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- PDB-7a1r: Crystal structure of the C2B domain of Trypanosoma brucei extende... -

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Basic information

Entry
Database: PDB / ID: 7a1r
TitleCrystal structure of the C2B domain of Trypanosoma brucei extended synaptotagmin (E-Syt)
ComponentsSynaptotagmin
KeywordsLIPID BINDING PROTEIN / C2 domain / Extended synaptotagmin / Lipid transfer / Trypanosoma
Function / homology
Function and homology information


lipid transport / lipid binding / endoplasmic reticulum / membrane
Similarity search - Function
Synaptotagmin, plant / Synaptotagmin, SMP domain / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. ...Synaptotagmin, plant / Synaptotagmin, SMP domain / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial-lipid-binding domain / Synaptotagmin-like mitochondrial lipid-binding proteins (SMP) domain profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Synaptotagmin
Similarity search - Component
Biological speciesTrypanosoma brucei equiperdum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsDong, G.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP28231-B28 Austria
Austrian Science FundP24383-B21 Austria
CitationJournal: Iscience / Year: 2021
Title: Structural studies of the shortest extended synaptotagmin with only two C2 domains from Trypanosoma brucei .
Authors: Stepinac, E. / Landrein, N. / Skwarzynska, D. / Wojcik, P. / Lesigang, J. / Lucic, I. / He, C.Y. / Bonhivers, M. / Robinson, D.R. / Dong, G.
History
DepositionAug 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Synaptotagmin
B: Synaptotagmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,96915
Polymers30,4792
Non-polymers49113
Water6,359353
1
A: Synaptotagmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4848
Polymers15,2391
Non-polymers2457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Synaptotagmin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4857
Polymers15,2391
Non-polymers2466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.908, 57.532, 84.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 474 through 503 or resid 505...
21(chain B and (resid 474 through 503 or resid 505...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 474 through 503 or resid 505...A474 - 503
121(chain A and (resid 474 through 503 or resid 505...A505 - 515
131(chain A and (resid 474 through 503 or resid 505...A518 - 523
141(chain A and (resid 474 through 503 or resid 505...A525 - 552
151(chain A and (resid 474 through 503 or resid 505...A554 - 560
161(chain A and (resid 474 through 503 or resid 505...A562 - 572
171(chain A and (resid 474 through 503 or resid 505...A575 - 583
181(chain A and (resid 474 through 503 or resid 505...A585
191(chain A and (resid 474 through 503 or resid 505...A588 - 592
1101(chain A and (resid 474 through 503 or resid 505...A594
1111(chain A and (resid 474 through 503 or resid 505...A596 - 597
211(chain B and (resid 474 through 503 or resid 505...B474 - 503
221(chain B and (resid 474 through 503 or resid 505...B505 - 515
231(chain B and (resid 474 through 503 or resid 505...B518 - 523
241(chain B and (resid 474 through 503 or resid 505...B525 - 552
251(chain B and (resid 474 through 503 or resid 505...B554 - 560
261(chain B and (resid 474 through 503 or resid 505...B562 - 572
271(chain B and (resid 474 through 503 or resid 505...B575 - 583
281(chain B and (resid 474 through 503 or resid 505...B585
291(chain B and (resid 474 through 503 or resid 505...B588 - 592
2101(chain B and (resid 474 through 503 or resid 505...B594
2111(chain B and (resid 474 through 503 or resid 505...B596 - 597

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Synaptotagmin


Mass: 15239.370 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei equiperdum (eukaryote)
Gene: DPX39_100143600 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3L6KWL9

