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- PDB-4rdq: Calcium-activated chloride channel bestrophin-1, from chicken, in... -

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Basic information

Entry
Database: PDB / ID: 4rdq
TitleCalcium-activated chloride channel bestrophin-1, from chicken, in complex with Fab antibody fragments, chloride and calcium
Components
  • (Fab antibody fragment, ...) x 2
  • Bestrophin-1Calcium-dependent chloride channel
KeywordsTRANSPORT PROTEIN / transmembrane protein / membrane protein / ion channel / calcium-activated chloride channel / CaCC / anion channel / membrane
Function / homologyBestrophin / Bestrophin/UPF0187 / Bestrophin-1 / Bestrophin, RFP-TM, chloride channel / Stimuli-sensing channels / transepithelial chloride transport / detection of light stimulus involved in visual perception / chloride channel activity / chloride channel complex / regulation of calcium ion transport ...Bestrophin / Bestrophin/UPF0187 / Bestrophin-1 / Bestrophin, RFP-TM, chloride channel / Stimuli-sensing channels / transepithelial chloride transport / detection of light stimulus involved in visual perception / chloride channel activity / chloride channel complex / regulation of calcium ion transport / basolateral plasma membrane / identical protein binding / metal ion binding / Bestrophin homolog
Function and homology information
Specimen sourceGallus gallus (chicken)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 2.85 Å resolution
AuthorsDickson, V.K. / Pedi, L. / Long, S.B.
CitationJournal: Nature / Year: 2014
Title: Structure and insights into the function of a Ca(2+)-activated Cl(-) channel.
Authors: Kane Dickson, V. / Pedi, L. / Long, S.B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 19, 2014 / Release: Oct 22, 2014
RevisionDateData content typeGroupProviderType
1.0Oct 22, 2014Structure modelrepositoryInitial release
1.1Oct 29, 2014Structure modelStructure summary
1.2Dec 24, 2014Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bestrophin-1
B: Bestrophin-1
C: Bestrophin-1
D: Bestrophin-1
E: Bestrophin-1
F: Fab antibody fragment, light chain
G: Fab antibody fragment, heavy chain
H: Fab antibody fragment, light chain
I: Fab antibody fragment, heavy chain
J: Fab antibody fragment, light chain
K: Fab antibody fragment, heavy chain
L: Fab antibody fragment, light chain
M: Fab antibody fragment, heavy chain
N: Fab antibody fragment, light chain
O: Fab antibody fragment, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)479,35750
Polyers472,96315
Non-polymers6,39435
Water18010
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)88800
ΔGint (kcal/M)-761
Surface area (Å2)142740
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)98.540, 242.904, 172.757
Angle α, β, γ (deg.)90.00, 93.68, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 1 types, 5 molecules ABCDE

#1: Protein/peptide
Bestrophin-1 / Calcium-dependent chloride channel / Best1


Mass: 47614.344 Da / Num. of mol.: 5 / Fragment: UNP residues 2-405 / Source: (gene. exp.) Gallus gallus (chicken) / Gene: Best1 bestrophin-1 / Production host: pichia pastoris (fungus) / References: UniProt: E1C3A0

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Fab antibody fragment, ... , 2 types, 10 molecules FHJLNGIKMO

#2: Protein/peptide
Fab antibody fragment, light chain


Mass: 23339.707 Da / Num. of mol.: 5 / Source: (natural) Mus musculus (house mouse) / Details: antibody secreted from hybridoma cells
#3: Protein/peptide
Fab antibody fragment, heavy chain


Mass: 23638.525 Da / Num. of mol.: 5 / Source: (natural) Mus musculus (house mouse) / Details: antibody secreted from hybridoma cells

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Non-polymers , 6 types, 45 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Formula: C3H8O3 / Glycerol
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Formula: Cl / Chloride
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Formula: Ca / Calcium
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Formula: K / Potassium
#8: Chemical
ChemComp-C6N / 6-cyclohexyl-2-(4-cyclohexylbutyl)-2-({[4-O-(alpha-D-glucopyranosyl)-beta-D-glucopyranosyl]oxy}methyl)hexyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1001.157 Da / Num. of mol.: 5 / Formula: C47H84O22
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Formula: H2O / Water

