1NLQ | pdb_00001nlq

The crystal structure of Drosophila NLP-core provides insight into pentamer formation and histone binding

• PDB DOI: https://doi.org/10.2210/pdb1NLQ/pdb

• Classification: CHAPERONE, LIGAND BINDING
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-01-07 Released: 2003-03-01 
• Deposition Author(s): Namboodiri, V.M.H., Dutta, S., Akey, I.V., Head, J.F., Akey, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.234 (DCC) 

Literature

The crystal structure of Drosophila NLP-core Provides Insight into Pentamer Formation and Histone Binding

Namboodiri, V.M.H., Dutta, S., Akey, I.V., Head, J.F., Akey, C.W.

(2003) Structure 11: 175-186

• PubMed: 12575937 
• DOI: https://doi.org/10.1016/s0969-2126(03)00007-8
• Primary Citation Related Structures: 
  1NLQ


• PubMed Abstract: 
  

  The nucleoplasmin-like protein from Drosophila (dNLP) functions as a chaperone for core histones and may remodel chromatin in embryos. We now report the crystal structure of a dNLP-core pentamer at 1.5 A resolution. The monomer has an eight-stranded, beta barrel topology that is similar to nucleoplasmin (Np). However, a signature beta hairpin is tucked in along the lateral surface of the dNLP-core pentamer, while it extends outward in the Np-core decamer. Drosophila NLP and Np both assemble histone octamers. This process may require each chaperone to form a decamer, which would create symmetric binding sites for the histones. Conformational differences between dNLP and Np may reflect their different oligomeric states, while a conserved, nonpolar subunit interface may allow conformational plasticity during histone binding.

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Organizational Affiliation: 
• Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.9 kDa 
• Atom Count: 4,147 
• Modeled Residue Count: 490 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoplasmin-like protein	A, B, C, D, E	108	Drosophila melanogaster	Mutation(s): 0  Gene Names: NLP OR CRP1 OR CG7917
UniProt
Find proteins for Q27415 (Drosophila melanogaster) Explore Q27415  Go to UniProtKB:  Q27415

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	F [auth A], G [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.254 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.234 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.608	α = 90
b = 60.089	β = 90.79
c = 73.426	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-03-01 
Deposition Author(s): Namboodiri, V.M.H., Dutta, S., Akey, I.V., Head, J.F., Akey, C.W.

Revision History  

• Version 1.0: 2003-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations