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PDBsum entry 1k5j
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protein Protein-protein interface(s) links
Chaperone PDB id
1k5j

 

 

 

 

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Contents
Protein chains
94 a.a. *
96 a.a. *
89 a.a. *
Waters ×147
* Residue conservation analysis
PDB id:
1k5j
Name: Chaperone
Title: The crystal structure of nucleoplasmin-core
Structure: Nucleoplasmin core. Chain: a, b, c, d, e. Fragment: nucleoplasmin core. Engineered: yes. Mutation: yes
Source: Xenopus laevis. African clawed frog. Organism_taxid: 8355. Gene: nucleoplasmin. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Pentamer (from PQS)
Resolution:
2.30Å     R-factor:   0.219     R-free:   0.252
Authors: S.Dutta,I.V.Akey,C.Dingwall,K.L.Hartman,T.Laue,R.T.Nolte,J.F.Head, C.W.Akey
Key ref:
S.Dutta et al. (2001). The crystal structure of nucleoplasmin-core: implications for histone binding and nucleosome assembly. Mol Cell, 8, 841-853. PubMed id: 11684019 DOI: 10.1016/S1097-2765(01)00354-9
Date:
10-Oct-01     Release date:   01-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05221  (NUPL_XENLA) -  Nucleoplasmin from Xenopus laevis
Seq:
Struc: 		200 a.a.
94 a.a.*
Protein chains
Pfam   ArchSchema ?
P05221  (NUPL_XENLA) -  Nucleoplasmin from Xenopus laevis
Seq:
Struc: 		200 a.a.
96 a.a.*
Protein chain
Pfam   ArchSchema ?
P05221  (NUPL_XENLA) -  Nucleoplasmin from Xenopus laevis
Seq:
Struc: 		200 a.a.
89 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/S1097-2765(01)00354-9 Mol Cell 8:841-853 (2001)
PubMed id: 11684019  
 
 
The crystal structure of nucleoplasmin-core: implications for histone binding and nucleosome assembly.
S.Dutta, I.V.Akey, C.Dingwall, K.L.Hartman, T.Laue, R.T.Nolte, J.F.Head, C.W.Akey.
 
  ABSTRACT  
 
The efficient assembly of histone complexes and nucleosomes requires the participation of molecular chaperones. Currently, there is a paucity of data on their mechanism of action. We now present the structure of an N-terminal domain of nucleoplasmin (Np-core) at 2.3 A resolution. The Np-core monomer is an eight-stranded beta barrel that fits snugly within a stable pentamer. In the crystal, two pentamers associate to form a decamer. We show that both Np and Np-core are competent to assemble large complexes that contain the four core histones. Further experiments and modeling suggest that these complexes each contain five histone octamers which dock to a central Np decamer. This work has important ramifications for models of histone storage, sperm chromatin decondensation, and nucleosome assembly.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structure of the Np Monomer and Pentamer(A) A face view of the Np-core pentamer is shown as a ribbon diagram, viewed from the pentamer-pentamer interface. A single monomer is highlighted in cranberry. Note the prominent β hairpin that extends radially from the subunit-subunit interface.(B) An Np-core monomer is shown at higher magnification, and each β strand is labeled.(C) The Np-core monomer in (B) was rotated vert, similar 90° away from the reader to present a side view, as seen from outside the pentamer. Positions of the conserved A1 tract (red dots), β hairpin, AKDE, and GSGP loops are indicated.(D) The Np-core monomer is shown in a similar orientation as in (C), except that it is viewed from the central 5-fold axis 		Figure 4.
Figure 4. Structure of the Np Decamer within Crystals(A) The Np decamer is shown, as viewed along the 5-fold axis. The two pentamers are offset by vert, similar 15°, and individual monomers within the top and bottom pentamers are labeled A′–E′ and A–E, respectively.(B) The Np decamer has an hourglass shape when viewed from the side, along a 2-fold axis. Localized negative charges are present near the pentamer-pentamer interface. In addition, a pair of opposing Lys57 residues are marked with an asterisk (see [D] and [F]).(C) A surface view of the Np pentamer is shown from within the pentamer-pentamer interface. Alternating positive (blue) and negative (red) charges that arise from Lys82 and Asp58 form an inner ring (black dots with white circles). At higher radius, Lys57 and Glu59 from the AKDE motif are revealed (see labeling key). The β hairpins form a distinctive projection.(D) A side view is shown of two Np monomers that face each other across the pentamer-pentamer interface. Lys82 and Asp58 form a pair of water-mediated, charge-based interactions that span the interface. In addition, Lys57 and Glu59 form an intramonomer salt bridge (see [F]).(E) A close-up is shown of a pair of charge-based interactions formed by Lys82, Asp58, and intervening waters.(F) A close-up is shown of an intramonomer salt bridge formed by Lys57, Glu59, and a bound water molecule. This salt bridge may neutralize potentially destabilizing interactions between opposing Lys57 residues (see [B] and [D])
 
