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- PDB-2a0l: Crystal structure of KvAP-33H1 Fv complex -

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Basic information

Entry
Database: PDB / ID: 2a0l
TitleCrystal structure of KvAP-33H1 Fv complex
Components
  • (33H1 Fv fragment) x 2
  • Voltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / voltage sensor / voltage-dependent K+ channel / K+ channel-Fv complex / ion channel
Function / homology
Function and homology information


delayed rectifier potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Helix Hairpins - #70 / Ion transport domain / Ion transport protein / Helix Hairpins / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Voltage-gated potassium channel
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.9 Å
AuthorsLee, S.Y. / Lee, A. / Chen, J. / Mackinnon, R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure of the KvAP voltage-dependent K+ channel and its dependence on the lipid membrane.
Authors: Lee, S.Y. / Lee, A. / Chen, J. / Mackinnon, R.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: 33H1 Fv fragment
D: 33H1 Fv fragment
E: 33H1 Fv fragment
F: 33H1 Fv fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,33410
Polymers101,1786
Non-polymers1564
Water00
1
A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: 33H1 Fv fragment
D: 33H1 Fv fragment
E: 33H1 Fv fragment
F: 33H1 Fv fragment
hetero molecules

A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: 33H1 Fv fragment
D: 33H1 Fv fragment
E: 33H1 Fv fragment
F: 33H1 Fv fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,66920
Polymers202,35612
Non-polymers3138
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)136.362, 136.362, 191.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-2-

K

21A-3-

K

31B-1-

K

41B-4-

K

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation : x. -y+1,-z

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Components

#1: Protein Voltage-gated potassium channel / KvAP


Mass: 26168.955 Da / Num. of mol.: 2 / Fragment: KvAP K+ channel
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: KVAP_AERPE / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue / References: UniProt: Q9YDF8
#2: Antibody 33H1 Fv fragment


Mass: 11238.435 Da / Num. of mol.: 2 / Fragment: Fv fragment,light chain / Source method: isolated from a natural source / Details: mouse hybridoma / Source: (natural) Mus musculus (house mouse)
#3: Antibody 33H1 Fv fragment


Mass: 13181.556 Da / Num. of mol.: 2 / Fragment: Fv fragment, heavy chain / Source method: isolated from a natural source / Details: mouse hybridoma / Source: (natural) Mus musculus (house mouse)
#4: 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: 1

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: sodium citrate, Tric-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONALS 8.2.121.1
SYNCHROTRONCHESS A130.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 10, 2004
ADSC QUANTUM 2102CCDNov 18, 2004
ADSC Q2103CCDDec 7, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Mx-ray1
3Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97951
ReflectionResolution: 3.9→57.7 Å / Num. obs: 16257 / Redundancy: 6.94 % / Rsym value: 0.09 / Net I/σ(I): 9.7
Reflection shellResolution: 3.9→4.1 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.465 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 3.9→57.89 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 6294012.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.392 789 4.9 %RANDOM
Rwork0.358 ---
obs0.358 16234 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 164.237 Å2 / ksol: 0.260472 e/Å3
Displacement parametersBiso mean: 187.8 Å2
Baniso -1Baniso -2Baniso -3
1-34.47 Å20 Å20 Å2
2--34.47 Å20 Å2
3----68.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.88 Å0.81 Å
Luzzati d res low-5 Å
Luzzati sigma a0.98 Å0.9 Å
Refinement stepCycle: LAST / Resolution: 3.9→57.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 4 0 6746
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it18.011.5
X-RAY DIFFRACTIONc_mcangle_it27.942
X-RAY DIFFRACTIONc_scbond_it18.272
X-RAY DIFFRACTIONc_scangle_it26.672.5
LS refinement shellResolution: 3.9→4.14 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.437 117 4.3 %
Rwork0.438 2586 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param

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