54        64        74        84        94       104       114       


Chain J from PDB  Type:PROTEIN  Length:106
 aligned with NPM_XENLA | P07222 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:107
                                    24        34        44        54        64        74        84        94       104       114       
            NPM_XENLA    15 PQNFLFGCELKADKKEYSFKVEDDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVAL 121
               SCOP domains d1xb9j_ J: Nucleophos min (NO38)                                                                            SCOP domains
               CATH domains 1xb9J00 J:15-121  [co de=2.60.120.340, no name defined]                                                     CATH domains
           Pfam domains (1) -Nucleoplasmin-1xb9J0 1 J:16-121                                                                            Pfam domains (1)
           Pfam domains (2) -Nucleoplasmin-1xb9J0 2 J:16-121                                                                            Pfam domains (2)
           Pfam domains (3) -Nucleoplasmin-1xb9J0 3 J:16-121                                                                            Pfam domains (3)
           Pfam domains (4) -Nucleoplasmin-1xb9J0 4 J:16-121                                                                            Pfam domains (4)
           Pfam domains (5) -Nucleoplasmin-1xb9J0 5 J:16-121                                                                            Pfam domains (5)
           Pfam domains (6) -Nucleoplasmin-1xb9J0 6 J:16-121                                                                            Pfam domains (6)
           Pfam domains (7) -Nucleoplasmin-1xb9J0 7 J:16-121                                                                            Pfam domains (7)
           Pfam domains (8) -Nucleoplasmin-1xb9J0 8 J:16-121                                                                            Pfam domains (8)
           Pfam domains (9) -Nucleoplasmin-1xb9J0 9 J:16-121                                                                            Pfam domains (9)
          Pfam domains (10) -Nucleoplasmin-1xb9J1 0 J:16-121                                                                            Pfam domains (10)
         Sec.struct. author .eeeeeeeee.....eeee..-......eeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1xb9 J  15 SQNFLFGCELKADKKEYSFKV-DDENEHQLSLRTVSLGASAKDELHVVEAEGINYEGKTIKIALASLKPSVQPTVSLGGFEITPPVILRLKSGSGPVYVSGQHLVAL 121
                                    24        34| |     44        54        64        74        84        94       104       114       
                                               35 |                                                                                    
                                                 37
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 10)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Jelly Rolls (1293)
(-)
Homologous Superfamily: [code=2.60.120.340, no name defined] (6)
(-)
African clawed frog (Xenopus laevis) (4)
1a1xb9C00C:15-120
1b1xb9D00D:15-119
1c1xb9F00F:15-120
1d1xb9G00G:15-121
1e1xb9E00E:15-120
1f1xb9J00J:15-121
1g1xb9B00B:15-121
1h1xb9H00H:15-122
1i1xb9I00I:15-121
1j1xb9A00A:15-122

(-) Pfam Domains  (1, 10)

Asymmetric Unit
(-)
Clan: no clan defined [family: Nucleoplasmin] (6)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J   (NPM_XENLA | P07222)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    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:0032071    regulation of endodeoxyribonuclease activity    Any process that modulates the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
    GO:0060699    regulation of endoribonuclease activity    Any process that modulates the rate, frequency or extent of the catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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 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
(no "Ligands, Modified Residues, Ions" information available for 1xb9)
 
  Sites
(no "Sites" information available for 1xb9)
 
  Cis Peptide Bonds
    Gly A:109 - Pro A:110   [ RasMol ]  
    Gly B:109 - Pro B:110   [ RasMol ]  
    Gly C:109 - Pro C:110   [ RasMol ]  
    Gly D:109 - Pro D:110   [ RasMol ]  
    Gly E:109 - Pro E:110   [ RasMol ]  
    Gly F:109 - Pro F:110   [ RasMol ]  
    Gly G:109 - Pro G:110   [ RasMol ]  
    Gly H:109 - Pro H:110   [ RasMol ]  
    Gly I:109 - Pro I:110   [ RasMol ]  
    Gly J:109 - Pro J:110   [ RasMol ]  
    Pro A:98 - Pro A:99   [ RasMol ]  
    Pro B:98 - Pro B:99   [ RasMol ]  
    Pro C:98 - Pro C:99   [ RasMol ]  
    Pro D:98 - Pro D:99   [ RasMol ]  
    Pro E:98 - Pro E:99   [ RasMol ]  
    Pro F:98 - Pro F:99   [ RasMol ]  
    Pro G:98 - Pro G:99   [ RasMol ]  
    Pro H:98 - Pro H:99   [ RasMol ]  
    Pro I:98 - Pro I:99   [ RasMol ]  
    Pro J:98 - Pro J:99   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1xb9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NPM_XENLA | P07222
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NPM_XENLA | P07222
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NPM_XENLA | P07222: 1xe0

(-) Related Entries Specified in the PDB File

1k5j A RELATED HISTONE CHAPERONE FROM XENOPUS LAEVIS
1nlq NUCLEOPLASMIN-LIKE PROTEIN FROM DROSOPHILA MELANOGLASTER
1xe0