[English] 日本語
Yorodumi
- PDB-6nyc: Munc13-1 C2B-domain, calcium free -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nyc
TitleMunc13-1 C2B-domain, calcium free
ComponentsMunc13-1
KeywordsMETAL BINDING PROTEIN / PHOSPHOLIPID BINDING PROTEIN
Function / homology
Function and homology information


dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / synaptic vesicle maturation / synaptic vesicle docking / regulation of synaptic vesicle priming / positive regulation of synaptic plasticity / positive regulation of dendrite extension / positive regulation of glutamate receptor signaling pathway / regulation of short-term neuronal synaptic plasticity ...dense core granule priming / neuronal dense core vesicle exocytosis / diacylglycerol binding / synaptic vesicle maturation / synaptic vesicle docking / regulation of synaptic vesicle priming / positive regulation of synaptic plasticity / positive regulation of dendrite extension / positive regulation of glutamate receptor signaling pathway / regulation of short-term neuronal synaptic plasticity / neurotransmitter secretion / innervation / regulation of amyloid precursor protein catabolic process / syntaxin binding / presynaptic active zone / syntaxin-1 binding / Golgi-associated vesicle / positive regulation of neurotransmitter secretion / spectrin binding / neuromuscular junction development / synaptic vesicle priming / synaptic vesicle exocytosis / excitatory synapse / amyloid-beta metabolic process / calyx of Held / synaptic membrane / SNARE binding / synaptic transmission, glutamatergic / neuromuscular junction / phospholipid binding / long-term synaptic potentiation / terminal bouton / synaptic vesicle membrane / presynapse / presynaptic membrane / cell differentiation / calmodulin binding / protein domain specific binding / axon / calcium ion binding / synapse / protein-containing complex binding / glutamatergic synapse / protein-containing complex / zinc ion binding / identical protein binding / plasma membrane
Similarity search - Function
Protein Unc-13 / Protein Unc-13, C2B domain / Mammalian uncoordinated homology 13, domain 2 / Munc13-homology domain 2 (MHD2) profile. / Domain of Unknown Function (DUF1041) / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) ...Protein Unc-13 / Protein Unc-13, C2B domain / Mammalian uncoordinated homology 13, domain 2 / Munc13-homology domain 2 (MHD2) profile. / Domain of Unknown Function (DUF1041) / MUN domain / Munc13 homology 1 / MUN domain / Munc13-homology domain 1 (MHD1) profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / C2 domain / Zinc finger phorbol-ester/DAG-type signature. / Protein kinase C conserved region 2 (CalB) / C2 domain / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C2 domain / C2 domain profile. / C1-like domain superfamily / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein unc-13 homolog A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.893 Å
AuthorsTomchick, D.R. / Rizo, J. / Machius, M. / Lu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS40944 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS051262 United States
Citation
Journal: Nat. Struct. Mol. Biol. / Year: 2010
Title: Munc13 C2B domain is an activity-dependent Ca2+ regulator of synaptic exocytosis.
Authors: Shin, O.H. / Lu, J. / Rhee, J.S. / Tomchick, D.R. / Pang, Z.P. / Wojcik, S.M. / Camacho-Perez, M. / Brose, N. / Machius, M. / Rizo, J. / Rosenmund, C. / Sudhof, T.C.
#1: Journal: Cell / Year: 2004
Title: Calmodulin and Munc13 form a Ca2+ sensor/effector complex that controls short-term synaptic plasticity.
Authors: Junge, H.J. / Rhee, J.S. / Jahn, O. / Varoqueaux, F. / Speiss, J. / Waxham, M.N. / Rosenmund, C. / Brose, N.
#2: Journal: Nature / Year: 1999
Title: Munc-13 is essential for fusion competence of glutamatergic synaptic vesicles.
Authors: Augustin, I. / Rosenmund, C. / Sudhof, T.C. / Brose, N.
#3: Journal: J. Biol. Chem. / Year: 1995
Title: Mammalian homologues of C. elegans unc-13 gene define novel family of C2-domain proteins.
Authors: Brose, N. / Hofmann, K. / Hata, Y. / Sudhof, T.C.
History
DepositionFeb 11, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 20, 2019ID: 3KWT
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Munc13-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2904
Polymers16,9371
Non-polymers3533
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.572, 101.141, 68.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Munc13-1 / Protein unc-13 homolog A


Mass: 16937.131 Da / Num. of mol.: 1 / Fragment: C2B domain, residues 675-820 / Mutation: L756W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Unc13a, Unc13h1 / Plasmid: pGEX-KT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q62768
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.11 % / Mosaicity: 0.635 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 30% PEG-MME 2000, 0.1 M bis-tris propane pH 6.8, 0.1 M NaCl, 0.5 mM TCEP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98066 Å
DetectorType: SBC-3 / Detector: CCD / Date: Nov 23, 2003 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98066 Å / Relative weight: 1
ReflectionResolution: 1.893→50 Å / Num. obs: 10420 / % possible obs: 86.5 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Χ2: 1.07 / Net I/σ(I): 17
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.9-1.933.30.3792790.993147.5
1.93-1.974.10.2943291.041155
1.97-2.014.40.2933461.001160.2
2.01-2.054.90.2284010.943166.4
2.05-2.095.50.2253861.086167.4
2.09-2.145.70.2034531.021174.8
2.14-2.196.10.1844661.068179.5
2.19-2.256.20.1735161.099187.3
2.25-2.326.60.1565491.059192.6
2.32-2.397.10.1425871.092197.7
2.39-2.487.80.1496011.1199.8
2.48-2.588.30.1355901.0921100
2.58-2.78.50.1075991.0891100
2.7-2.848.60.0856111.0991100
2.84-3.028.70.0635991.0761100
3.02-3.258.60.056121.0731100
3.25-3.588.50.046001.075199.8
3.58-4.098.50.0426111.0271100
4.09-5.1680.0376271.066199.8
5.16-26.437.90.0376581.072197.5

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RSY

1rsy


Resolution: 1.893→26.43 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 34.31
RfactorNum. reflection% reflection
Rfree0.2478 500 4.81 %
Rwork0.2091 --
obs0.211 10400 86.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.26 Å2 / Biso mean: 52.568 Å2 / Biso min: 20.37 Å2
Refinement stepCycle: final / Resolution: 1.893→26.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 47 20 1009
Biso mean--57.54 38.23 -
Num. residues----117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8935-2.08390.2836810.22411649173059
2.0839-2.38530.26781260.21742434256086
2.3853-3.00460.28011320.25328662998100
3.0046-26.43230.23281610.192529513112100
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)
10.3239-0.3539-0.27230.78140.62920.69370.0841-0.37060.19730.22160.02070.4442-0.2007-0.2616-0.00080.2920.0462-0.01680.2630.00440.345914.308943.436432.7927
20.62670.3684-0.50091.48050.73491.1664-0.05030.0472-0.2591-0.0950.1118-0.3680.08990.04990.00170.2263-0.0219-0.01790.2498-0.05440.25520.257133.487330.8271
32.025-0.29470.19841.7791-0.60951.0010.04650.2189-0.6933-0.27330.0730.39340.3472-0.45160.06280.2529-0.0215-0.01410.3287-0.0960.240215.06431.17127.8389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 780 through 819 )A780 - 819
2X-RAY DIFFRACTION2chain 'A' and (resid 687 through 737 )A687 - 737
3X-RAY DIFFRACTION3chain 'A' and (resid 738 through 779 )A738 - 779

+
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