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(-) Description

Title :  STRUCTURAL POLYMORPHISM IN THE N-TERMINAL OLIGOMERIZATION DOMAIN OF NPM1
 
Authors :  D. Mitrea, G. Royappa, M. Buljan, M. Yun, N. Pytel, J. Satumba, A. Nourse M. M. Babu, S. W. White, R. W. Kriwacki
Date :  17 Oct 13  (Deposition) - 12 Mar 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Histone Chaperone, Nucleolar Protein, Phosphoprotein, Structural Polymorphism, Pentamer, Ribosome Biogenesis, Regulated Unfolding, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Mitrea, C. R. Grace, M. Buljan, M. K. Yun, N. J. Pytel, J. Satumba, A. Nourse, C. G. Park, M. Madan Babu, S. W. White, R. W. Kriwacki
Structural Polymorphism In The N-Terminal Oligomerization Domain Of Npm1.
Proc. Natl. Acad. Sci. Usa V. 111 4466 2014
PubMed-ID: 24616519  |  Reference-DOI: 10.1073/PNAS.1321007111

(-) Compounds

Molecule 1 - NUCLEOPHOSMIN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN OF NPM1, UNP RESIDUES 1-130
    Gene: NPM1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: NPM, NUCLEOLAR PHOSPHOPROTEIN B23, NUCLEOLAR PROTEIN NO38, NUMATRIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1CO5Ligand/IonCOBALT (II) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:28 , HIS A:30BINDING SITE FOR RESIDUE CO A 601
2AC2SOFTWAREASP B:28 , HIS B:30 , HOH B:355 , HOH B:357 , HOH B:358BINDING SITE FOR RESIDUE CO B 201
3AC3SOFTWAREASP C:28 , HIS C:30BINDING SITE FOR RESIDUE CO C 201
4AC4SOFTWAREASP D:28 , HIS D:30BINDING SITE FOR RESIDUE CO D 201
5AC5SOFTWAREASP E:28 , HIS E:30BINDING SITE FOR RESIDUE CO E 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4N8M)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Pro A:96 -Pro A:97
2Gly A:107 -Pro A:108
3Pro B:96 -Pro B:97
4Gly B:107 -Pro B:108
5Pro C:96 -Pro C:97
6Gly C:107 -Pro C:108
7Pro D:96 -Pro D:97
8Gly D:107 -Pro D:108
9Pro E:96 -Pro E:97
10Gly E:107 -Pro E:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N8M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N8M)

(-) Exons   (0, 0)

(no "Exon" information available for 4N8M)

(-) 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:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee.....eee....hhh.eeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4n8m A  13 RPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAVE 120
                                    22        32        42        52        62        72        82        92       102       112        


Chain B from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d4n8mb_ B: automated matches                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.....eee.......eeeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4n8m B  13 RPQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAV 119
                                    22        32        42        52        62        72        82        92       102       112       


Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eee....hhh.eeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4n8m C  14 PQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAV 119
                                    23        33        43        53        63        73        83        93       103       113      


Chain D from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eee.......eeeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4n8m D  14 PQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVA 118
                                    23        33        43        53        63        73        83        93       103       113     


Chain E from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....eee.......eeeeeeeeeee........eeeeeeee.....eeeeeeeee......eeeeeeeee...eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4n8m E  14 PQNYLFGCELKADKDYHFKVDNDENEHQLSLRTVSLGAGAKDELHIVEAEAMNYEGSPIKVTLATLKMSVQPTVSLGGFEITPPVVLRLKCGSGPVHISGQHLVAV 119
                                    23        33        43        53        63        73        83        93       103       113
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N8M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N8M)

(-) Gene Ontology  (80, 80)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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