PDB-3ogc: KcsA E71A variant in presence of Na+

ID or keywords:

Entry

Database: PDB / ID: 3ogc

Title

KcsA E71A variant in presence of Na+

Components

Voltage-gated potassium channel
antibody Fab fragment heavy chain
antibody Fab fragment light chain

Keywords

MEMBRANE PROTEIN /

Voltage-gated channel / antibody fab complex

Function / homology

Function and homology information

monoatomic ion transmembrane transport / identical protein binding /

plasma membrane
Similarity search - Function

Biological species

Mus musculus (house mouse)

Streptomyces lividans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.8 Å

Authors

McCoy, J.G. / Nimigean, C.M.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Mechanism for selectivity-inactivation coupling in KcsA potassium channels.
Authors: Cheng, W.W. / McCoy, J.G. / Thompson, A.N. / Nichols, C.G. / Nimigean, C.M.

History

Deposition	Aug 16, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 16, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ogc.cif.gz	220.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ogc.ent.gz	179.1 KB	Display	PDB format
PDBx/mmJSON format	3ogc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/og/3ogc ftp://data.pdbj.org/pub/pdb/validation_reports/og/3ogc	HTTPS FTP

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Related structure data

Related structure data	2atkS S: Starting model for refinement
Similar structure data	3or6-1 3stl-1 2ih1-1 2itd-1 5ebw-1 1k4c-1 2hvj-1 2w0f-1 1k4d-1 2hvk-1 1r3j-1 6w0g-1 3or7-1 1r3l-1 2itc-1 1r3i-1 2p7t-3 5j9p-1 2boc-1 1s5h-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#38 - Feb 2003 Potassium Channels similarity (3) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (2)

Deposited unit

A: antibody Fab fragment heavy chain

B: antibody Fab fragment light chain

C: Voltage-gated potassium channel

hetero molecules

61 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: antibody Fab fragment heavy chain

B: antibody Fab fragment light chain

C: Voltage-gated potassium channel

hetero molecules

A: antibody Fab fragment heavy chain

B: antibody Fab fragment light chain

C: Voltage-gated potassium channel

hetero molecules

A: antibody Fab fragment heavy chain

B: antibody Fab fragment light chain

C: Voltage-gated potassium channel

hetero molecules

A: antibody Fab fragment heavy chain

B: antibody Fab fragment light chain

C: Voltage-gated potassium channel

hetero molecules

defined by author
244 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	154.735, 154.735, 75.401
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	79
Space group name H-M	I4

Components on special symmetry positions

ID	Model	Components
1	1	C-1000- NA
2	1	C-1001- NA

#1: Antibody	antibody Fab fragment heavy chain Mass: 23411.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody	antibody Fab fragment light chain Mass: 23435.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse)
#3: Protein	Voltage-gated potassium channel / Mass: 14105.556 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2-124 / Mutation: E71A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Plasmid: pASK90 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0A334
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.7 Å³/Da / Density % sol: 66.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 400, MgAcetate, MES, pH 6.5, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction

Mean temperature: 93 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X25 / Wavelength: 1.1 Å

Detector

Type: ADSC Q315 / Detector: CCD / Date: Apr 24, 2010

Radiation

Monochromator: Double silicon(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1 Å / Relative weight: 1

Reflection

Resolution: 3.8→38.7 Å / Num. obs: 8872 / % possible obs: 99.8 % / Redundancy: 3.6 % / R_merge(I) obs: 0.107 / Net I/σ(I): 7.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	% possible all
3.8-3.89	3.6	0.445	100
3.89-3.99	3.6	0.433	100
3.99-4.09	3.6	0.341	99.8
4.09-4.21	3.6	0.263	99.8
4.21-4.35	3.6	0.196	100
4.35-4.5	3.7	0.154	100
4.5-4.69	3.7	0.144	100
4.69-4.9	3.7	0.133	99.8
4.9-5.16	3.7	0.129	100
5.16-5.48	3.7	0.134	99.8
5.48-5.9	3.7	0.13	100
5.9-6.49	3.6	0.113	100
6.49-7.43	3.6	0.078	100
7.43-9.35	3.6	0.037	99.7
9.35-50	3.6	0.024	98.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	3.93 Å	42.57 Å
Translation	3.93 Å	42.57 Å

