[English] 日本語
Yorodumi
- PDB-4lcv: Crystal Structure of DOC2B C2A domain -

+
Open data


ID or keywords:

Loading...

-
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


calcium ion-regulated exocytosis of neurotransmitter / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / 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 ...calcium ion-regulated exocytosis of neurotransmitter / spontaneous neurotransmitter secretion / positive regulation of vesicle fusion / calcium-dependent activation of synaptic vesicle fusion / 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 / protein localization / synapse / calcium ion binding / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more