[English] 日本語
Yorodumi
- PDB-6lpc: Crystal Structure of rat Munc18-1 with K332E/K333E mutation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lpc
TitleCrystal Structure of rat Munc18-1 with K332E/K333E mutation
ComponentsSyntaxin-binding protein 1
KeywordsEXOCYTOSIS / Synaptic exocytosis / Membrane fusion / SNAREs-binding
Function / homology
Function and homology information


positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / regulation of vesicle fusion / developmental process involved in reproduction / axon target recognition / extrinsic component of presynaptic membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle ...positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / regulation of vesicle fusion / developmental process involved in reproduction / axon target recognition / extrinsic component of presynaptic membrane / regulation of synaptic vesicle priming / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / presynaptic dense core vesicle exocytosis / negative regulation of synaptic transmission, GABAergic / platelet degranulation / neuromuscular synaptic transmission / positive regulation of calcium ion-dependent exocytosis / synaptic vesicle maturation / presynaptic active zone cytoplasmic component / positive regulation of mast cell degranulation / vesicle docking involved in exocytosis / neurotransmitter secretion / platelet alpha granule / presynaptic cytosol / parallel fiber to Purkinje cell synapse / syntaxin-1 binding / SNARE complex assembly / long-term synaptic depression / synaptic vesicle priming / syntaxin binding / exocytosis / positive regulation of exocytosis / phospholipase binding / negative regulation of protein-containing complex assembly / phagocytic vesicle / presynaptic active zone membrane / vesicle-mediated transport / SNARE binding / secretory granule / establishment of localization in cell / protein localization to plasma membrane / intracellular protein transport / terminal bouton / platelet aggregation / cellular response to type II interferon / presynapse / response to estradiol / postsynapse / neuron apoptotic process / negative regulation of neuron apoptotic process / molecular adaptor activity / protein stabilization / axon / protein domain specific binding / glutamatergic synapse / protein kinase binding / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sec1-like, domain 1 / Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family
Similarity search - Domain/homology
Syntaxin-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.402 Å
AuthorsWang, X.P. / Gong, J.H. / Wang, S. / Zhu, L. / Yang, X.Y. / Xu, Y.Y. / Yang, X.F. / Ma, C.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670846 China
National Basic Research Program of China (973 Program)2015CB910800 China
National Natural Science Foundation of China (NSFC)31721002 China
National Natural Science Foundation of China (NSFC)31670850 China
CitationJournal: Embo J. / Year: 2020
Title: Munc13 activates the Munc18-1/syntaxin-1 complex and enables Munc18-1 to prime SNARE assembly.
Authors: Wang, X. / Gong, J. / Zhu, L. / Wang, S. / Yang, X. / Xu, Y. / Yang, X. / Ma, C.
History
DepositionJan 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Syntaxin-binding protein 1
B: Syntaxin-binding protein 1


Theoretical massNumber of molelcules
Total (without water)135,3312
Polymers135,3312
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer, but displaying dimerization in crystal packing.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-26 kcal/mol
Surface area46090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.475, 80.475, 247.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 6 or (resid 7...
21(chain B and (resid 1 through 61 or (resid 62...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLEULEU(chain A and (resid 1 through 6 or (resid 7...AA1 - 61 - 6
12LYSLYSALAALA(chain A and (resid 1 through 6 or (resid 7...AA7 - 87 - 8
13METMETTHRTHR(chain A and (resid 1 through 6 or (resid 7...AA1 - 5881 - 588
14METMETTHRTHR(chain A and (resid 1 through 6 or (resid 7...AA1 - 5881 - 588
15METMETTHRTHR(chain A and (resid 1 through 6 or (resid 7...AA1 - 5881 - 588
16METMETTHRTHR(chain A and (resid 1 through 6 or (resid 7...AA1 - 5881 - 588
21METMETILEILE(chain B and (resid 1 through 61 or (resid 62...BB1 - 611 - 61
22ASNASNGLUGLU(chain B and (resid 1 through 61 or (resid 62...BB62 - 6662 - 66
23METMETLEULEU(chain B and (resid 1 through 61 or (resid 62...BB1 - 5851 - 585
24METMETLEULEU(chain B and (resid 1 through 61 or (resid 62...BB1 - 5851 - 585
25METMETLEULEU(chain B and (resid 1 through 61 or (resid 62...BB1 - 5851 - 585
26METMETLEULEU(chain B and (resid 1 through 61 or (resid 62...BB1 - 5851 - 585

-
Components

#1: Protein Syntaxin-binding protein 1 / Munc18-1 / N-Sec1 / Protein unc-18 homolog 1 / Unc18-1 / Protein unc-18 homolog A / Unc-18A / p67 / rbSec1


Mass: 67665.570 Da / Num. of mol.: 2 / Mutation: K332E, K333E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stxbp1, Unc18a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61765

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 4 M ammonium acetate, 0.1 M sodium acetate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 21586 / % possible obs: 100 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.033 / Rrim(I) all: 0.078 / Χ2: 1.029 / Net I/σ(I): 25.2
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2162 / CC1/2: 0.934 / CC star: 0.983 / Rpim(I) all: 0.281 / Rrim(I) all: 0.658 / Χ2: 0.66 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
PHASERphasing
SCALAdata scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PUJ

3puj


Resolution: 3.402→49.072 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 39.96
RfactorNum. reflection% reflection
Rfree0.3306 1102 5.14 %
Rwork0.2809 --
obs0.2834 21456 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 252.62 Å2 / Biso mean: 135.813 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.402→49.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7114 0 0 0 7114
Num. residues----1000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057241
X-RAY DIFFRACTIONf_angle_d0.8349914
X-RAY DIFFRACTIONf_chiral_restr0.0471206
X-RAY DIFFRACTIONf_plane_restr0.0061289
X-RAY DIFFRACTIONf_dihedral_angle_d4.5224353
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3590X-RAY DIFFRACTION11.268TORSIONAL
12B3590X-RAY DIFFRACTION11.268TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.402-3.55680.43551610.3734251399
3.5568-3.74430.39591340.349251599
3.7443-3.97880.40521280.33532567100
3.9788-4.28580.34691360.30722534100
4.2858-4.71680.36511340.29922556100
4.7168-5.39860.33091490.29962541100
5.3986-6.79880.33661260.33052564100
6.7988-49.0720.27331340.2167256499

+
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