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- PDB-4wis: Crystal structure of the lipid scramblase nhTMEM16 in crystal form 1 -

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Basic information

Entry
Database: PDB / ID: 4wis
TitleCrystal structure of the lipid scramblase nhTMEM16 in crystal form 1
Componentslipid scramblase
KeywordsLIPID TRANSPORT / membrane protein / calcium activation / transport protein
Function / homology: / Alpha-beta plait domain in TMEM16 lipid scramblase / : / Anoctamin / Calcium-activated chloride channel / membrane / identical protein binding / metal ion binding / Plasma membrane channel protein
Function and homology information
Biological speciesNectria haematococca (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsDutzler, R. / Brunner, J.D. / Lim, N.K. / Schenck, S.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
European Research Council339116-AnoBest Switzerland
SNSFTransCure Switzerland
CitationJournal: Nature / Year: 2014
Title: X-ray structure of a calcium-activated TMEM16 lipid scramblase.
Authors: Brunner, J.D. / Lim, N.K. / Schenck, S. / Duerst, A. / Dutzler, R.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Apr 25, 2018Group: Author supporting evidence / Data collection / Structure summary
Category: entity / pdbx_audit_support / reflns_shell
Item: _entity.pdbx_description / _pdbx_audit_support.funding_organization / _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lipid scramblase
B: lipid scramblase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,5606
Polymers166,4002
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-124 kcal/mol
Surface area63800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.480, 113.690, 235.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein lipid scramblase


Mass: 83200.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nectria haematococca (fungus) / Strain: 77-13-4 / ATCC MYA-4622 / FGSC 9596 / MPVI / Gene: NECHADRAFT_66456 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: C7Z7K1
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 21-23% PEG 400, 100 mM Capso pH 9.4, 100 mM MgCl2, 100 mM NaCl
PH range: 9.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9797 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 39477 / % possible obs: 88.1 % / Redundancy: 12.7 % / Net I/σ(I): 20.1
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.235 / Mean I/σ(I) obs: 2.6 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
SHELXphasing
SHARPphasing
DMphasing
Omodel building
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.3→14.984 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2847 1954 5.01 %
Rwork0.2375 --
obs0.2399 38985 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→14.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10570 0 4 0 10574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310846
X-RAY DIFFRACTIONf_angle_d0.73614716
X-RAY DIFFRACTIONf_dihedral_angle_d14.363892
X-RAY DIFFRACTIONf_chiral_restr0.0291618
X-RAY DIFFRACTIONf_plane_restr0.0031864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.38160.36181280.31372594X-RAY DIFFRACTION99
3.3816-3.47190.32541490.29022583X-RAY DIFFRACTION99
3.4719-3.57280.33211370.26522625X-RAY DIFFRACTION99
3.5728-3.68640.32211350.24722617X-RAY DIFFRACTION100
3.6864-3.81610.27411330.23242604X-RAY DIFFRACTION99
3.8161-3.96620.29511500.23872603X-RAY DIFFRACTION99
3.9662-4.1430.27181400.22572629X-RAY DIFFRACTION99
4.143-4.35640.27291360.22982642X-RAY DIFFRACTION99
4.3564-4.62180.24431390.21372631X-RAY DIFFRACTION99
4.6218-4.96660.26151280.21052676X-RAY DIFFRACTION100
4.9666-5.44450.25451350.23142664X-RAY DIFFRACTION99
5.4445-6.18330.34191310.26392690X-RAY DIFFRACTION100
6.1833-7.61610.33441550.27572703X-RAY DIFFRACTION100
7.6161-14.98430.25871580.21862770X-RAY DIFFRACTION99
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)
15.1862-0.7587-1.08922.64720.7645.2642-0.15-0.6153-0.34910.1698-0.25970.9384-0.5044-1.50850.26320.75960.1444-0.01251.1818-0.08791.3724-23.36740.200981.865
26.0307-1.14-0.621.79620.29382.503-0.2399-0.5195-0.7670.30170.07980.4460.4287-0.32870.17590.8104-0.0646-0.13810.59030.1121.0239-0.935426.107679.1918
34.08750.01590.50373.8857-0.44783.4464-0.0901-1.08280.31860.94040.0684-0.1355-0.16180.0901-0.08150.80860.0371-0.05940.789-0.09480.767516.140442.621688.8794
43.9078-0.1393-0.12731.9011-0.49983.5838-0.0377-0.4766-0.03970.41680.0219-0.1710.03690.1629-0.0140.74590.0088-0.23730.55670.10490.877311.78230.054181.5072
51.6361-0.03780.82510.6071-0.43234.8222-0.32221.07970.0613-0.6540.13630.22950.8496-0.091-0.27041.5811-0.2483-0.37911.57430.07441.3646-5.989125.341422.7576
62.8707-0.00410.30961.6138-0.02242.8293-0.06970.8921-0.0611-0.7785-0.13590.22640.0212-0.36780.18260.93460.0673-0.12960.8207-0.01860.97158.189837.570130.6859
73.41580.04390.44192.64260.10912.22430.20520.8054-0.2785-0.3097-0.0478-0.43490.20360.4322-0.13530.75280.1124-0.06040.7661-0.0620.860334.498130.053940.7288
82.9227-0.027-1.66481.0604-0.17572.3697-0.02470.060.28840.03760.04510.0867-0.0615-0.3958-0.02540.65430.0281-0.16080.55580.04860.89634.927741.174556.0719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 245 )
3X-RAY DIFFRACTION3chain 'A' and (resid 246 through 463 )
4X-RAY DIFFRACTION4chain 'A' and (resid 464 through 625 )
5X-RAY DIFFRACTION5chain 'A' and (resid 626 through 719 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 245 )
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 463 )
8X-RAY DIFFRACTION8chain 'B' and (resid 464 through 719 )

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