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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: 4.36 / Density percent sol: 71.8 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 5% PEG 4000, 75 mM KCl, 75 mM NaCl, 50 mM sodium acetate pH 4.0, 20% glycerol, 0.5 mM Cymal-6-NG (detergent), 10 mM Tris-HCl pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Collection date: Apr 19, 2013
RadiationMonochromator: Si(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 61.1 Å2 / D resolution high: 2.85 Å / D resolution low: 40 Å / Number obs: 188162 / Observed criterion sigma F: 0 / Observed criterion sigma I: -3 / Rsym value: 0.113 / NetI over sigmaI: 14.2 / Redundancy: 6.8 % / Percent possible obs: 100
Reflection shellHighest resolution: 2.85 Å / Lowest resolution: 2.95 Å / MeanI over sigI obs: 1.1 / Number unique all: 18682 / Redundancy: 6.7 % / Percent possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
CNS1.3refinement
REFMACrefinement
PHENIX(phenix.refine: 1.9_1678)refinement
HKL-3000data reduction
HKL-3000data scaling
RefineMethod to determine structure: SAD / Overall SU ML: 0.39 / R Free selection details: RANDOM / Sigma F: 0 / Overall phase error: 27.53 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.7 Å / Solvent vdw probe radii: 1 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2341 / R factor R work: 0.2167 / R factor obs: 0.2176 / Highest resolution: 2.85 Å / Lowest resolution: 39.891 Å / Number reflection R free: 9438 / Number reflection all: 188162 / Number reflection obs: 187788 / Percent reflection R free: 5.03 / Percent reflection obs: 99.74
Refine hist #LASTHighest resolution: 2.85 Å / Lowest resolution: 39.891 Å
Number of atoms included #LASTProtein: 30715 / Nucleic acid: 0 / Ligand: 400 / Solvent: 10 / Total: 31125
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00331985
X-RAY DIFFRACTIONf_angle_d0.93143700
X-RAY DIFFRACTIONf_dihedral_angle_d15.41011245
X-RAY DIFFRACTIONf_chiral_restr0.0384945
X-RAY DIFFRACTIONf_plane_restr0.0055505
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.85000.39900.37792.8824313587898.00
2.88240.35810.35832.91633345890100.00
2.91630.37740.34922.95183325879100.00
2.95180.35470.35292.9892314594599.00
2.98920.32320.33583.02853185874100.00
3.02850.33410.32663.07003135974100.00
3.07000.33650.32633.11383445856100.00
3.11380.33330.30983.1603320589799.00
3.16030.30330.29423.20963305913100.00
3.20960.30660.29783.26223145984100.00
3.26220.29900.28283.31853125895100.00
3.31850.28640.27133.37883185980100.00
3.37880.25470.26663.44372635972100.00
3.44370.24770.23433.51403405969100.00
3.51400.23560.22193.59033305874100.00
3.59030.24130.21533.67382975978100.00
3.67380.24400.20533.76562935949100.00
3.76560.23470.20073.86733215972100.00
3.86730.20490.19503.98103395911100.00
3.98100.21510.18664.10942956006100.00
4.10940.20820.18214.25613395910100.00
4.25610.17190.17334.42632805988100.00
4.42630.19780.16334.62753075972100.00
4.62750.21600.18204.87113025955100.00
4.87110.19740.18605.17563235964100.00
5.17560.21400.20135.57433095971100.00
5.57430.23910.20906.13342905994100.00
6.13340.23950.20957.01682926015100.00
7.01680.19320.16858.82463255988100.00
8.82460.19230.198739.8949331599799.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.5506-0.0284-0.09960.2055-0.04050.43990.0232-0.21960.2248-0.01330.0297-0.0977-0.06490.0399-0.00000.4375-0.01770.01900.4455-0.17110.544249.130884.706941.2728