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
MOLREP		phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
DENZO		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ATK

2atk

Resolution: 3.8→38.7 Å / Cor.coef. F_o:F_c: 0.865 / Cor.coef. F_o:F_c free: 0.853 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 92.814 / SU ML: 0.591 / SU R Cruickshank DPI: 0.6761 / Cross valid method: THROUGHOUT / ESU R Free: 0.761 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28289	423	4.8 %	RANDOM
R_work	0.24711	-	-	-
obs	0.24872	8449	99.26 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 80.148 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.93 Å²	0 Å²	0 Å²
2-	-	4.93 Å²	0 Å²
3-	-	-	-9.86 Å²

Refinement step

Cycle: LAST / Resolution: 3.8→38.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4072	0	2	0	4074

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	4179
X-RAY DIFFRACTION	r_angle_refined_deg	0.791	1.942	5704
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.829	5	531
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.032	23.438	160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.64	15	646
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.566	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	649
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	3150
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.031	1.5	2660
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.064	2	4303
X-RAY DIFFRACTION	r_scbond_it	0.113	3	1519
X-RAY DIFFRACTION	r_scangle_it	0.211	4.5	1401
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.801→3.9 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.281	28	-
R_work	0.269	580	-
obs	-	-	93.39 %

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	8.689	-1.1789	3.6728	5.575	-1.5081	12.5121	0.4653	-1.1039	-0.9239	0.0247	0.1488	1.0234	1.3833	-1.6465	-0.6141	0.3539	-0.221	-0.026	0.4107	-0.0253	0.7825	-37.4005	-15.6612	-26.3164
2	5.6683	-1.1926	-0.274	12.6405	6.5673	8.1902	0.2344	0.0914	0.6489	-0.4043	-0.1565	-0.1131	-0.0098	-0.2804	-0.0779	0.0402	-0.0322	-0.0492	0.4496	0.1048	0.5089	-29.3265	-7.872	-28.7296
3	4.0248	-3.1862	2.4331	5.9147	2.4284	7.1136	-0.4018	-0.4656	-0.0094	-0.3372	0.429	0.1278	-1.1227	-0.3478	-0.0273	0.2544	0.0151	-0.0394	0.8069	0.0907	1.0905	-37.4261	-5.6931	-28.0493
4	11.5217	-1.6964	8.7339	4.0991	0.7457	8.4638	0.4261	-0.5045	-0.846	-0.1417	0.0989	0.6459	0.3299	-0.9939	-0.525	0.1515	-0.1467	0.0244	0.5823	0.1044	0.6093	-32.8081	-14.1769	-32.8387
5	2.5584	-0.6868	-0.478	2.2284	2.5931	4.7199	-0.26	0.4053	-0.1679	-0.0673	-0.481	0.3736	0.7335	-0.8548	0.741	0.6683	-0.3059	-0.1442	0.9729	-0.1015	0.7863	-43.3704	-32.9977	-50.3351
