PDB-6u9t: Wild-type MthK pore in 50 mM K+

Basic information

• Entry: Database: PDB / ID: 6u9t
• Title: Wild-type MthK pore in 50 mM K+
• Components: Calcium-gated potassium channel MthK
• Keywords: TRANSPORT PROTEIN / Potassium ion channel MthK

Function / homology

Function:

monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / metal ion binding / plasma membrane

Domain/homology:

: / Regulator of K+ conductance, N-terminal / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. / Potassium channel domain / Ion channel / NAD(P)-binding domain superfamily

Component:

HEXANE-1,6-DIOL / : / Calcium-gated potassium channel MthK

• Biological species: Methanothermobacter thermautotrophicus (archaea)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
• Authors: Posson, D.J. / Nimigean, C.M.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM088352	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	F32GM087865	United States

• Citation: Journal: Proc.Natl.Acad.Sci.USA / Year: 2020; Title: Selectivity filter ion binding affinity determines inactivation in a potassium channel.; Authors: Boiteux, C. / Posson, D.J. / Allen, T.W. / Nimigean, C.M.

History

Deposition	Sep 9, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 4, 2020	Provider: repository / Type: Initial release
Revision 1.1	Nov 18, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 9, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: Calcium-gated potassium channel MthK

hetero molecules

Summary:

• 9.29 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	9,293	7
Polymers	8,980	1
Non-polymers	314	6
Water	558	31

1

A: Calcium-gated potassium channel MthK

hetero molecules

A: Calcium-gated potassium channel MthK

hetero molecules

A: Calcium-gated potassium channel MthK

hetero molecules

A: Calcium-gated potassium channel MthK

hetero molecules

Summary:

• defined by author&software
• 37.2 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	37,173	28
Polymers	35,918	4
Non-polymers	1,255	24
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_565	-x,-y+1,z	1
crystal symmetry operation	3_555	-y+1/2,x+1/2,z	1
crystal symmetry operation	4_455	y-1/2,-x+1/2,z	1

Calculated values:

Buried area	6570 Å2
ΔGint	-62 kcal/mol
Surface area	15630 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	63.811, 63.811, 44.050
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	90
Space group name H-M	P4212
Space group name Hall	P4ab2ab
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z #3: y+1/2,-x+1/2,z #4: x+1/2,-y+1/2,-z #5: -x+1/2,y+1/2,-z #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-101- K
2	1	A-102- K
3	1	A-103- K
4	1	A-104- K
5	1	A-105- K

Components

#1: Protein

A Calcium-gated potassium channel MthK

Details:

Mass: 8979.500 Da / Num. of mol.: 1 / Fragment: UNP residues 18-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564

#2: Chemical

A-101 A-102 A-103 A-104 A-105
ChemComp-K / POTASSIUM ION

Details:

Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION

#3: Chemical

A-106 ChemComp-HEZ / HEXANE-1,6-DIOL

Details:

Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: Y

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.5 ų/Da / Density % sol: 50.74 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 ; Details: 1:1 protein (in 100 mM sodium chloride, 1 mM potassium chloride, 10 mM MOPS, pH 8.0) + 3.5-4.0 M 1,6-hexanediol, 100 mM MES-NaOH, pH 6.75

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.979 Å / Relative weight: 1
• Reflection: Resolution: 1.55→31.91 Å / Num. obs: 13679 / % possible obs: 99.72 % / Redundancy: 23.3 % / B_iso Wilson estimate: 22.11 Ų / CC_1/2: 1 / R_merge(I) obs: 0.06349 / R_pim(I) all: 0.01327 / R_rim(I) all: 0.0649 / Net I/σ(I): 32.28
• Reflection shell: Resolution: 1.55→1.607 Å / Redundancy: 13.6 % / R_merge(I) obs: 1.502 / Num. unique obs: 1297 / CC_1/2: 0.682 / R_pim(I) all: 0.4156 / R_rim(I) all: 1.56 / % possible all: 97.59

Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
XDS		data reduction
PHENIX		phasing
XDS		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LDC

3ldc

Resolution: 1.55→31.9 Å / SU ML: 0.1633 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3571

	Rfactor	Num. reflection	% reflection
Rfree	0.2102	1378	10.17 %
Rwork	0.1925	-	-
obs	0.1941	13666	99.72 %

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
• Displacement parameters: B_iso mean: 29.81 Ų

Refinement step

Cycle: LAST / Resolution: 1.55→31.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	637	0	13	31	681

