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- PDB-4npk: Extended-Synaptotagmin 2, C2A- and C2B-domains, calcium bound -

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Basic information

Entry
Database: PDB / ID: 4npk
TitleExtended-Synaptotagmin 2, C2A- and C2B-domains, calcium bound
ComponentsExtended synaptotagmin-2
KeywordsMEMBRANE PROTEIN / CALCIUM/PHOSPHOLIPID BINDING PROTEIN / C2 domain / ER to plasma membrane / membrane traffic / protein targeting / Plasma membrane
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
Extended synaptotagmin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.552 Å
AuthorsTomchick, D.R. / Rizo, J. / Xu, J.
Citation
Journal: Structure / Year: 2014
Title: Structure and ca(2+)-binding properties of the tandem c2 domains of e-syt2.
Authors: Xu, J. / Bacaj, T. / Zhou, A. / Tomchick, D.R. / Sudhof, T.C. / Rizo, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: E-Syts, a family of membranous Ca2+-sensor proteins with multiple C2 domains.
Authors: Min, S.W. / Chang, W.P. / Sudhof, T.C.
History
DepositionNov 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extended synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3854
Polymers34,2651
Non-polymers1203
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.840, 53.194, 85.276
Angle α, β, γ (deg.)90.000, 99.950, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Extended synaptotagmin-2 / E-Syt2 / Chr2Syt


Mass: 34265.121 Da / Num. of mol.: 1 / Fragment: C2A and C2B domains / Mutation: A512V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESYT2, extended-synaptotagmin 2, FAM62B, KIAA1228 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0FGR8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 6% PEG 8000, 0.1 M Hepes pH 8.0, 0.125 M NaCl, 2.5% glycerol, 0.02 M CaCl2, 0.5 mM TCEP, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2012 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 12318 / Num. obs: 12318 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 68.45 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 33.4
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.45 / Num. unique all: 263 / % possible all: 38

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4NPJ

4npj


Resolution: 2.552→28.986 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 42.82 / Stereochemistry target values: ML
Details: Used reference model restraints. Reference model was
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 604 4.94 %RANDOM
Rwork0.2216 ---
all0.2249 12224 --
obs0.2249 12224 87.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 275.75 Å2 / Biso mean: 133.5576 Å2 / Biso min: 69.44 Å2
Refine analyzeLuzzati sigma a free: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.552→28.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 3 4 2185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092240
X-RAY DIFFRACTIONf_angle_d1.2053003
X-RAY DIFFRACTIONf_chiral_restr0.045337
X-RAY DIFFRACTIONf_plane_restr0.008388
X-RAY DIFFRACTIONf_dihedral_angle_d13.432853
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.5523-2.80890.417930.315817821875178254
2.8089-3.21490.37911770.323731783355317897
3.2149-4.04870.35771630.254233003463330099
4.0487-28.98790.23171710.185533603531336099
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)
11.5728-0.9747-0.14641.07440.25660.2878-0.3274-0.4386-0.2296-0.33060.0453-0.24940.36070.1333-0.00010.86710.033-0.03210.9540.06680.8068-27.13541.718831.594
21.05350.43-1.02251.4805-1.37551.3591-0.0256-0.1640.3122-0.16970.43040.03350.0353-0.27710.00010.8112-0.0410.00990.9015-0.10010.9302-23.904811.641530.781
32.1798-0.7921-0.6229-0.39020.30671.5907-0.0375-0.53480.2015-0.1589-0.0453-0.14650.13980.30560.00010.91760.0581-0.00221.00920.02280.9484-11.01389.570624.7056
40.2228-0.0523-0.01170.2089-0.28520.11140.37051.03990.1261-0.11110.03190.10560.97980.2484-01.3310.03350.11581.47080.12571.2516-20.209914.6566-4.2628
5-0.0191-0.49220.1058-0.2351-0.58850.5990.86540.13290.8660.7134-0.34690.4012-0.2849-1.11150.07460.96650.32910.15371.12860.33491.2253-20.415219.90591.5795
60.53370.091-0.4890.0159-0.12790.31480.47710.35770.0213-0.0555-0.0107-0.23190.74110.1086-0.00030.9617-0.14120.14830.9316-0.14760.9995-16.44888.6333-0.1475
71.9857-0.7664-1.6164-1.15470.03710.91130.44380.15440.3472-0.0489-0.0937-0.04-0.270.23390.00031.09060.06490.0570.76670.11890.947-6.424915.38292.908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 380 through 439 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 440 through 482 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 483 through 546 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 547 through 569 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 570 through 592 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 593 through 611 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 612 through 659 )A0

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