[English] 日本語
Yorodumi
- PDB-3c98: Revised structure of the munc18a-syntaxin1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c98
TitleRevised structure of the munc18a-syntaxin1 complex
Components
  • Syntaxin-1A
  • Syntaxin-binding protein 1
KeywordsENDOCYTOSIS/EXOCYTOSIS / protein complex / Alternative splicing / Cytoplasm / Membrane / Phosphoprotein / Protein transport / Transport / Coiled coil / Neurotransmitter transport / Transmembrane / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
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 / axon target recognition / developmental process involved in reproduction / regulation of vesicle fusion / negative regulation of synaptic transmission, GABAergic / myosin head/neck binding / Other interleukin signaling ...positive regulation of vesicle docking / regulation of acrosomal vesicle exocytosis / positive regulation of glutamate secretion, neurotransmission / negative regulation of SNARE complex assembly / axon target recognition / developmental process involved in reproduction / regulation of vesicle fusion / negative regulation of synaptic transmission, GABAergic / myosin head/neck binding / Other interleukin signaling / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / platelet degranulation / presynaptic dense core vesicle exocytosis / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / extrinsic component of presynaptic membrane / Glutamate Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / synaptic vesicle maturation / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / positive regulation of norepinephrine secretion / positive regulation of catecholamine secretion / Dopamine Neurotransmitter Release Cycle / synaptic vesicle docking / regulation of synaptic vesicle priming / regulated exocytosis / presynaptic active zone cytoplasmic component / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of calcium ion-dependent exocytosis / positive regulation of mast cell degranulation / vesicle docking / regulation of exocytosis / secretion by cell / chloride channel inhibitor activity / platelet alpha granule / SNARE complex / SNAP receptor activity / calcium-ion regulated exocytosis / neuromuscular synaptic transmission / vesicle fusion / actomyosin / hormone secretion / LGI-ADAM interactions / ATP-dependent protein binding / neurotransmitter secretion / vesicle docking involved in exocytosis / long-term synaptic depression / protein localization to membrane / syntaxin binding / insulin secretion / syntaxin-1 binding / SNARE complex assembly / positive regulation of neurotransmitter secretion / neurotransmitter transport / myosin binding / synaptic vesicle priming / parallel fiber to Purkinje cell synapse / response to gravity / exocytosis / modulation of excitatory postsynaptic potential / positive regulation of exocytosis / synaptic vesicle exocytosis / protein sumoylation / synaptic vesicle endocytosis / positive regulation of excitatory postsynaptic potential / negative regulation of protein-containing complex assembly / calcium channel inhibitor activity / phospholipase binding / presynaptic cytosol / phagocytic vesicle / presynaptic active zone membrane / endomembrane system / acrosomal vesicle / secretory granule / SNARE binding / protein localization to plasma membrane / intracellular protein transport / establishment of localization in cell / postsynaptic density membrane / cellular response to type II interferon / platelet aggregation / kinase binding / Schaffer collateral - CA1 synapse / terminal bouton / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / response to estradiol / presynapse / presynaptic membrane / neuron apoptotic process / nuclear membrane / protein-macromolecule adaptor activity / molecular adaptor activity / negative regulation of neuron apoptotic process / transmembrane transporter binding / postsynapse / neuron projection
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / Sec1/Munc18 (SM) protein, domain 2 / Syntaxin Binding Protein 1; Chain A, domain 2 / Sec1/Munc18 (SM) protein, domain 3a / Sec1/Munc18 (SM) protein, domain 1 / Sec1-like, domain 1 / Sec1-like protein / Sec1-like, domain 2 / Sec1-like superfamily / Sec1-like, domain 3a / Sec1 family / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / Syntaxin / Syntaxin/epimorphin, conserved site / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Complex / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Syntaxin-1A / Syntaxin-binding protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.601 Å
AuthorsHattendorf, D.A. / Misura, K.M. / Burkhardt, P. / Scheller, R.H. / Fasshauer, D. / Weis, W.I.
Citation
Journal: Embo J. / Year: 2008
Title: Munc18a controls SNARE assembly through its interaction with the syntaxin N-peptide
Authors: Burkhardt, P. / Hattendorf, D.A. / Weis, W.I. / Fasshauer, D.
#1: Journal: Nature / Year: 2000
Title: Three-dimensional structure of the neuronal-Sec1-syntaxin 1a complex
Authors: Misura, K.M. / Scheller, R.H. / Weis, W.I.
History
DepositionFeb 15, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionMar 25, 2008ID: 1DN1
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,5232
Polymers101,5232
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-17.5 kcal/mol
Surface area37430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.070, 158.070, 81.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

