3L4B

Crystal Structure of an Octomeric Two-Subunit TrkA K+ Channel Ring Gating Assembly, TM1088A:TM1088B, from Thermotoga maritima

• PDB DOI: https://doi.org/10.2210/pdb3L4B/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-18 Released: 2010-02-16 
• Deposition Author(s): Deller, M.C., Johnson, H.A., Miller, M., Spraggon, G., Wilson, I.A., Lesley, S.A., Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.308 
• R-Value Work: 0.259 
• R-Value Observed: 0.261 

Starting Model: experimental

Literature

Crystal Structure of an Octomeric Two-Subunit TrkA K+ Channel Ring Gating Assembly, TM1088A:TM1088B, from Thermotoga maritima

Deller, M.C., Johnson, H.A., Miller, M., Spraggon, G., Lesley, S.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 161.86 kDa 
• Atom Count: 9,045 
• Modelled Residue Count: 1,361 
• Deposited Residue Count: 1,444 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TrkA K+ Channel protein TM1088A	A, B, E, F	143	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM1088
UniProt
Find proteins for D3KFX7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore D3KFX7  Go to UniProtKB:  D3KFX7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TrkA K+ Channel protein TM1088B	C, D, G, H	218	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM1088
UniProt
Find proteins for D3KFX8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore D3KFX8  Go to UniProtKB:  D3KFX8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	I [auth A], J [auth B], L [auth E], M [auth F]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
UNX	K [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.308 
• R-Value Work: 0.259 
• R-Value Observed: 0.261 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.778	α = 90
b = 96.778	β = 90
c = 305.098	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Deller, M.C., Johnson, H.A., Miller, M., Spraggon, G., Wilson, I.A., Lesley, S.A., Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2020-09-02
  Changes: Derived calculations, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description