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- PDB-4h37: Crystal structure of a voltage-gated K+ channel pore domain in a ... -

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Basic information

Entry
Database: PDB / ID: 4h37
TitleCrystal structure of a voltage-gated K+ channel pore domain in a closed state in lipid membranes
ComponentsLmo2059 protein
KeywordsMEMBRANE PROTEIN / MODULE / PORE MODULE / ION CHANNEL / MEMBRANE
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / potassium ion transmembrane transport / membrane
Similarity search - Function
Helix Hairpins - #70 / Potassium channel domain / Ion channel / Voltage-dependent channel domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsSantos, J.S. / Asmar-Rovira, G.A. / Han, G.W. / Liu, W. / Syeda, R. / Cherezov, V. / Baker, K.A. / Stevens, R.C. / Montal, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of a Voltage-gated K+ Channel Pore Module in a Closed State in Lipid Membranes.
Authors: Santos, J.S. / Asmar-Rovira, G.A. / Han, G.W. / Liu, W. / Syeda, R. / Cherezov, V. / Baker, K.A. / Stevens, R.C. / Montal, M.
History
DepositionSep 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo2059 protein
B: Lmo2059 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2796
Polymers31,1232
Non-polymers1564
Water00
1
A: Lmo2059 protein
B: Lmo2059 protein
hetero molecules

A: Lmo2059 protein
B: Lmo2059 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,55912
Polymers62,2464
Non-polymers3138
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6650 Å2
ΔGint-61 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.100, 80.670, 55.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

K

21A-202-

K

31A-203-

K

41A-204-

K

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Components

#1: Protein Lmo2059 protein


Mass: 15561.433 Da / Num. of mol.: 2
Fragment: KVLM PORE MODULE, TRUNCATED C-TERMINUS (UNP RESIDUES 98-233)
Mutation: A98C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo2059 / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q8Y5K1
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.06 %
Crystal growTemperature: 293 K / pH: 6.25
Details: 25% (v/v) PEG-MME-550, 0.35 M sodium nitrate, 50 mM ADA, 50 mM sodium malonate pH 7.0, Lipidic Cubic Phase (LCP), temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2011
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.35→32.6 Å / Num. obs: 3736 / % possible obs: 95.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 101.9 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 15.8
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.1 / % possible all: 86

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EFF, 2ATK , 2A79 AND 1ORQ

3eff

2atk

2a79

1orq


Resolution: 3.35→32.6 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.341 534 14.29 %RANDOM
Rwork0.314 ---
obs0.318 3736 95.5 %-
Displacement parametersBiso mean: 192.51 Å2
Baniso -1Baniso -2Baniso -3
1-9.2681 Å20 Å20 Å2
2--36.1359 Å20 Å2
3----45.404 Å2
Refine analyzeLuzzati coordinate error obs: 1.95 Å
Refinement stepCycle: LAST / Resolution: 3.35→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 4 0 1307
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011337HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.941833HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 3.35→3.75 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3071 140 14.03 %
Rwork0.264 858 -
all0.2703 998 -
obs--95.48 %
Refinement TLS params.

T22: -0.6079 Å2 / 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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1350.37371.416416.63093.04890.5255-0.02840.398-0.19190.14510.01470.03930.0588-0.20720.01370.59280.0166-0.07570.01430.6077-7.8178-10.341525.9932
22.9192-2.7463-1.483315.66841.07542.4693-0.06060.33790.02180.04780.1180.22230.00090.0402-0.05740.6079-0.0232-0.1609-0.0670.6078-10.32167.661525.7507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|14 - A|99 }A14 - 99
2X-RAY DIFFRACTION2{ B|14 - B|99 }B14 - 99

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