#1: Protein Syntaxin-binding protein 1 / munc18A / Unc-18 homolog / Unc-18A / Unc-18-1 / N- Sec1 / rbSec1 / p67


Mass: 69071.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pQE9 / Production host: Escherichia coli (E. coli) / References: UniProt: P61765
#2: Protein Syntaxin-1A / syntaxin1 / Synaptotagmin-associated 35 kDa protein / P35A / Neuron- specific antigen HPC-1


Mass: 32451.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pQE9 / Production host: Escherichia coli (E. coli) / References: UniProt: P32851
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG400, Ammonium Acetate, Sodium Acetate, EDTA, 2-mercaptoethanol, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9798
SYNCHROTRONSSRL BL9-220.9252, 0.9795, 0.9798
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 4, 1999
ADSC QUANTUM 42CCDJul 4, 1999
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.92521
30.97951
ReflectionResolution: 2.6→33.88 Å / Num. all: 32718 / Num. obs: 32178 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.409 / Num. unique all: 3091 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.601→33.88 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / Isotropic thermal model: isotropic / σ(F): 0.03 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2332 8.01 %RANDOM
Rwork0.203 26798 --
obs0.208 29130 90.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.889 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso max: 216.89 Å2 / Biso mean: 74.012 Å2 / Biso min: 28.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.111 Å2-0 Å2-0 Å2
2---0.111 Å2-0 Å2
3---0.222 Å2
Refinement stepCycle: LAST / Resolution: 2.601→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6327 0 0 69 6396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036422
X-RAY DIFFRACTIONf_angle_d0.6698642
X-RAY DIFFRACTIONf_chiral_restr0.047983
X-RAY DIFFRACTIONf_plane_restr0.0021109
X-RAY DIFFRACTIONf_dihedral_angle_d14.9642492
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.601-2.6540.319910.2961262135372.47
2.654-2.7120.3971270.3051387151481.53
2.712-2.7750.3571350.2881422155783.26
2.775-2.8450.3831520.2971419157184.46
2.845-2.9210.3531210.2781503162486.29
2.921-3.0070.3341200.2781520164088.08
3.007-3.1040.3141410.2651541168289.66
3.104-3.2150.3061340.2561601173592.93
3.215-3.3440.3351420.2441570171291.5
3.344-3.4960.2821490.241605175492.71
3.496-3.680.2851430.2171524166788.48
3.68-3.910.2871320.2041638177093.35
3.91-4.2120.2281340.1791668180294.44
4.212-4.6340.1971330.1421725185897.48
4.634-5.3030.2131580.1511752191099.07
5.303-6.6730.2541600.1871777193798.93
6.673-33.8840.1781600.1571884204498.41
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)
13.212-0.64620.12183.1179-0.9311.7027-0.145-0.4806-0.3920.55860.07870.14590.07850.14460.00010.7065-0.00750.12870.55980.03680.412253.917555.245222.9154
23.39810.2154-0.09492.2196-0.86933.3697-0.0604-0.4263-0.37980.50210.01960.67270.2212-0.0250.00010.5428-0.01490.15910.43240.06330.72529.735759.098412.9113
33.33160.98520.58322.09060.52952.0055-0.0780.16630.2212-0.2607-0.01970.5789-0.3378-0.0691-00.55870.0801-0.00660.3873-0.00320.670930.987273.702-3.122
40.05030.05610.0282-0.01250.0380.06210.0227-0.08790.59670.53360.301-0.119-0.1368-0.1522-0.00041.38990.00090.50791.82090.12720.995348.591846.756836.158
51.2253-0.1106-0.08624.21731.0181.75660.0433-0.12470.3663-0.01990.0514-0.0425-0.4980.0926-00.8155-0.19090.05880.7406-0.0290.475862.377490.997820.6303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 4-136A4 - 136
2X-RAY DIFFRACTION2chain A and (resid 137-235 or resid 532-592)A137 - 235
3X-RAY DIFFRACTION2chain A and (resid 137-235 or resid 532-592)A532 - 592
4X-RAY DIFFRACTION3chain A and resid 236-505A236 - 505
5X-RAY DIFFRACTION4chain B and resid 2-9B2 - 9
6X-RAY DIFFRACTION5chain B and resid 27-248B27 - 248

+
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