5NFD

Antiparallel monomeric coiled coil of Kif21A

• PDB DOI: https://doi.org/10.2210/pdb5NFD/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-03-13 Released: 2018-05-02 
• Deposition Author(s): Kraatz, S.H.W., Bianchi, S., Steinmetz, M.O.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.239 
• R-Value Work: 0.197 
• R-Value Observed: 0.202 

Literature

Combinatorial use of disulfide bridges and native sulfur-SAD phasing for rapid structure determination of coiled-coils.

Kraatz, S.H.W., Bianchi, S., Steinmetz, M.O.

(2018) Biosci Rep 38

• PubMed: 30135143 
• DOI: https://doi.org/10.1042/BSR20181073
• Primary Citation of Related Structures:  
  5NFD, 5NG4


• PubMed Abstract: 
  

  Coiled-coils are ubiquitous protein-protein interaction motifs found in many eukaryotic proteins. The elongated, flexible and often irregular nature of coiled-coils together with their tendency to form fibrous arrangements in crystals imposes challenges on solving the phase problem by molecular replacement. Here, we report the successful combinatorial use of native and rational engineered disulfide bridges together with sulfur-SAD phasing as a powerful tool to stabilize and solve the structure of coiled-coil domains in a straightforward manner. Our study is a key example of how modern sulfur SAD combined with mutagenesis can help to advance and simplify the structural study of challenging coiled-coil domains by X-ray crystallography.

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Organizational Affiliation: 

Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.93 kDa 
• Atom Count: 1,344 
• Modelled Residue Count: 153 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF21A	A, B	82	Homo sapiens	Mutation(s): 1  Gene Names: KIF21A, KIAA1708, KIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z4S6 (Homo sapiens) Explore Q7Z4S6  Go to UniProtKB:  Q7Z4S6
PHAROS:  Q7Z4S6 GTEx:  ENSG00000139116

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.239 
• R-Value Work: 0.197 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.97	α = 90
b = 41.67	β = 90
c = 123.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Kraatz, S.H.W., Bianchi, S., Steinmetz, M.O.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030B_138659
Swiss National Science Foundation	Switzerland	31003A_166608

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2018-09-05
  Changes: Data collection, Database references
• Version 1.2: 2018-10-03
  Changes: Data collection, Database references