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- PDB-5tod: Transmembrane protein 24 SMP domain -

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Basic information

Entry
Database: PDB / ID: 5tod
TitleTransmembrane protein 24 SMP domain
ComponentsTransmembrane protein 24
KeywordsLIPID TRANSPORT / lipid transfer protein / SMP / membrane contact sites
Function / homology
Function and homology information


endoplasmic reticulum-plasma membrane contact site / phosphatidylinositol transfer activity / cortical endoplasmic reticulum / insulin binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phosphatidylinositol binding / membrane => GO:0016020 / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
C2 domain-containing protein 2-like / Synaptotagmin-like, mitochondrial and lipid-binding domain / Synaptotagmin-like, mitochondrial and lipid-binding domain / C2 domain profile.
Similarity search - Domain/homology
Phospholipid transfer protein C2CD2L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.96 Å
AuthorsLees, J.A. / Reinisch, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM80616 United States
CitationJournal: Science / Year: 2017
Title: Lipid transport by TMEM24 at ER-plasma membrane contacts regulates pulsatile insulin secretion.
Authors: Lees, J.A. / Messa, M. / Sun, E.W. / Wheeler, H. / Torta, F. / Wenk, M.R. / De Camilli, P. / Reinisch, K.M.
History
DepositionOct 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Derived calculations
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Transmembrane protein 24
A: Transmembrane protein 24
B: Transmembrane protein 24
C: Transmembrane protein 24
D: Transmembrane protein 24
E: Transmembrane protein 24


Theoretical massNumber of molelcules
Total (without water)126,3566
Polymers126,3566
Non-polymers00
Water00
1
F: Transmembrane protein 24


Theoretical massNumber of molelcules
Total (without water)21,0591
Polymers21,0591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Transmembrane protein 24


Theoretical massNumber of molelcules
Total (without water)21,0591
Polymers21,0591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Transmembrane protein 24


Theoretical massNumber of molelcules
Total (without water)21,0591
Polymers21,0591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Transmembrane protein 24


Theoretical massNumber of molelcules
Total (without water)21,0591
Polymers21,0591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Transmembrane protein 24


Theoretical massNumber of molelcules
Total (without water)21,0591
Polymers21,0591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
E: Transmembrane protein 24


Theoretical massNumber of molelcules
Total (without water)21,0591
Polymers21,0591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-43 kcal/mol
Surface area44220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.395, 117.098, 148.133
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
Transmembrane protein 24 / C2 domain-containing protein 2-like


Mass: 21059.260 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C2CD2L, KIAA0285, TMEM24, DLNB23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14523

