5IQZ | pdb_00005iqz

Crystal structure of N-terminal domain of Human SIRT7

• PDB DOI: https://doi.org/10.2210/pdb5IQZ/pdb

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


• Deposited: 2016-03-11 Released: 2016-07-27 
• Deposition Author(s): Thakur, K.G., Priyanka, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the N-terminal domain of human SIRT7 reveals a three-helical domain architecture

Priyanka, A., Solanki, V., Parkesh, R., Thakur, K.G.

(2016) Proteins 84: 1558-1563

• PubMed: 27287224 
• DOI: https://doi.org/10.1002/prot.25085
• Primary Citation Related Structures: 
  5IQZ


• PubMed Abstract: 
  

  Human SIRT7 is an NAD(+) dependent deacetylase, which belongs to sirtuin family of proteins. SIRT7, like other sirtuins has conserved catalytic domain and is flanked by N- and C-terminal domains reported to play vital functional roles. Here, we report the crystal structure of the N-terminal domain of human SIRT7 (SIRT7(NTD) ) at 2.3 Å resolution as MBP-SIRT7(NTD) fusion protein. SIRT7(NTD) adopts three-helical domain architecture and comparative structural analyses suggest similarities to some DNA binding motifs and transcription regulators. We also report here the importance of N- and C-terminal domains in soluble expression of SIRT7. Proteins 2016; 84:1558-1563. © 2016 Wiley Periodicals, Inc.

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Organizational Affiliation: 
• Structural Biology Laboratory, G. N. Ramachandran Protein Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.
Computational Medicinal Chemistry and Fluorescent Chemosensors Laboratory, G. N. Ramachandran Protein Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India.
Structural Biology Laboratory, G. N. Ramachandran Protein Centre, CSIR-Institute of Microbial Technology, Chandigarh, 160036, India. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 49.51 kDa 
• Atom Count: 3,558 
• Modeled Residue Count: 426 
• Deposited Residue Count: 443 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIRT7 protein	A	443	Homo sapiens	Mutation(s): 0  Gene Names: sirt7 EC: 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q9NRC8 (Homo sapiens) Explore Q9NRC8  Go to UniProtKB:  Q9NRC8
PHAROS:  Q9NRC8 GTEx:  ENSG00000187531
UniProt Groups	Q9NRC8P0AEX9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.237 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.49	α = 90
b = 49.33	β = 101.2
c = 65.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data processing
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building
iMOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Thakur, K.G., Priyanka, A.

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary