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- PDB-4lcv: Crystal Structure of DOC2B C2A domain -

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Basic information

Entry
Database: PDB / ID: 4lcv
TitleCrystal Structure of DOC2B C2A domain
ComponentsDouble C2-like domain-containing protein beta
KeywordsMETAL BINDING PROTEIN / C2 / Calcium binding protein
Function / homology
Function and homology information


spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / calcium-dependent phospholipid binding / syntaxin binding / exocytosis / positive regulation of insulin secretion ...spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / calcium ion-regulated exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis / extrinsic component of synaptic vesicle membrane / calcium-dependent phospholipid binding / syntaxin binding / exocytosis / positive regulation of insulin secretion / intracellular protein localization / calcium ion binding / synapse / glutamatergic synapse / plasma membrane / cytoplasm
Similarity search - Function
Double C2 protein, alpha/beta/gamma / Rabphilin/DOC2/Noc2 / : / Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily ...Double C2 protein, alpha/beta/gamma / Rabphilin/DOC2/Noc2 / : / Synaptotagmin / 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
BETA-MERCAPTOETHANOL / CITRATE ANION / Double C2-like domain-containing protein beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGiladi, M. / Almagor, L. / Hirsch, J.A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The C2B Domain Is the Primary Ca(2+) Sensor in DOC2B: A Structural and Functional Analysis.
Authors: Giladi, M. / Michaeli, L. / Almagor, L. / Bar-On, D. / Buki, T. / Ashery, U. / Khananshvili, D. / Hirsch, J.A.
History
DepositionJun 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Double C2-like domain-containing protein beta
B: Double C2-like domain-containing protein beta
C: Double C2-like domain-containing protein beta
D: Double C2-like domain-containing protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,60612
Polymers61,8754
Non-polymers7328
Water4,702261
1
A: Double C2-like domain-containing protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6433
Polymers15,4691
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Double C2-like domain-containing protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5652
Polymers15,4691
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Double C2-like domain-containing protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6454
Polymers15,4691
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Double C2-like domain-containing protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7543
Polymers15,4691
Non-polymers2852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.632, 95.151, 67.816
Angle α, β, γ (deg.)90.00, 99.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Double C2-like domain-containing protein beta / Doc2-beta


Mass: 15468.713 Da / Num. of mol.: 4 / Fragment: C2A domain (UNP residues 125-255)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Doc2b / Production host: Escherichia coli (E. coli) / References: UniProt: P70610

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Non-polymers , 5 types, 269 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M LiSO4, 25% PEG 3350, 0.1 M Na-Citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2012
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 34604 / Num. obs: 34604 / % possible obs: 94.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2→2.06 Å / % possible all: 73.6

