5E5B | pdb_00005e5b

Crystal structure of Human Spt16 N-terminal domain

• PDB DOI: https://doi.org/10.2210/pdb5E5B/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-08 Released: 2016-02-10 
• Deposition Author(s): Marciano, G., Huang, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.176 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structure of the human histone chaperone FACT Spt16 N-terminal domain.

Marciano, G., Huang, D.T.

(2016) Acta Crystallogr F Struct Biol Commun 72: 121-128

• PubMed: 26841762 
• DOI: https://doi.org/10.1107/S2053230X15024565
• Primary Citation Related Structures: 
  5E5B


• PubMed Abstract: 
  

  The histone chaperone FACT plays an important role in facilitating nucleosome assembly and disassembly during transcription. FACT is a heterodimeric complex consisting of Spt16 and SSRP1. The N-terminal domain of Spt16 resembles an inactive aminopeptidase. How this domain contributes to the histone chaperone activity of FACT remains elusive. Here, the crystal structure of the N-terminal domain (NTD) of human Spt16 is reported at a resolution of 1.84 Å. The structure adopts an aminopeptidase-like fold similar to those of the Saccharomyces cerevisiae and Schizosaccharomyces pombe Spt16 NTDs. Isothermal titration calorimetry analyses show that human Spt16 NTD binds histones H3/H4 with low-micromolar affinity, suggesting that Spt16 NTD may contribute to histone binding in the FACT complex. Surface-residue conservation and electrostatic analysis reveal a conserved acidic patch that may be involved in histone binding.

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Organizational Affiliation: 
• Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, Scotland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.72 kDa 
• Atom Count: 3,878 
• Modeled Residue Count: 431 
• Deposited Residue Count: 431 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACT complex subunit SPT16	A	431	Homo sapiens	Mutation(s): 0  Gene Names: SUPT16H, FACT140, FACTP140
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5B9 (Homo sapiens) Explore Q9Y5B9  Go to UniProtKB:  Q9Y5B9
PHAROS:  Q9Y5B9 GTEx:  ENSG00000092201

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.176 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 246.57	α = 90
b = 246.57	β = 90
c = 246.57	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Marciano, G., Huang, D.T.

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description