  The above figures are reprinted by permission from Cell Press: Mol Cell (2001, 8, 841-853) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21329878 A.Bowman, R.Ward, N.Wiechens, V.Singh, H.El-Mkami, D.G.Norman, and T.Owen-Hughes (2011).
The histone chaperones Nap1 and Vps75 bind histones H3 and H4 in a tetrameric conformation.
  Mol Cell, 41, 398-408.  
21220123 S.Yuan, X.Yu, M.Topf, L.Dorstyn, S.Kumar, S.J.Ludtke, and C.W.Akey (2011).
Structure of the Drosophila apoptosome at 6.9 å resolution.
  Structure, 19, 128-140.
PDB codes: 1vt4 3iz8
20444609 C.Das, J.K.Tyler, and M.E.Churchill (2010).
The histone shuffle: histone chaperones in an energetic dance.
  Trends Biochem Sci, 35, 476-489.  
20142844 H.Li, and S.Luan (2010).
AtFKBP53 is a histone chaperone required for repression of ribosomal RNA gene expression in Arabidopsis.
  Cell Res, 20, 357-366.  
20141833 M.Ransom, B.K.Dennehey, and J.K.Tyler (2010).
Chaperoning histones during DNA replication and repair.
  Cell, 140, 183-195.  
20504901 P.Drané, K.Ouararhni, A.Depaux, M.Shuaib, and A.Hamiche (2010).
The death-associated protein DAXX is a novel histone chaperone involved in the replication-independent deposition of H3.3.
  Genes Dev, 24, 1253-1265.  
19067583 C.A.Galea, A.A.High, J.C.Obenauer, A.Mishra, C.G.Park, M.Punta, A.Schlessinger, J.Ma, B.Rost, C.A.Slaughter, and R.W.Kriwacki (2009).
Large-scale analysis of thermostable, mammalian proteins provides insights into the intrinsically disordered proteome.
  J Proteome Res, 8, 211-226.  
19176479 J.Gill, M.Yogavel, A.Kumar, H.Belrhali, S.K.Jain, M.Rug, M.Brown, A.G.Maier, and A.Sharma (2009).
Crystal structure of malaria parasite nucleosome assembly protein: DISTINCT MODES OF PROTEIN LOCALIZATION AND HISTONE RECOGNITION.
  J Biol Chem, 284, 10076-10087.
PDB code: 3fs3
18367526 C.B.Buck, N.Cheng, C.D.Thompson, D.R.Lowy, A.C.Steven, J.T.Schiller, and B.L.Trus (2008).
Arrangement of L2 within the papillomavirus capsid.
  J Virol, 82, 5190-5197.  
17541954 C.Iribarren, V.Morin, M.Puchi, and M.Imschenetzky (2008).
Sperm nucleosomes disassembly is a requirement for histones proteolysis during male pronucleus formation.
  J Cell Biochem, 103, 447-455.  
18547526 I.Vakonakis, T.Langenhan, S.Prömel, A.Russ, and I.D.Campbell (2008).
Solution structure and sugar-binding mechanism of mouse latrophilin-1 RBL: a 7TM receptor-attached lectin-like domain.
  Structure, 16, 944-953.  
18332108 K.Murano, M.Okuwaki, M.Hisaoka, and K.Nagata (2008).
Transcription regulation of the rRNA gene by a multifunctional nucleolar protein, B23/nucleophosmin, through its histone chaperone activity.
  Mol Cell Biol, 28, 3114-3126.  
18456819 R.M.Finn, K.Browne, K.C.Hodgson, and J.Ausió (2008).
sNASP, a histone H1-specific eukaryotic chaperone dimer that facilitates chromatin assembly.
  Biophys J, 95, 1314-1325.  
17289584 E.Luk, N.D.Vu, K.Patteson, G.Mizuguchi, W.H.Wu, A.Ranjan, J.Backus, S.Sen, M.Lewis, Y.Bai, and C.Wu (2007).
Chz1, a nuclear chaperone for histone H2AZ.
  Mol Cell, 25, 357-368.  
17879352 H.H.Lee, H.S.Kim, J.Y.Kang, B.I.Lee, J.Y.Ha, H.J.Yoon, S.O.Lim, G.Jung, and S.W.Suh (2007).
Crystal structure of human nucleophosmin-core reveals plasticity of the pentamer-pentamer interface.