6	5.3234	-0.9719	-2.0522	14.0206	2.5034	3.959	-0.2658	-0.1895	-0.3003	-0.3528	0.3172	0.8566	0.4042	-0.1782	-0.0514	0.6728	-0.3456	-0.1809	0.799	-0.1088	0.5534	-41.7574	-31.9641	-48.8479
7	11.189	0.6091	-0.5077	0.0565	-0.0205	0.053	0.6463	-0.9774	-2.7734	0.0707	-0.447	-0.3122	0.1354	-0.2261	-0.1993	1.8676	-1.6982	-0.274	2.5738	0.7263	1.8217	-50.2321	-37.8902	-49.2847
8	3.7611	0.7683	-0.8177	6.242	3.5002	6.7117	0.0442	0.6993	-0.2388	-0.5765	0.1938	-0.3081	0.1134	0.2583	-0.2381	0.262	-0.0057	-0.0617	0.3992	0.0157	0.3552	-13.59	-17.747	-38.5
9	3.2996	1.686	0.563	3.968	0.9872	3.9389	-0.0166	0.0964	-0.5723	0.477	0.164	0.1042	0.9899	0.219	-0.1474	0.3346	-0.0217	-0.0687	0.2933	0.0116	0.5446	-15.1958	-21.3424	-33.0116
10	0.042	0.0966	0.0371	2.3392	1.0632	0.5759	-0.0149	0.1947	-0.0834	-0.1447	0.2046	-0.0242	0.1346	-0.0893	-0.1897	0.8706	-0.2532	-0.2114	1.2105	-0.0393	0.6624	-33.7689	-29.8174	-54.9439
11	6.5829	-0.7682	1.8701	1.003	2.2304	7.498	0.1599	0.598	0.4009	-0.3117	-0.1814	0.0176	-0.2442	-0.4117	0.0215	0.967	-0.2423	-0.1414	0.6956	-0.1209	0.6952	-32.8633	-28.7429	-61.6458
12	5.3049	-1.7066	3.2548	3.9156	-2.0765	5.0896	0.086	0.3745	-0.7435	-0.7965	0.0048	0.6256	0.085	-0.3322	-0.0908	1.1404	-0.1501	-0.152	1.1076	-0.1732	0.6953	-41.4833	-32.2333	-68.3606
13	14.0127	-6.0632	21.4936	20.2174	-3.6876	34.7598	0.0919	-0.0823	-0.388	1.4829	0.6996	-0.4913	0.609	0.1003	-0.7915	0.3173	-0.1345	0.1076	0.3524	0.0269	0.6161	-12.031	-10.2461	13.4956
14	3.4845	-2.1328	6.7718	1.3369	-3.3398	34.0281	-0.0506	0.0862	-0.2577	0.0803	-0.1428	0.1705	1.1117	-2.1047	0.1934	0.0945	-0.1619	-0.0095	0.2865	0.009	0.5245	-19.6099	-6.4979	-9.6597
15	3.5038	0.0635	6.904	7.8966	-5.8799	18.1713	0.1955	0.4717	-0.021	-0.7888	0.1289	0.3523	0.9951	0.8321	-0.3244	0.1222	-0.0086	0.0625	0.2187	-0.0247	0.3464	-13.1768	-7.4171	-14.0384
16	28.4919	-17.4709	10.6695	16.4746	-1.0112	9.3054	-0.2753	0.185	0.484	0.1405	-0.1627	-0.0378	-0.1443	0.0208	0.438	0.401	-0.2684	0.0481	0.2119	0.0705	0.3906	-10.8581	0.4115	-12.9123
17	13.6542	-6.1066	18.3395	3.3845	-9.355	29.1964	-0.2737	-0.575	-0.3902	0.4977	0.0214	-0.1794	-0.065	-0.0174	0.2523	0.5993	-0.0258	-0.08	0.2538	-0.0152	0.5366	-3.9824	-4.4973	12.4426

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 33
2	X-RAY DIFFRACTION	2	A	34 - 62
3	X-RAY DIFFRACTION	3	A	63 - 88
4	X-RAY DIFFRACTION	4	A	89 - 120
5	X-RAY DIFFRACTION	5	A	121 - 165
6	X-RAY DIFFRACTION	6	A	166 - 208
7	X-RAY DIFFRACTION	7	A	209 - 219
8	X-RAY DIFFRACTION	8	B	1 - 41
9	X-RAY DIFFRACTION	9	B	42 - 97
10	X-RAY DIFFRACTION	10	B	98 - 130
11	X-RAY DIFFRACTION	11	B	131 - 173
12	X-RAY DIFFRACTION	12	B	174 - 212
13	X-RAY DIFFRACTION	13	C	22 - 35
14	X-RAY DIFFRACTION	14	C	36 - 54
15	X-RAY DIFFRACTION	15	C	55 - 73
16	X-RAY DIFFRACTION	16	C	74 - 88
17	X-RAY DIFFRACTION	17	C	89 - 124

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