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.575 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1727 4.99 %RANDOM
Rwork0.1872 ---
obs0.1894 34576 94.28 %-
all-34581 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 39 261 4236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124063
X-RAY DIFFRACTIONf_angle_d1.0475528
X-RAY DIFFRACTIONf_dihedral_angle_d13.9951485
X-RAY DIFFRACTIONf_chiral_restr0.062645
X-RAY DIFFRACTIONf_plane_restr0.009699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06280.26621070.24732052X-RAY DIFFRACTION70
2.0628-2.12940.28951250.23182340X-RAY DIFFRACTION82
2.1294-2.20550.25821360.22432600X-RAY DIFFRACTION90
2.2055-2.29380.29431450.21492790X-RAY DIFFRACTION96
2.2938-2.39820.25531500.21432849X-RAY DIFFRACTION99
2.3982-2.52460.29121510.21272864X-RAY DIFFRACTION99
2.5246-2.68280.22731510.19892864X-RAY DIFFRACTION99
2.6828-2.88990.24941520.2032870X-RAY DIFFRACTION99
2.8899-3.18070.25661510.1972866X-RAY DIFFRACTION99
3.1807-3.64080.21911520.16482903X-RAY DIFFRACTION99
3.6408-4.58640.20981530.15012904X-RAY DIFFRACTION100
4.5864-47.58890.18281540.18122947X-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)
18.75835.34090.06983.90160.06721.3969-0.10110.31250.4135-0.04470.13020.1796-0.13270.0039-0.06110.18070.0724-0.01110.13920.00710.1679-13.5367-8.2415-13.4152
25.7171-3.4468-0.51782.98131.84092.90130.0697-0.53680.01580.2347-0.0661-0.00150.29210.5640.14430.24850.0501-0.11030.2667-0.05370.2313-3.2347-6.5222-5.5799
35.13831.2928-0.18261.6414-0.30991.62980.08920.5716-0.1579-0.176-0.0998-0.26040.0060.10810.02910.20830.0806-0.0010.18950.02430.1679-7.9421-9.6647-11.2726
42.0345-1.0102-0.40891.3466-0.02760.07460.005-0.71250.55080.26130.0416-0.53140.15210.7444-0.0920.27540.0641-0.07450.4726-0.01620.373.3608-4.2319-5.2762
53.25971.4847-1.77325.13450.08161.9305-0.0432-0.37610.74970.0291-0.17190.0427-0.1240.06690.2570.19680.0567-0.03990.1593-0.00770.2493-13.5728-1.4902-8.8028
62.3463-0.47221.90242.69470.57796.47060.32010.1106-0.33030.21120.0412-0.57570.34920.3591-0.34820.1020.02240.02310.15580.02890.1771-20.86367.29-18.3477
71.21621.51461.3352.75923.41484.2488-0.0062-0.10430.1718-0.3165-0.25950.1534-0.4708-0.46580.25020.22530.0684-0.0270.2196-0.01750.2094-23.905617.2109-14.4804
82.61740.62470.98038.4217.45472.2412-0.04210.24410.0752-0.40650.08410.327-0.64770.1449-0.19770.43570.02010.03530.23970.09470.1873-20.48311.6972-27.5577
95.10230.6540.71582.16686.78817.24390.1387-0.12850.8986-0.80750.2161-0.3666-0.93190.0322-0.38690.47080.05560.07310.20280.0690.2931-17.879221.895-16.7563
107.36593.04384.31287.59634.44769.22780.35730.1913-0.1633-0.2450.0208-0.57080.34810.3405-0.43670.1960.09-0.00920.16970.04310.2736-16.67786.4644-18.6765
113.51850.81630.61520.8013-0.35111.9533-0.1141-0.1794-0.4822-0.0903-0.0004-0.28690.12890.27450.09390.1654-0.03370.02250.19460.07410.29055.340316.794714.1975
128.3082-2.31182.5594.5156-1.67623.04950.11040.1321-0.0231-0.1375-0.2515-0.5615-0.01340.37640.19980.1773-0.05440.00090.15040.050.27857.242921.905812.2118
132.1003-9.38727.9458.7015-6.17245.68070.4780.9104-0.0874-0.3358-0.5032-0.14940.31420.4367-0.03770.1509-0.0536-0.03640.22020.01830.3154-3.758118.38994.6386
149.04192.4595-3.53813.7893-5.44747.79220.4380.1322-0.7050.23570.43851.45830.549-0.4717-0.74680.5572-0.24830.01060.46010.00880.704123.388116.53297.6642
152.0214-8.86541.20528.1791-0.93212.6649-0.11860.7756-0.97060.2105-0.2109-0.0480.35360.22690.240.2577-0.02360.00010.17330.03050.40712.169711.58647.7122
166.736-5.35172.2585.6334-1.29171.02260.1572-0.0062-0.3887-0.3940.00260.09580.105-0.002-0.11960.2176-0.0826-0.01820.18280.03570.3342-5.124114.402515.4295
172.47850.91521.45673.3284-1.99683.3233-0.0227-0.2523-0.7591-0.28070.34580.45120.6423-0.7644-0.36410.2943-0.1158-0.05450.33820.15070.37071.896-0.0129-44.2117
183.0232-0.9041-0.27530.5004-0.60471.8949-0.2531-0.6971-0.79190.00571.12441.08650.8929-1.0249-0.37960.3676-0.4726-0.35490.42960.19780.7805-2.0137-4.2377-43.2535
196.9225-3.19880.38149.86893.98236.1882-0.291-1.1507-0.03480.58080.68930.01160.582-1.0176-0.46190.2911-0.0645-0.02540.41130.23180.27042.64185.2452-32.9527
201.99833.55415.98233.73563.52167.08870.17140.0724-1.51030.3859-0.16880.37170.0621-0.0152-0.04680.7518-0.19420.01450.44030.02440.9397-0.5385-20.7179-43.7396
213.17571.3748-0.47262.01648.24138.483-0.0299-0.2119-0.92020.76610.5542-0.28380.8855-0.0021-0.36620.3345-0.0229-0.14340.22160.10010.42088.866-1.2841-39.0656
221.9987-1.3878-0.24683.15682.05738.64540.64280.02550.4383-0.3292-0.45530.1499-0.5025-0.8384-0.28670.33340.11780.07080.46040.13250.34390.362517.035-40.1372
234.4128-1.5271-1.44175.57671.72523.46190.2522-0.188-0.79660.57230.0046-0.85710.4676-0.2-0.26190.2963-0.08-0.14830.20240.09940.466210.52461.6372-44.7839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 126:151 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 152:181 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 182:210 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 211:225 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 226:253 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 124:141 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 142:203 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 204:218 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 219:237 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 238:254 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 125:171 )
12X-RAY DIFFRACTION12CHAIN C AND (RESID 172:203 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 204:218 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 219:225 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 226:237 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 238:253 )
17X-RAY DIFFRACTION17CHAIN D AND (RESID 126:171 )
18X-RAY DIFFRACTION18CHAIN D AND (RESID 172:200 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 201:218 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 219:225 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 226:237 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 238:243 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 244:254 )

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