  Proteins, 69, 672-678.
PDB code: 2p1b
17937816 J.Dundas, T.A.Binkowski, B.DasGupta, and J.Liang (2007).
Topology independent protein structural alignment.
  BMC Bioinformatics, 8, 388.  
17984962 L.De Koning, A.Corpet, J.E.Haber, and G.Almouzni (2007).
Histone chaperones: an escort network regulating histone traffic.
  Nat Struct Mol Biol, 14, 997.  
17292837 M.Agez, J.Chen, R.Guerois, C.van Heijenoort, J.Y.Thuret, C.Mann, and F.Ochsenbein (2007).
Structure of the histone chaperone ASF1 bound to the histone H3 C-terminal helix and functional insights.
  Structure, 15, 191-199.
PDB code: 2iij
17510054 S.Bañuelos, M.J.Omaetxebarria, I.Ramos, M.R.Larsen, I.Arregi, O.N.Jensen, J.M.Arizmendi, A.Prado, and A.Muga (2007).
Phosphorylation of both nucleoplasmin domains is required for activation of its chromatin decondensation activity.
  J Biol Chem, 282, 21213-21221.  
17360516 S.Muto, M.Senda, Y.Akai, L.Sato, T.Suzuki, R.Nagai, T.Senda, and M.Horikoshi (2007).
Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone chaperone activity.
  Proc Natl Acad Sci U S A, 104, 4285-4290.
PDB code: 2e50
16510276 A.Gunjan, J.Paik, and A.Verreault (2006).
The emergence of regulated histone proteolysis.
  Curr Opin Genet Dev, 16, 112-118.  
17000757 B.Friedrich, C.Quensel, T.Sommer, E.Hartmann, and M.Köhler (2006).
Nuclear localization signal and protein context both mediate importin alpha specificity of nuclear import substrates.
  Mol Cell Biol, 26, 8697-8709.  
16940514 H.Si, S.C.Verma, and E.S.Robertson (2006).
Proteomic analysis of the Kaposi's sarcoma-associated herpesvirus terminal repeat element binding proteins.
  J Virol, 80, 9017-9030.  
16449640 H.Tamada, N.Van Thuan, P.Reed, D.Nelson, N.Katoku-Kikyo, J.Wudel, T.Wakayama, and N.Kikyo (2006).
Chromatin decondensation and nuclear reprogramming by nucleoplasmin.
  Mol Cell Biol, 26, 1259-1271.  
16751661 J.M.Eirín-López, L.J.Frehlick, and J.Ausió (2006).
Long-term evolution and functional diversification in the members of the nucleophosmin/nucleoplasmin family of nuclear chaperones.
  Genetics, 173, 1835-1850.  
16646973 L.J.Frehlick, J.M.Eirín-López, E.D.Jeffery, D.F.Hunt, and J.Ausió (2006).
The characterization of amphibian nucleoplasmins yields new insight into their role in sperm chromatin remodeling.
  BMC Genomics, 7, 99.  
17113241 M.J.Lim, and X.W.Wang (2006).
Nucleophosmin and human cancer.
  Cancer Detect Prev, 30, 481-490.  
16716593 R.J.Ellis (2006).
Molecular chaperones: assisting assembly in addition to folding.
  Trends Biochem Sci, 31, 395-401.  
16679321 T.Enomoto, M.S.Lindström, A.Jin, H.Ke, and Y.Zhang (2006).
Essential role of the B23/NPM core domain in regulating ARF binding and B23 stability.
  J Biol Chem, 281, 18463-18472.  
16984370 T.Naoe, T.Suzuki, H.Kiyoi, and T.Urano (2006).
Nucleophosmin: a versatile molecule associated with hematological malignancies.
  Cancer Sci, 97, 963-969.  
16287087 Y.Qiu, V.Tereshko, Y.Kim, R.Zhang, F.Collart, M.Yousef, A.Kossiakoff, and A.Joachimiak (2006).
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.
  Proteins, 62, 8.
PDB code: 1r4v
15687486 K.F.Tóth, J.Mazurkiewicz, and K.Rippe (2005).
Association states of nucleosome assembly protein 1 and its complexes with histones.
