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- PDB-7mdj: The structure of KcsA in complex with a synthetic Fab -

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Basic information

Entry
Database: PDB / ID: 7mdj
TitleThe structure of KcsA in complex with a synthetic Fab
Components
  • Fab heavy chain
  • Fab light chain
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / ion channel
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 / Potassium channel domain / Ion channel / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciessynthetic construct (others)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsRohaim, A. / Slezak, T. / Blackowicz, L. / Kossiakoff, A. / Roux, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Gen.Physiol. / Year: 2022
Title: Engineering of a synthetic antibody fragment for structural and functional studies of K+ channels.
Authors: Rohaim, A. / Slezak, T. / Koh, Y.H. / Blachowicz, L. / Kossiakoff, A.A. / Roux, B.
History
DepositionApr 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3517
Polymers61,1953
Non-polymers1564
Water2,288127
1
A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab heavy chain
B: Fab light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,40528
Polymers244,78012
Non-polymers62616
Water21612
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
Unit cell
Length a, b, c (Å)138.409, 138.409, 71.160
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-201-

K

21C-202-

K

31C-203-

K

41C-204-

K

51C-322-

HOH

61C-324-

HOH

71C-326-

HOH

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Components

#1: Antibody Fab heavy chain


Mass: 24379.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab light chain


Mass: 23604.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 13211.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM sodium acetate/50 mM ammonium acetate, 50 mM magnesium acetate, 25% PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50.01 Å / Num. obs: 17621 / % possible obs: 99.9 % / Redundancy: 6.2 % / CC1/2: 0.99 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.75 Å / Num. unique obs: 17621 / CC1/2: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W0I

6w0i


Resolution: 2.75→50.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.953 / SU B: 45.775 / SU ML: 0.414 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.423 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 832 4.7 %RANDOM
Rwork0.2013 ---
obs0.2044 16764 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 401.98 Å2 / Biso mean: 122.052 Å2 / Biso min: 67.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å2-0 Å2
2--0.45 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 2.75→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 4 130 4008
Biso mean--129.57 118.87 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133993
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173686
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.6395447
X-RAY DIFFRACTIONr_angle_other_deg1.2111.5728493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8835511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.521.977172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.10115612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9311520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024538
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02918
LS refinement shellResolution: 2.751→2.822 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 58 -
Rwork0.383 1231 -
all-1289 -
obs--99.61 %
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)
11.343-0.32821.24190.0988-0.25552.0781-0.22-0.46910.24060.0270.13320.0249-0.2485-0.43210.08680.08360.0584-0.15780.1930.03130.6-39.29921.192-39.884
20.5752-0.41850.83661.0699-0.41.51360.1092-0.1138-0.0598-0.1864-0.02050.36750.2249-0.0996-0.08860.0638-0.0161-0.12130.13160.10180.4989-36.4226.753-50.672
31.0548-0.22050.84521.5784-1.28461.5655-0.128-0.21810.09150.38680.17790.0952-0.2789-0.3368-0.04990.23360.05610.04510.229-0.02710.1552-10.695.734-3.894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 221
2X-RAY DIFFRACTION2B2 - 198
3X-RAY DIFFRACTION3C22 - 123

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