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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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100-200 mM MgCl2, 100 mM bis-tris propane pH 6.5-8.0, 45% PEG 200
PH range: 6.5-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2014
RadiationMonochromator: Cryogenically cooled single-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.958→148.13 Å / Num. obs: 30469 / % possible obs: 98.1 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 28.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.96→58.55 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.07
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1942 6.5 %THIN SHELL
Rwork0.239 ---
obs0.241 29860 96.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.96→58.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6900 0 0 0 6900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027031
X-RAY DIFFRACTIONf_angle_d0.5049605
X-RAY DIFFRACTIONf_dihedral_angle_d11.4444318
X-RAY DIFFRACTIONf_chiral_restr0.0431174
X-RAY DIFFRACTIONf_plane_restr0.0031229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9596-3.03360.3996920.38091378X-RAY DIFFRACTION68
3.0336-3.11560.36281110.34581893X-RAY DIFFRACTION92
3.1156-3.20730.38181720.3111933X-RAY DIFFRACTION97
3.2073-3.31080.339940.27792022X-RAY DIFFRACTION98
3.3108-3.42910.34181920.26921974X-RAY DIFFRACTION99
3.4291-3.56640.3056980.26042065X-RAY DIFFRACTION99
3.5664-3.72870.26251950.23941965X-RAY DIFFRACTION99
3.7287-3.92520.2571990.23962111X-RAY DIFFRACTION100
3.9252-4.17110.28281970.23052007X-RAY DIFFRACTION100
4.1711-4.4930.2235990.19912111X-RAY DIFFRACTION100
4.493-4.9450.19651370.16892073X-RAY DIFFRACTION100
4.945-5.660.2251600.21892062X-RAY DIFFRACTION100
5.66-7.1290.2879990.25952165X-RAY DIFFRACTION100
7.129-58.56040.23731970.24772159X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.94430.491-0.05910.2556-0.0921.5370.13260.34290.27070.27680.179-0.38340.0241-0.20330.00080.69380.00170.11430.92450.00790.720248.981472.6408109.5498
21.47382.1171-0.45444.746-2.24381.86470.63980.8343-0.7537-0.3682-1.0254-1.0735-1.0261-0.5365-0.27891.10790.12020.05350.7687-0.1341.016348.783770.0082119.4213
32.0101-0.2123-0.99882.7933-0.56712.04030.07990.2871-0.0476-0.3701-0.13970.5889-0.0444-0.9686-0.00020.44380.1086-0.0250.93530.10490.80242.201874.227110.5475
41.0153-0.6876-0.60110.49970.16730.8002-0.0051-0.368-0.01730.76840.1635-0.18460.11340.02330.00040.57520.1349-0.12290.7265-0.02690.495662.629977.351285.3675
51.53110.64340.09772.7756-0.32442.7426-0.2904-0.32840.1264-0.05760.32440.3754-0.3739-0.3073-0.00050.4940.0636-0.03440.5571-0.00420.57858.960879.295878.9093
60.6379-1.1497-0.35681.59591.25261.52350.016-0.2222-0.233-0.0074-0.05670.2979-0.0592-0.1348-0.00090.51520.0189-0.11260.48910.01320.452362.515668.851576.9962
70.8442-1.0315-0.50361.71530.42261.0230.17190.37090.37390.66630.06830.30220.1445-0.12640.00160.6620.00710.07930.54890.11060.643577.594458.468392.2848
80.78260.2193-0.78660.3407-0.02841.31460.34190.00720.12560.2283-0.1012-0.14470.3182-0.0050.00070.6223-0.04580.00020.57470.00870.589584.72459.838987.1961
90.99780.87180.91880.69520.38631.8436-0.23450.5476-0.6943-0.07020.1733-0.26241.0682-1.3835-0.02620.61980.0566-0.0350.55740.05050.607777.173443.987493.1013
101.87491.80820.30023.01740.01020.6532-0.0131-0.1277-0.1421-0.01540.1371-0.26640.04250.08530.00040.48860.0676-0.00180.4850.02010.539189.417959.5191.3494
111.5875-1.13640.0620.7581-0.11971.0080.05171.14290.5034-0.76560.3126-1.0526-0.6120.6623-0.01510.65450.10330.26530.87560.07330.75467.395659.5092118.1222
121.0427-0.2477-0.68320.2342-0.32261.24510.0260.43540.50030.32960.14250.25020.12530.11080.00120.63410.07250.17020.52430.06350.621765.71160.5957126.2952
130.75970.79660.57831.01880.72590.52010.4927-0.78210.19130.15980.4106-0.481-0.90141.08610.00690.6650.0630.13980.6074-0.03370.624882.194354.4339124.0119
140.604-0.315-1.02152.2828-0.02971.6465-0.06760.2366-0.2458-0.1807-0.07340.33110.4164-0.1931-0.0010.64610.04130.12980.55770.02640.565962.561654.5906122.3292
151.62961.26730.59221.60271.40542.045-0.01620.124-0.20150.3185-0.08020.00480.36390.0002-0.00380.4916-0.05370.08530.5223-0.0440.481882.271285.037595.0258
162.2908-0.07380.04220.0553-0.14280.1417-0.54790.0698-1.8576-0.86780.3156-0.0617-0.48430.0877-0.0010.94690.02840.07120.5293-0.01440.671286.090779.679886.6853
171.1722-1.09710.69631.2787-0.33660.7154-0.1467-0.31370.05650.49140.3783-0.84020.48640.31350.00040.5593-0.04880.03710.5722-0.12750.680595.907888.9152103.1641
181.16080.02150.51852.43710.6451.30670.02490.0510.2378-0.18390.01020.0016-0.09250.1320.00020.4201-0.07590.06840.4382-0.01390.504382.569190.633489.4358
191.02810.0466-1.09011.63840.31411.20950.01460.6431-0.1175-1.2669-0.35960.5585-0.2208-0.1309-0.00480.8681-0.02250.0670.5965-0.0260.791466.038286.557117.9158
200.942-0.3205-0.56880.5281-0.4610.83430.69520.20650.0936-0.6127-0.4693-0.37150.2502-0.25330.00010.73520.14360.05190.66580.05010.688463.979385.804126.2184
211.1312-0.76580.25850.6209-0.43340.17530.07420.97910.63630.7590.5369-0.1346-0.7686-1.12740.00220.78980.06260.23590.67310.04810.822466.7288100.8177116.7098
221.02910.9243-0.06792.43440.13310.2290.0975-0.1392-0.0560.76470.0029-0.0149-0.38820.06030.00030.5761-0.00150.10320.5035-0.02030.579670.538585.1954127.5693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'F' and (resid 90 through 125 )
2X-RAY DIFFRACTION2chain 'F' and (resid 126 through 134 )
3X-RAY DIFFRACTION3chain 'F' and (resid 135 through 256 )
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 255 )
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 114 )
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 140 )
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 160 )
10X-RAY DIFFRACTION10chain 'B' and (resid 161 through 255 )
11X-RAY DIFFRACTION11chain 'C' and (resid 97 through 114 )
12X-RAY DIFFRACTION12chain 'C' and (resid 115 through 140 )
13X-RAY DIFFRACTION13chain 'C' and (resid 141 through 160 )
14X-RAY DIFFRACTION14chain 'C' and (resid 161 through 256 )
15X-RAY DIFFRACTION15chain 'D' and (resid 89 through 125 )
16X-RAY DIFFRACTION16chain 'D' and (resid 126 through 134 )
17X-RAY DIFFRACTION17chain 'D' and (resid 135 through 160 )
18X-RAY DIFFRACTION18chain 'D' and (resid 161 through 256 )
19X-RAY DIFFRACTION19chain 'E' and (resid 89 through 114 )
20X-RAY DIFFRACTION20chain 'E' and (resid 115 through 140 )
21X-RAY DIFFRACTION21chain 'E' and (resid 141 through 160 )
22X-RAY DIFFRACTION22chain 'E' and (resid 161 through 256 )

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