6IVM | pdb_00006ivm

Crystal structure of a membrane protein P143A

• PDB DOI: https://doi.org/10.2210/pdb6IVM/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2018-12-04 Released: 2019-11-06 
• Deposition Author(s): Kittredge, A., Fukuda, F., Zhang, Y., Yang, T.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Dual Ca2+-dependent gates in human Bestrophin1 underlie disease-causing mechanisms of gain-of-function mutations.

Ji, C., Kittredge, A., Hopiavuori, A., Ward, N., Chen, S., Fukuda, Y., Zhang, Y., Yang, T.

(2019) Commun Biol 2: 240-240

• PubMed: 31263784 
• DOI: https://doi.org/10.1038/s42003-019-0433-3
• Primary Citation Related Structures: 
  6IV0, 6IV1, 6IV2, 6IV3, 6IV4, 6IVJ, 6IVK, 6IVL, 6IVM, 6IVN, 6IVO, 6IVP, 6IVQ, 6IVR, 6IVW, 6JLF


• PubMed Abstract: 
  

  Mutations of human BEST1 , encoding a Ca ²⁺ -activated Cl ^- channel (hBest1), cause macular degenerative disorders. Best1 homolog structures reveal an evolutionarily conserved channel architecture highlighted by two landmark restrictions (named the "neck" and "aperture", respectively) in the ion conducting pathway, suggesting a unique dual-switch gating mechanism, which, however, has not been characterized well. Using patch clamp and crystallography, we demonstrate that both the neck and aperture in hBest1 are Ca ²⁺ -dependent gates essential for preventing channel leakage resulting from Ca ²⁺ -independent, spontaneous gate opening. Importantly, three patient-derived mutations (D203A, I205T and Y236C) lead to Ca ²⁺ -independent leakage and elevated Ca ²⁺ -dependent anion currents due to enhanced opening of the gates. Moreover, we identify a network of residues critically involved in gate operation. Together, our results suggest an indispensable role of the neck and aperture of hBest1 for channel gating, and uncover disease-causing mechanisms of hBest1 gain-of-function mutations.

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Organizational Affiliation: 
• Department of Pharmacology and Physiology, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642 USA.
2Guangdong Provincial Key Laboratory of Biomedical Imaging, Department of Experimental Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, 519000 Zhuhai, Guangzhou China.
3Division of Advance Pharmaco-Science, Graduate School of Pharmaceutical Science, Osaka University, Yamadaoka 1-6, Suita, Osaka 565-0871 Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 171.09 kDa 
• Atom Count: 10,888 
• Modeled Residue Count: 1,349 
• Deposited Residue Count: 1,485 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ibestrophin	A, B, C, D, E	297	Klebsiella pneumoniae	Mutation(s): 1  Gene Names:  yneE, AGG09_26735, B1727_16705, B4U21_14105, B4U25_16730, B4U27_02655, B4U30_16350, B4U35_20780, BB785_13310, BN49_2925, C3483_12335, C7V41_19985, CPT10_17935, CWN54_25435, CWQ24_13475, DM060_34770, DM071_16710, DM078_14870, DM083_28480, DMR37_19630, DXF97_13395, NCTC11679_02573, NCTC13465_00112, NCTC5052_01714, NCTC8849_03195, NCTC9637_03467, NCTC9645_05950, NCTC9661_03571, SAMEA104305404_11875, SAMEA23986918_00256, SAMEA24002668_02597, SAMEA24012418_00268, SAMEA3649709_04169, SAMEA3673019_02937, SAMEA3727643_02313, SAMEA4394730_00268 Membrane Entity: Yes
UniProt
Find proteins for W9BH30 (Klebsiella pneumoniae) Explore W9BH30  Go to UniProtKB:  W9BH30

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	Z [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
LEU	N [auth B]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
ZN	BA [auth D], CA [auth D], DA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], IA [auth E], JA [auth E], NA [auth E], O [auth B], P [auth B], Q [auth B], T [auth C], U [auth C], V [auth C], Y [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	M [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	AA [auth C], S [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
CL	EA [auth D], FA [auth D], GA [auth D], J [auth A], K [auth A], KA [auth E], L [auth A], LA [auth E], MA [auth E], R [auth B], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	HA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.243 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.965	α = 90
b = 158.808	β = 90
c = 161.682	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Kittredge, A., Fukuda, F., Zhang, Y., Yang, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.2: 2024-05-29
  Changes: Data collection