  J Biol Chem, 280, 15690-15699.  
15713634 K.Matsumoto, K.J.Tanaka, and M.Tsujimoto (2005).
An acidic protein, YBAP1, mediates the release of YB-1 from mRNA and relieves the translational repression activity of YB-1.
  Mol Cell Biol, 25, 1779-1792.  
16107701 V.Swaminathan, A.H.Kishore, K.K.Febitha, and T.K.Kundu (2005).
Human histone chaperone nucleophosmin enhances acetylation-dependent chromatin transcription.
  Mol Cell Biol, 25, 7534-7545.  
15284896 A.Prado, I.Ramos, L.J.Frehlick, A.Muga, and J.Ausió (2004).
Nucleoplasmin: a nuclear chaperone.
  Biochem Cell Biol, 82, 437-445.  
15576023 R.N.Dutnall (2004).
Nucleosome assembly: more than electric in the making?
  Structure, 12, 2098-2100.  
15574324 S.D.Benson, J.K.Bamford, D.H.Bamford, and R.M.Burnett (2004).
Does common architecture reveal a viral lineage spanning all three domains of life?
  Mol Cell, 16, 673-685.  
15576029 V.M.Namboodiri, I.V.Akey, M.S.Schmidt-Zachmann, J.F.Head, and C.W.Akey (2004).
The structure and function of Xenopus NO38-core, a histone chaperone in the nucleolus.
  Structure, 12, 2149-2160.
PDB codes: 1xb9 1xe0
15583381 V.M.Namboodiri, M.S.Schmidt-Zachmann, J.F.Head, and C.W.Akey (2004).
Purification, crystallization and preliminary X-ray analysis of the N-terminal domain of NO38, a nucleolar protein from Xenopus laevis.
  Acta Crystallogr D Biol Crystallogr, 60, 2325-2327.  
12791680 C.Arnan, N.Saperas, C.Prieto, M.Chiva, and J.Ausió (2003).
Interaction of nucleoplasmin with core histones.
  J Biol Chem, 278, 31319-31324.  
12581654 C.W.Akey, and K.Luger (2003).
Histone chaperones and nucleosome assembly.
  Curr Opin Struct Biol, 13, 6.  
12928440 S.J.McBryant, Y.J.Park, S.M.Abernathy, P.J.Laybourn, J.K.Nyborg, and K.Luger (2003).
Preferential binding of the histone (H3-H4)2 tetramer by NAP1 is mediated by the amino-terminal histone tails.
  J Biol Chem, 278, 44574-44583.  
14680630 S.M.Daganzo, J.P.Erzberger, W.M.Lam, E.Skordalakes, R.Zhang, A.A.Franco, S.J.Brill, P.D.Adams, J.M.Berger, and P.D.Kaufman (2003).
Structure and function of the conserved core of histone deposition protein Asf1.
  Curr Biol, 13, 2148-2158.
PDB code: 1roc
12009903 A.Hierro, J.M.Arizmendi, S.Bañuelos, A.Prado, and A.Muga (2002).
Electrostatic interactions at the C-terminal domain of nucleoplasmin modulate its chromatin decondensation activity.
  Biochemistry, 41, 6408-6413.  
11777905 C.A.Johnson, D.A.White, J.S.Lavender, L.P.O'Neill, and B.M.Turner (2002).
Human class I histone deacetylase complexes show enhanced catalytic activity in the presence of ATP and co-immunoprecipitate with the ATP-dependent chaperone protein Hsp70.
  J Biol Chem, 277, 9590-9597.  
12058066 M.Okuwaki, M.Tsujimoto, and K.Nagata (2002).
The RNA binding activity of a ribosome biogenesis factor, nucleophosmin/B23, is modulated by phosphorylation with a cell cycle-dependent kinase and by association with its subtype.
  Mol Biol Cell, 13, 2016-2030.  
12370244 S.K.Lyman, T.Guan, J.Bednenko, H.Wodrich, and L.Gerace (2002).
Influence of cargo size on Ran and energy requirements for nuclear protein import.
  J Cell Biol, 159, 55-67.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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