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Non-polymers , 5 types, 366 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.87 % / Description: Plate-like
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium cacodylate (pH 6.5), 0.15 M sodium acetate, 28% (v/v) polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 43547 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.08 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.039 / Rrim(I) all: 0.092 / Net I/σ(I): 10.39
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 4297 / CC1/2: 0.644 / CC star: 0.885 / Rpim(I) all: 0.429 / Rrim(I) all: 1.035 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→19.86 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1907 1984 4.56 %
Rwork0.1695 41538 -
obs0.1705 43522 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.46 Å2 / Biso mean: 24.73 Å2 / Biso min: 5.47 Å2
Refinement stepCycle: final / Resolution: 1.5→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 16 353 2279
Biso mean--24.74 36.69 -
Num. residues----242
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A608X-RAY DIFFRACTION5.882TORSIONAL
12B608X-RAY DIFFRACTION5.882TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.28011390.28132874301398
1.54-1.580.28441400.251629373077100
1.58-1.620.26351330.226329333066100
1.62-1.680.22011350.20472917305299
1.68-1.740.21391500.19022925307599
1.74-1.810.191380.18362940307899
1.81-1.890.19741370.170129493086100
1.89-1.990.21521460.160629643110100
1.99-2.110.18751360.153529763112100
2.11-2.270.20251450.157929713116100
2.27-2.50.18171440.168629823126100
2.5-2.860.18091450.176929873132100
2.86-3.60.18161420.15653029317199
3.6-19.860.16081540.15313154330899
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)
10.26710.06720.30920.51170.60080.41340.0707-0.01820.02370.0826-0.0990.08360.06420.0175-0.00020.1371-0.0002-0.00580.14290.00720.139716.747212.149754.695
20.03230.02660.03960.02480.0155-0.01440.0045-0.1251-0.01650.11560.00820.10010.0707-0.069400.11260.0092-0.01040.1418-0.00010.164110.18516.902850.3448
30.0032-0.01320.00580.02990.04090.0838-0.0106-0.08140.0281-0.1318-0.06630.475-0.12490.0530.00010.13950.0185-0.00590.1849-0.01140.21856.662822.734646.0993
40.03470.0250.01060.00970.04290.09990.01330.0723-0.08520.08870.0548-0.10270.09810.115100.13950.0275-0.01910.1305-0.00690.124920.00877.465750.5125
50.05910.012-0.0210.00920.01190.0522-0.0124-0.15630.1144-0.05120.0207-0.1107-0.13560.1084-0.00020.15440.0077-0.02120.16060.01690.186115.43924.837445.7915
60.0074-0.0216-0.00250.0349-0.00150.00430.01260.05820.30720.3017-0.04440.4665-0.00160.0284-0.00070.33120.02010.0820.1763-0.03490.34787.912835.631552.6818
70.02950.004-0.08010.111-0.00980.10180.1107-0.0813-0.02560.3316-0.11640.3530.0773-0.13780.00190.14740.01370.02120.1386-0.00570.16110.266816.972754.5857
80.04530.00450.03910.00820.00770.0232-0.30270.407-0.1239-0.45030.07180.1568-0.19410.0244-0.00080.1456-0.0006-0.0080.1884-0.02410.19375.49042.394949.3883
90.80.79680.22212.2724-0.18330.98720.017-0.13750.24350.3333-0.11040.5527-0.3593-0.0502-0.1490.1862-0.01110.02790.1134-0.01480.111112.24422.568258.4931
100.4339-0.0612-0.44780.3111-0.02010.5332-0.1207-0.11380.2046-0.0484-0.08220.2229-0.10460.1855-0.17280.223-0.0036-0.07170.2358-0.02270.174523.116727.118858.1453
110.018-0.00540.01340.049-0.02770.03130.1408-0.354-0.23660.1824-0.0603-0.01520.2382-0.09750.00050.2795-0.00050.06060.20860.02780.159613.683413.089264.4983
120.18270.1286-0.07190.17490.10250.1849-0.0668-0.04860.1969-0.0194-0.1502-0.253-0.27010.2237-0.01850.2592-0.0189-0.04830.15880.00370.149920.083427.298552.4865
130.0885-0.0221-0.1050.0827-0.10250.1849-0.05250.08570.03860.10520.0892-0.0180.0653-0.05870.00140.1224-0.0055-0.03650.1774-0.0120.15629.421921.5232.6777
140.5419-0.2246-0.02180.1788-0.08210.05540.02350.0793-0.118-0.2668-0.0651-0.18340.04660.0391-0.00160.178-0.0007-0.00340.1379-0.00840.173817.05766.573529.9465
150.0130.0462-0.01890.01870.06570.2396-0.0043-0.08810.1914-0.0106-0.1229-0.1541-0.1214-0.0135-0.01250.1259-0.0113-0.01040.17740.01890.182522.678422.424837.9892
160.0044-0.01370.01290.056-0.01040.06860.0664-0.138-0.01790.1297-0.06640.25710.25-0.2853-00.1611-0.0418-0.01570.17290.00060.16459.56916.701134.235
170.0722-0.05820.1190.2595-0.06050.1457-0.0722-0.0389-0.0462-0.1127-0.1222-0.2018-0.1426-0.0187-0.01280.1619-0.0196-0.02790.16410.01160.190317.72829.745134.392
180.457-0.1870.02692.65520.66130.2638-0.00840.07690.0626-0.2778-0.01-0.3885-0.08860.0732-0.08870.099-0.02870.01440.0947-0.00360.10219.607215.295729.0265
190.44680.15680.07980.1952-0.22840.3795-0.18090.2870.2036-0.09720.134-0.0845-0.02170.0596-0.07260.2191-0.0161-0.04070.18960.02020.18738.832122.245424.1848
200.2368-0.1897-0.41420.62720.22540.695-0.2660.03610.23320.14670.11160.4746-0.0159-0.0591-0.10880.17770.0326-0.06840.1399-0.00810.16679.517426.785430.6258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 474 through 498 )A474 - 498
2X-RAY DIFFRACTION2chain 'A' and (resid 499 through 505 )A499 - 505
3X-RAY DIFFRACTION3chain 'A' and (resid 506 through 511 )A506 - 511
4X-RAY DIFFRACTION4chain 'A' and (resid 512 through 524 )A512 - 524
5X-RAY DIFFRACTION5chain 'A' and (resid 525 through 531 )A525 - 531
6X-RAY DIFFRACTION6chain 'A' and (resid 532 through 537 )A532 - 537
7X-RAY DIFFRACTION7chain 'A' and (resid 538 through 545 )A538 - 545
8X-RAY DIFFRACTION8chain 'A' and (resid 546 through 552 )A546 - 552
9X-RAY DIFFRACTION9chain 'A' and (resid 553 through 567 )A553 - 567
10X-RAY DIFFRACTION10chain 'A' and (resid 568 through 578 )A568 - 578
11X-RAY DIFFRACTION11chain 'A' and (resid 579 through 583 )A579 - 583
12X-RAY DIFFRACTION12chain 'A' and (resid 584 through 594 )A584 - 594
13X-RAY DIFFRACTION13chain 'B' and (resid 474 through 486 )B474 - 486
14X-RAY DIFFRACTION14chain 'B' and (resid 487 through 505 )B487 - 505
15X-RAY DIFFRACTION15chain 'B' and (resid 506 through 511 )B506 - 511
16X-RAY DIFFRACTION16chain 'B' and (resid 512 through 524 )B512 - 524
17X-RAY DIFFRACTION17chain 'B' and (resid 525 through 537 )B525 - 537
18X-RAY DIFFRACTION18chain 'B' and (resid 538 through 567 )B538 - 567
19X-RAY DIFFRACTION19chain 'B' and (resid 568 through 583 )B568 - 583
20X-RAY DIFFRACTION20chain 'B' and (resid 584 through 594 )B584 - 594

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