1NN7 | pdb_00001nn7

Crystal Structure Of The Tetramerization Domain Of The Shal Voltage-Gated Potassium Channel

• PDB DOI: https://doi.org/10.2210/pdb1NN7/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-01-13 Released: 2003-07-15 
• Deposition Author(s): Zhou, W., Choe, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.277 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.236 (DCC) 

Starting Model: experimental

Literature

Determining the basis of channel-tetramerization specificity by x-ray crystallography and a sequence-comparison algorithm: Family values (FamVal)

Nanao, M.H., Zhou, W., Pfaffinger, P.J., Choe, S.

(2003) Proc Natl Acad Sci U S A 100: 8670-8675

• PubMed: 12835418 
• DOI: https://doi.org/10.1073/pnas.1432840100
• Primary Citation Related Structures: 
  1NN7


• PubMed Abstract: 
  

  We have developed a semiempirical algorithm called Family Values (FamVal), which identifies residues that encode functional specificity in a protein sequence. Given a multiple sequence alignment (MSA) grouped into functionally distinct subfamilies, FamVal calculates a specificity score for each subfamily at every amino acid position of an MSA. This algorithm was used to predict specificity-encoding positions within the tetramerization assembly (T1) domain of voltage-gated potassium (Kv) channel subfamilies Kv3 and Kv4. The importance of one such position (Arg to Ala at MSA position 93) was confirmed by in vitro pull-down assays. The structural basis of this assembly discrimination was elucidated by determining the crystal structure of the Kv4 T1 domain and comparing it to the Kv3 T1 domain.

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Organizational Affiliation: 
• Structural Biology Laboratory, The Salk Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 12.85 kDa 
• Atom Count: 945 
• Modeled Residue Count: 105 
• Deposited Residue Count: 105 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
potassium channel Kv4.2	A	105	Rattus norvegicus	Mutation(s): 0  Gene Names: Kcnd2
UniProt
Find proteins for Q63881 (Rattus norvegicus) Explore Q63881  Go to UniProtKB:  Q63881

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.277 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.236 (DCC) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.999	α = 90
b = 59.999	β = 90
c = 61.593	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-15 
Deposition Author(s): Zhou, W., Choe, S.

Revision History  

• Version 1.0: 2003-07-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2018-04-04
  Changes: Advisory, Data collection
• Version 1.4: 2023-08-16
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description