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- PDB-4npj: Extended-Synaptotagmin 2, C2A- and C2B-domains -

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Basic information

Entry
Database: PDB / ID: 4npj
TitleExtended-Synaptotagmin 2, C2A- and C2B-domains
ComponentsExtended synaptotagmin-2
KeywordsMEMBRANE PROTEIN / CALCIUM/PHOSPHOLIPID BINDING PROTEIN / C2 domain / membrane traffic / protein targeting / Plasma membrane / ER to 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
ACETATE ION / Extended synaptotagmin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.101 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _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.ptnr3_auth_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_asym_id / _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_asym_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
B: Extended synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7228
Polymers68,4742
Non-polymers2476
Water2,666148
1
A: Extended synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3083
Polymers34,2371
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extended synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4145
Polymers34,2371
Non-polymers1774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Extended synaptotagmin-2
hetero molecules

A: Extended synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7228
Polymers68,4742
Non-polymers2476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z+1/41
Buried area3490 Å2
ΔGint-53 kcal/mol
Surface area30060 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-51 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.300, 62.300, 226.395
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 34237.070 Da / Num. of mol.: 2 / Fragment: C2 and C2B domains (unp residues 363-660)
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 2.25 M LiCl, 0.1 M sodium acetate, 0.125 M NaCl, 2.5% glycerol, 25% ethylene glycol, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.38592
SYNCHROTRONAPS 19-ID20.97912
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDAug 8, 2012monochromator
ADSC QUANTUM 315r2CCDOct 18, 2012monochromator
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHx-ray1
2SAGITALLY FOCUSED Si(111)SADx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.385921
20.979121
ReflectionResolution: 2.1→50 Å / Num. all: 48539 / Num. obs: 48539 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 41.96 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.066 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.1-2.143.20.5011.4618300.9773.8
2.14-2.183.50.50220960.9883.3
2.18-2.223.80.54822420.9789.4
2.22-2.2640.50123631.01495.8
2.26-2.314.50.43424940.97298.6
2.31-2.374.90.40424720.936100
2.37-2.425.20.37324840.937100
2.42-2.495.60.33325210.954100
2.49-2.565.90.30924731.00199.9
2.56-2.656.10.28224820.999100
2.65-2.746.10.20525320.971100
2.74-2.856.10.14825100.98399.8
2.85-2.986.10.10824801.06599.9
2.98-3.146.20.08425001.187100
3.14-3.336.10.06824961.09699.9
3.33-3.596.10.06324961.17399.8
3.59-3.956.10.05925081.25799.8
3.95-4.526.10.04524991.2699.8
4.52-5.76.30.04125231.116100
5.7-506.40.04125381.18199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.101→41.892 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 2468 5.1 %RANDOM
Rwork0.1999 ---
obs0.2019 48422 96.88 %-
all-48422 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.48 Å2 / Biso mean: 78.5058 Å2 / Biso min: 28.14 Å2
Refine analyzeLuzzati sigma a free: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.101→41.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 12 148 4797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054735
X-RAY DIFFRACTIONf_angle_d0.9046400
X-RAY DIFFRACTIONf_chiral_restr0.034721
X-RAY DIFFRACTIONf_plane_restr0.004835
X-RAY DIFFRACTIONf_dihedral_angle_d14.8581820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.1005-2.14090.39291080.294619792087197974
2.1409-2.18460.32711050.29121692274216984
2.1846-2.23210.33241430.293724222565242292
2.2321-2.2840.33891480.282425272675252797
2.284-2.34120.29361270.271926162743261699
2.3412-2.40450.32581620.261263627982636100
2.4045-2.47520.3131320.2528262627582626100
2.4752-2.55510.31521330.2562261827512618100
2.5551-2.64640.30881340.2552262527592625100
2.6464-2.75230.25421310.2451267428052674100
2.7523-2.87760.2921430.2451259627392596100
2.8776-3.02920.27631360.2315266628022666100
3.0292-3.2190.23121300.2293262127512621100
3.219-3.46740.27041440.2149265427982654100
3.4674-3.81610.22841500.1858260027502600100
3.8161-4.36780.19211490.1582264527942645100
4.3678-5.5010.1771690.143261827872618100
5.501-41.90060.21761240.172626622786266299
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)
12.02940.3915-1.6642-0.239-0.87423.07940.0035-0.1705-0.2918-0.52960.3407-0.0336-1.4824-0.1756-0.07911.0683-0.21930.13190.4081-0.06380.36688.7713-14.718-34.7645
20.8627-1.15-1.06170.68860.8080.2538-0.5707-0.6669-0.10860.71960.50970.13020.45641.58950.04230.58010.1746-0.0241.4239-0.08520.3915-2.4076-17.238225.175
33.697-0.2139-2.14271.55541.80364.7632-0.3361-0.88480.09230.24170.4585-0.2603-0.46980.7832-0.13940.31550.0982-0.00481.3709-0.06580.38365.4623-16.550110.5215
43.7641-0.03010.18692.09841.37896.4061-0.0918-0.2609-0.677-0.11580.2217-0.12320.61610.9863-0.06510.19660.10290.10520.58160.0440.55949.5512-32.0166-16.6409
50.1172-0.4746-1.12251.09691.93272.7809-0.2016-0.1650.08020.01850.0466-0.0605-0.97980.40940.06580.65080.1921-0.02270.8193-0.09990.3296-14.1741-10.097612.5902
64.22960.0742-1.66552.59060.43756.41330.08480.7105-0.3878-0.6062-0.2482-0.257-0.8134-0.3660.07160.40350.09710.02270.458-0.04910.3992-6.0062-24.4256-33.358
73.06960.3509-1.36241.47340.89194.48490.03740.6492-0.0762-0.604-0.25550.2155-1.0349-1.45840.06990.54980.3554-0.07370.7435-0.0040.3919-16.6402-20.1125-25.2579
83.86180.4276-1.1972.1991.94884.1755-0.1785-1.2539-0.81590.0712-0.24350.16320.7491-0.81060.14520.07870.05730.12470.95110.23120.5128-15.5806-30.7108-0.5741
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 363 through 384 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 385 through 413 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 414 through 535 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 536 through 659 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 364 through 384 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 385 through 466 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 467 through 546 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 547 through 659 )B0

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