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- PDB-4p42: Extended-Synaptotagmin 2, SMP - C2A - C2B Domains -

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Basic information

Entry
Database: PDB / ID: 4p42
TitleExtended-Synaptotagmin 2, SMP - C2A - C2B Domains
ComponentsExtended synaptotagmin-2
KeywordsLIPID TRANSPORT / endocytosis / signal transduction / membrane contact site / lipid binding
Function / homology
Function and homology information


endoplasmic reticulum-plasma membrane tethering / endoplasmic reticulum-plasma membrane contact site / organelle membrane contact site / Glycosphingolipid transport / phosphatidylcholine binding / phosphatidylethanolamine binding / calcium-dependent phospholipid binding / lipid transport / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol binding ...endoplasmic reticulum-plasma membrane tethering / endoplasmic reticulum-plasma membrane contact site / organelle membrane contact site / Glycosphingolipid transport / phosphatidylcholine binding / phosphatidylethanolamine binding / calcium-dependent phospholipid binding / lipid transport / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol binding / cytoplasmic side of plasma membrane / endocytosis / cadherin binding / calcium ion binding / endoplasmic reticulum membrane / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Extended synaptotagmin, C2A domain / Extended synaptotagmin, C2B domain / Extended synaptotagmin, C-terminal C2 domain / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) ...Extended synaptotagmin, C2A domain / Extended synaptotagmin, C2B domain / Extended synaptotagmin, C-terminal C2 domain / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Extended synaptotagmin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.44 Å
AuthorsSchauder, C.M. / Wu, X. / Reinisch, K.M.
CitationJournal: Nature / Year: 2014
Title: Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer.
Authors: Schauder, C.M. / Wu, X. / Saheki, Y. / Narayanaswamy, P. / Torta, F. / Wenk, M.R. / De Camilli, P. / Reinisch, K.M.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 2.0Dec 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / entity / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / refine / refine_hist / struct_keywords / symmetry
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _refine.pdbx_diffrn_id / _struct_keywords.text / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extended synaptotagmin-2
B: Extended synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1146
Polymers108,4212
Non-polymers2,6944
Water3,819212
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-94 kcal/mol
Surface area41480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.332, 88.382, 167.190
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 Extended synaptotagmin-2 / E-Syt2 / Chr2Syt


Mass: 54210.277 Da / Num. of mol.: 2 / Fragment: SMP-C2A-C2B Domains (UNP residues 191-662)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESYT2, FAM62B, KIAA1228 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: A0FGR8
#2: Chemical ChemComp-EGC / 2-(2-{2-[2-(2-{2-[2-(2-{2-[4-(1,1,3,3-TETRAMETHYL-BUTYL)-PHENOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOX Y}-ETHOXY)-ETHANOL / TRITON X-100


Mass: 602.797 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58O10 / Comment: detergent*YM
#3: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 1500, MIB Buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792, 1.907
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
21.9071
ReflectionResolution: 2.44→47.14 Å / Num. obs: 41769 / % possible obs: 98.86 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 2.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1452) / Classification: refinement
RefinementResolution: 2.44→47.14 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 21.8 / Phase error: 26.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 2000 4.79 %
Rwork0.2102 --
obs0.2124 41769 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7143 0 138 212 7493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037421
X-RAY DIFFRACTIONf_angle_d0.84610025
X-RAY DIFFRACTIONf_dihedral_angle_d14.1862886
X-RAY DIFFRACTIONf_chiral_restr0.0311141
X-RAY DIFFRACTIONf_plane_restr0.0031260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.50010.31471400.2832795X-RAY DIFFRACTION100
2.5001-2.56770.33441420.27152810X-RAY DIFFRACTION100
2.5677-2.64330.33421400.26642787X-RAY DIFFRACTION100
2.6433-2.72860.33011410.2662797X-RAY DIFFRACTION100
2.7286-2.82610.3291410.26362820X-RAY DIFFRACTION100
2.8261-2.93920.31731410.25852802X-RAY DIFFRACTION100
2.9392-3.0730.32321410.26162809X-RAY DIFFRACTION100
3.073-3.2350.27581420.25312830X-RAY DIFFRACTION100
3.235-3.43760.30591440.23722828X-RAY DIFFRACTION100
3.4376-3.70290.26521420.21692846X-RAY DIFFRACTION100
3.7029-4.07540.24671430.19342842X-RAY DIFFRACTION100
4.0754-4.66460.19951440.15632877X-RAY DIFFRACTION100
4.6646-5.87520.21281460.16252888X-RAY DIFFRACTION100
5.8752-47.14960.18951530.18633038X-RAY DIFFRACTION100
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)
10.51720.2533-0.1444.6294-1.39891.65480.06150.1430.0041-0.37830.04920.01150.01350.0626-0.07330.3232-0.0314-0.01050.4054-0.00310.3211-64.2322-72.210817.7065
21.57030.9199-0.58671.0059-0.28740.91710.0868-0.0241-0.00960.1361-0.07370.08050.0719-0.1957-0.03850.32570.0378-0.01860.3480.01770.3072-100.518-91.129544.9088
35.1283-1.16621.53772.81270.00492.47990.0540.02490.1574-0.1121-0.1039-0.2305-0.28390.29240.06010.4393-0.06720.02920.3702-0.04910.2954-80.9004-83.810157.1123
43.11181.3354-1.94891.6951-1.05472.8163-0.11970.1837-0.1266-0.08360.0806-0.08310.0634-0.06910.05780.3870.0145-0.06110.3135-0.03430.3364-81.0253-102.540432.5641
55.4547-0.21081.20041.0401-0.43263.00070.31160.5253-0.571-0.4532-0.15670.18480.07620.12420.01440.35820.1569-0.0660.4013-0.05730.4125-91.9379-109.87810.8495
64.4124-4.64091.64847.1649-2.67062.53120.61020.7535-0.0864-0.5901-0.7054-0.3650.53990.66660.02760.41610.142-0.02630.5913-0.04880.3797-87.9265-111.7924.7066
75.7588-1.0973-4.18821.98410.78296.57360.02250.0845-0.0144-0.0007-0.16690.06150.1477-0.27020.14970.24830.0333-0.03360.2960.03660.3268-110.6455-94.885219.6595
84.4285-1.3707-2.43451.8171.5224.21520.09660.29070.1153-0.1184-0.1862-0.0231-0.0462-0.29190.09850.3030.0327-0.0180.32770.04920.2893-109.9061-91.502116.7047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 163 through 311 )
2X-RAY DIFFRACTION2chain 'A' and (resid 312 through 507)
3X-RAY DIFFRACTION3chain 'A' and (resid 508 through 630 )
4X-RAY DIFFRACTION4chain 'B' and (resid 164 through 331 )
5X-RAY DIFFRACTION5chain 'B' and (resid 332 through 424 )
6X-RAY DIFFRACTION6chain 'B' and (resid 425 through 492 )
7X-RAY DIFFRACTION7chain 'B' and (resid 493 through 544 )
8X-RAY DIFFRACTION8chain 'B' and (resid 545 through 630 )

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