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- PDB-4mvu: Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium ... -

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Basic information

Entry
Database: PDB / ID: 4mvu
TitleStructural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / Tetrameric / Voltage-gated Ion Channel / Voltage-gated Calcium Channel / Calcium Selective / Transport Protein / Membrane
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity / identical protein binding / metal ion binding
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Helix Hairpins - #70 / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Similarity search - Component
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.198 Å
AuthorsTang, L. / Gamal El-Din, T.M. / Payandeh, J. / Martinez, G.Q. / Heard, T.M. / Scheuer, T. / Zheng, N. / Catterall, W.A.
CitationJournal: Nature / Year: 2014
Title: Structural basis for Ca2+ selectivity of a voltage-gated calcium channel.
Authors: Tang, L. / Gamal El-Din, T.M. / Payandeh, J. / Martinez, G.Q. / Heard, T.M. / Scheuer, T. / Zheng, N. / Catterall, W.A.
History
DepositionSep 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
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 / 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_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: Ion transport protein
B: Ion transport protein
C: Ion transport protein
D: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,93823
Polymers109,9554
Non-polymers10,98319
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-161 kcal/mol
Surface area45560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.765, 177.685, 131.205
Angle α, β, γ (deg.)90.00, 132.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ion transport protein


Mass: 27488.709 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (bacteria) / Strain: RM4018 / Gene: Abu_1752 / Plasmid: PFASTBAC DUAL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE


Mass: 678.940 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: CHAPSO:DMPC bicelles, 0.1M Na-Acetate, pH4.75, 2M Ammonium Sulfate, 28% Glucose, 15mM Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.75 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.75 Å / Relative weight: 1
ReflectionResolution: 3.198→30 Å / Num. all: 46122 / Num. obs: 46122 / % possible obs: 93.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 3.198→3.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RVY

3rvy


Resolution: 3.198→29.89 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.917 / SU B: 14.615 / SU ML: 0.256 / Cross valid method: THROUGHOUT / ESU R: 0.569 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26254 2335 5.1 %RANDOM
Rwork0.23671 ---
obs0.23802 43749 93.2 %-
all-43749 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.553 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å2-1.09 Å2
2--3.45 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 3.198→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7196 0 191 4 7391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.027572
X-RAY DIFFRACTIONr_bond_other_d0.0040.027528
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.97210276
X-RAY DIFFRACTIONr_angle_other_deg0.849317200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0275872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40921.667288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.89151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1381540
X-RAY DIFFRACTIONr_chiral_restr0.0750.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027956
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021852
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_it9.2239.3553500
X-RAY DIFFRACTIONr_mcbond_other9.2239.3553499
X-RAY DIFFRACTIONr_mcangle_it13.96114.0164368
X-RAY DIFFRACTIONr_mcangle_other13.96514.0244369
X-RAY DIFFRACTIONr_scbond_it8.2619.8064072
X-RAY DIFFRACTIONr_scbond_other8.2919.8074073
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.67614.4815909
X-RAY DIFFRACTIONr_long_range_B_refined19.14388.50531846
X-RAY DIFFRACTIONr_long_range_B_other19.14288.50631846
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.198→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 188 -
Rwork0.366 3361 -
obs--98.17 %

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