20.3517-0.0571-0.05580.29840.02210.20640.0163-0.35970.06040.06800.0491-0.04420.03440.06770.00000.39190.0137-0.03140.6268-0.17310.442549.063772.903560.2726
30.26750.0133-0.03890.26520.22390.37810.0107-0.2638-0.09570.03980.0111-0.05260.07940.05020.00000.38190.0360-0.03200.5112-0.04600.376048.987551.224454.9372
40.35400.10980.01470.3584-0.08920.31310.0131-0.0035-0.0218-0.05820.0386-0.06830.02230.02290.00000.45300.02550.00850.4279-0.08050.465048.994749.621232.6430
50.5605-0.05570.06140.42580.12960.22160.0147-0.07200.1808-0.06140.0184-0.0333-0.04960.0465-0.00000.4253-0.00610.03540.3961-0.08490.475149.072470.307024.1802
60.5052-0.3326-0.12811.4172-0.08830.6569-0.25520.16090.17630.0326-0.1585-0.1836-0.2072-0.13760.00000.7309-0.0391-0.13970.6215-0.12200.864459.0613117.296027.1937
70.2282-0.0059-0.30140.63970.26150.9366-0.0574-0.31470.1237-0.02090.2488-0.1108-0.1201-0.03660.00750.60490.0720-0.05041.0033-0.34400.607057.394297.105286.1151
80.29790.45680.17690.74690.03900.75870.2395-0.4280-0.22930.4775-0.1144-0.09090.40550.19570.00001.02150.0483-0.12281.16540.19170.720457.029633.771885.9242
90.6334-0.1755-0.28051.58020.02230.9165-0.1672-0.0598-0.1841-0.00700.1393-0.21810.09820.01240.00000.65030.01690.01310.5011-0.07140.663457.022814.835125.8713
100.8332-0.79650.38581.19440.00851.15130.15440.12010.0369-0.4296-0.1163-0.16680.01310.17650.00000.8320-0.00340.11790.54620.01010.579257.659666.2308-10.9610
110.3253-0.0095-0.19860.5910-0.25490.15430.2854-0.0067-0.22150.0476-0.0439-0.1888-0.2603-0.0713-0.00001.53150.0492-0.19990.84350.10641.116660.4914152.197519.6285
120.6938-0.44320.26530.43330.26830.8652-0.07210.4001-0.20660.37810.16710.0206-0.35110.2547-0.00001.15000.01460.02360.8586-0.16960.718254.8384116.3181116.1061
130.0587-0.0105-0.08370.0246-0.06640.1033-0.6871-0.4258-0.70330.58750.1674-0.00040.7691-0.2048-0.00002.47500.41110.20542.45870.82371.624253.900310.8746113.5577
140.57980.1481-0.54100.69520.06670.5222-0.0429-0.04550.1034-0.07200.2220-0.18460.1559-0.0686-0.00001.02060.05750.16340.7114-0.11890.986056.0367-19.548516.3715
150.04040.1021-0.10300.0315-0.08390.0723-0.50961.10810.1057-0.97890.3015-0.1352-0.05520.50630.00192.1115-0.30090.11341.96080.12891.022656.328969.4245-46.7202
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 103) or (chain 'G' and resid 1 through 113)
7X-RAY DIFFRACTION7(chain 'H' and resid 1 through 103) or (chain 'I' and resid 1 through 113)
8X-RAY DIFFRACTION8(chain 'J' and resid 1 through 103) or (chain 'K' and resid 1 through 113)
9X-RAY DIFFRACTION9(chain 'L' and resid 1 through 103) or (chain 'M' and resid 1 through 113)
10X-RAY DIFFRACTION10(chain 'N' and resid 1 through 103) or (chain 'O' and resid 1 through 113)
11X-RAY DIFFRACTION11(chain 'F' and resid 104 through 212) or (chain 'G' and resid 114 through 217)
12X-RAY DIFFRACTION12(chain 'H' and resid 104 through 212) or (chain 'I' and resid 114 through 217)
13X-RAY DIFFRACTION13(chain 'J' and resid 104 through 212) or (chain 'K' and resid 114 through 217)
14X-RAY DIFFRACTION14(chain 'L' and resid 104 through 212) or (chain 'M' and resid 114 through 217)
15X-RAY DIFFRACTION15(chain 'N' and resid 104 through 212) or (chain 'O' and resid 114 through 217)

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