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0043	687
X-RAY DIFFRACTION	f_angle_d	0.5882	946
X-RAY DIFFRACTION	f_chiral_restr	0.0413	119
X-RAY DIFFRACTION	f_plane_restr	0.0041	111
X-RAY DIFFRACTION	f_dihedral_angle_d	2.0888	501

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
1.55-1.607	0.2906	156	0.3074	1297	X-RAY DIFFRACTION	97.59
1.58-1.61	0.256	141	0.2748	1253	X-RAY DIFFRACTION	99.93
1.61-1.65	0.2616	147	0.2505	1256	X-RAY DIFFRACTION	100
1.65-1.69	0.2468	158	0.2366	1242	X-RAY DIFFRACTION	99.86
1.69-1.73	0.2229	130	0.2273	1264	X-RAY DIFFRACTION	99.93
1.73-1.78	0.2548	127	0.2107	1265	X-RAY DIFFRACTION	100
1.78-1.83	0.2205	146	0.1998	1263	X-RAY DIFFRACTION	100
1.83-1.89	0.2202	133	0.1967	1274	X-RAY DIFFRACTION	100
1.89-1.95	0.2034	155	0.1749	1233	X-RAY DIFFRACTION	100
1.95-2.03	0.1986	132	0.1823	1259	X-RAY DIFFRACTION	100
2.03-2.12	0.1817	158	0.1852	1261	X-RAY DIFFRACTION	100
2.12-2.24	0.2217	149	0.1857	1236	X-RAY DIFFRACTION	100
2.24-2.38	0.2124	168	0.1757	1235	X-RAY DIFFRACTION	100
2.38-2.56	0.1885	134	0.1671	1262	X-RAY DIFFRACTION	100
2.56-2.82	0.1948	131	0.1601	1271	X-RAY DIFFRACTION	100
2.82-3.23	0.1632	117	0.1777	1294	X-RAY DIFFRACTION	100
3.23-4.06	0.1901	144	0.1874	1260	X-RAY DIFFRACTION	100
4.06-31.9	0.2512	129	0.2126	1277	X-RAY DIFFRACTION	99.86

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°2)	L12 (°2)	L13 (°2)	L22 (°2)	L23 (°2)	L33 (°2)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å2)	T12 (Å2)	T13 (Å2)	T22 (Å2)	T23 (Å2)	T33 (Å2)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.62116808408	2.37974169211	3.92787735909	5.48744226261	-1.07644436356	4.51354214175	-0.0217703061663	-0.54571159285	-0.129733223663	0.454741039385	0.240596042711	0.253289220731	-0.00148114623895	-0.152760535267	-0.216148874398	0.233294266773	0.0924662819163	0.0233086699238	0.287241295127	0.0182911700378	0.20605486949	8.44046520261	15.2710780587	6.63359867006
2	2.44295951544	-1.06367073718	-0.0420296577345	5.48258242186	-1.21147092641	2.52309606795	0.115756696034	0.216616085023	-0.160273891333	-0.325688331945	-0.052952756708	-0.0247740718198	0.375783292464	0.121055748473	-0.0698441988758	0.22592129517	0.0223393421097	-0.027625534505	0.205719682464	-0.020433970684	0.171730091292	4.74867486162	18.7703771413	-11.7541425244
3	4.4893274535	0.347408551966	3.31640915456	3.02942906768	0.633624035526	8.66438545842	0.0247773161366	-0.147514416506	-0.309511235808	0.0968923391509	0.130866297371	0.0353890392366	0.225538733044	-0.144280697119	-0.142231666946	0.169756744988	0.00607192032476	0.00746367287627	0.123697163854	0.0246957408688	0.161580628259	-1.62038914404	19.029187444	-3.59057963781
4	6.9566903945	2.30386966845	-1.23788828392	9.66172872635	5.91005117819	9.39169224885	-0.267933787473	-1.65032236438	0.889827806923	1.93517852208	-0.00206833328534	-0.639461759335	-0.548491608969	1.51425692704	0.329817485875	0.841841598956	0.0229964239672	-0.203182428791	0.743642231861	-0.0663780107717	0.628663253123	13.6169410884	27.1131114896	10.7915577343

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 18:31)
2	X-RAY DIFFRACTION	2	(chain A and resid 32:68)
3	X-RAY DIFFRACTION	3	(chain A and resid 69:91)
4	X-RAY DIFFRACTION	4	(chain A and resid 92:99)