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

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Basic information

Entry
Database: PDB / ID: 3ogc
TitleKcsA E71A variant in presence of Na+
Components
  • Voltage-gated potassium channel
  • antibody Fab fragment heavy chain
  • antibody Fab fragment light chain
KeywordsMEMBRANE PROTEIN / Voltage-gated channel / antibody fab complex
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Voltage-gated potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsMcCoy, J.G. / Nimigean, C.M.
CitationJournal: 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
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: 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
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9995
Polymers60,9533
Non-polymers462
Water00
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


Theoretical massNumber of molelcules
Total (without water)243,99420
Polymers243,81012
Non-polymers1848
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9460 Å2
ΔGint-119 kcal/mol
Surface area19060 Å2
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 number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-1000-

NA

21C-1001-

NA

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Components

#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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 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

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Apr 24, 2010
RadiationMonochromator: Double silicon(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.8→38.7 Å / Num. obs: 8872 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
3.8-3.893.60.445100
3.89-3.993.60.433100
3.99-4.093.60.34199.8
4.09-4.213.60.26399.8
4.21-4.353.60.196100
4.35-4.53.70.154100
4.5-4.693.70.144100
4.69-4.93.70.13399.8
4.9-5.163.70.129100
5.16-5.483.70.13499.8
5.48-5.93.70.13100
5.9-6.493.60.113100
6.49-7.433.60.078100
7.43-9.353.60.03799.7
9.35-503.60.02498.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.93 Å42.57 Å
Translation3.93 Å42.57 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ATK

2atk


Resolution: 3.8→38.7 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.28289 423 4.8 %RANDOM
Rwork0.24711 ---
obs0.24872 8449 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.148 Å2
Baniso -1Baniso -2Baniso -3
1-4.93 Å20 Å20 Å2
2--4.93 Å20 Å2
3----9.86 Å2
Refinement stepCycle: LAST / Resolution: 3.8→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 0 2 0 4074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224179
X-RAY DIFFRACTIONr_angle_refined_deg0.7911.9425704
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8295531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03223.438160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6415646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5661522
X-RAY DIFFRACTIONr_chiral_restr0.0470.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213150
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0311.52660
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.06424303
X-RAY DIFFRACTIONr_scbond_it0.11331519
X-RAY DIFFRACTIONr_scangle_it0.2114.51401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.801→3.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 28 -
Rwork0.269 580 -
obs--93.39 %
Refinement TLS params.

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

IDL11 (°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)
18.689-1.17893.67285.575-1.508112.51210.4653-1.1039-0.92390.02470.14881.02341.3833-1.6465-0.61410.3539-0.221-0.0260.4107-0.02530.7825-37.4005-15.6612-26.3164
25.6683-1.1926-0.27412.64056.56738.19020.23440.09140.6489-0.4043-0.1565-0.1131-0.0098-0.2804-0.07790.0402-0.0322-0.04920.44960.10480.5089-29.3265-7.872-28.7296
34.0248-3.18622.43315.91472.42847.1136-0.4018-0.4656-0.0094-0.33720.4290.1278-1.1227-0.3478-0.02730.25440.0151-0.03940.80690.09071.0905-37.4261-5.6931-28.0493
411.5217-1.69648.73394.09910.74578.46380.4261-0.5045-0.846-0.14170.09890.64590.3299-0.9939-0.5250.1515-0.14670.02440.58230.10440.6093-32.8081-14.1769-32.8387
52.5584-0.6868-0.4782.22842.59314.7199-0.260.4053-0.1679-0.0673-0.4810.37360.7335-0.85480.7410.6683-0.3059-0.14420.9729-0.10150.7863-43.3704-32.9977-50.3351
65.3234-0.9719-2.052214.02062.50343.959-0.2658-0.1895-0.3003-0.35280.31720.85660.4042-0.1782-0.05140.6728-0.3456-0.18090.799-0.10880.5534-41.7574-31.9641-48.8479
711.1890.6091-0.50770.0565-0.02050.0530.6463-0.9774-2.77340.0707-0.447-0.31220.1354-0.2261-0.19931.8676-1.6982-0.2742.57380.72631.8217-50.2321-37.8902-49.2847
83.76110.7683-0.81776.2423.50026.71170.04420.6993-0.2388-0.57650.1938-0.30810.11340.2583-0.23810.262-0.0057-0.06170.39920.01570.3552-13.59-17.747-38.5
93.29961.6860.5633.9680.98723.9389-0.01660.0964-0.57230.4770.1640.10420.98990.219-0.14740.3346-0.0217-0.06870.29330.01160.5446-15.1958-21.3424-33.0116
100.0420.09660.03712.33921.06320.5759-0.01490.1947-0.0834-0.14470.2046-0.02420.1346-0.0893-0.18970.8706-0.2532-0.21141.2105-0.03930.6624-33.7689-29.8174-54.9439
116.5829-0.76821.87011.0032.23047.4980.15990.5980.4009-0.3117-0.18140.0176-0.2442-0.41170.02150.967-0.2423-0.14140.6956-0.12090.6952-32.8633-28.7429-61.6458
125.3049-1.70663.25483.9156-2.07655.08960.0860.3745-0.7435-0.79650.00480.62560.085-0.3322-0.09081.1404-0.1501-0.1521.1076-0.17320.6953-41.4833-32.2333-68.3606
1314.0127-6.063221.493620.2174-3.687634.75980.0919-0.0823-0.3881.48290.6996-0.49130.6090.1003-0.79150.3173-0.13450.10760.35240.02690.6161-12.031-10.246113.4956
143.4845-2.13286.77181.3369-3.339834.0281-0.05060.0862-0.25770.0803-0.14280.17051.1117-2.10470.19340.0945-0.1619-0.00950.28650.0090.5245-19.6099-6.4979-9.6597
153.50380.06356.9047.8966-5.879918.17130.19550.4717-0.021-0.78880.12890.35230.99510.8321-0.32440.1222-0.00860.06250.2187-0.02470.3464-13.1768-7.4171-14.0384
1628.4919-17.470910.669516.4746-1.01129.3054-0.27530.1850.4840.1405-0.1627-0.0378-0.14430.02080.4380.401-0.26840.04810.21190.07050.3906-10.85810.4115-12.9123
1713.6542-6.106618.33953.3845-9.35529.1964-0.2737-0.575-0.39020.49770.0214-0.1794-0.065-0.01740.25230.5993-0.0258-0.080.2538-0.01520.5366-3.9824-4.497312.4426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 33
2X-RAY DIFFRACTION2A34 - 62
3X-RAY DIFFRACTION3A63 - 88
4X-RAY DIFFRACTION4A89 - 120
5X-RAY DIFFRACTION5A121 - 165
6X-RAY DIFFRACTION6A166 - 208
7X-RAY DIFFRACTION7A209 - 219
8X-RAY DIFFRACTION8B1 - 41
9X-RAY DIFFRACTION9B42 - 97
10X-RAY DIFFRACTION10B98 - 130
11X-RAY DIFFRACTION11B131 - 173
12X-RAY DIFFRACTION12B174 - 212
13X-RAY DIFFRACTION13C22 - 35
14X-RAY DIFFRACTION14C36 - 54
15X-RAY DIFFRACTION15C55 - 73
16X-RAY DIFFRACTION16C74 - 88
17X-RAY DIFFRACTION17C89 - 124

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