[English] 日本語
Yorodumi
- PDB-2xhe: Crystal structure of the Unc18-syntaxin 1 complex from Monosiga b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xhe
TitleCrystal structure of the Unc18-syntaxin 1 complex from Monosiga brevicollis
Components
  • SYNTAXIN1
  • UNC18
KeywordsEXOCYTOSIS / EXOCYTOSIS COMPLEX / SNARE / NEURO FUSION / SM PROTEIN / CHOANOFLAGELLATES
Function / homology
Function and homology information


acrosome reaction / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / vesicle docking involved in exocytosis / syntaxin binding / exocytosis / endomembrane system / vesicle-mediated transport ...acrosome reaction / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / vesicle docking involved in exocytosis / syntaxin binding / exocytosis / endomembrane system / vesicle-mediated transport / SNARE binding / secretory granule / intracellular protein transport / cell differentiation / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Syntaxin-2 / 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 superfamily ...Syntaxin-2 / 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 superfamily / Sec1 family / Syntaxin / Syntaxin N-terminal domain / Syntaxin, N-terminal domain / SNARE domain / 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
Predicted protein / Predicted protein
Similarity search - Component
Biological speciesMONOSIGA BREVICOLLIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBurkhardt, P. / Stegmann, C.M. / Wahl, M.C. / Fasshauer, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Primordial Neurosecretory Apparatus Identified in the Choanoflagellate Monosiga Brevicollis.
Authors: Burkhardt, P. / Stegmann, C.M. / Cooper, B. / Kloepper, T.H. / Imig, C. / Varoqueaux, F. / Wahl, M.C. / Fasshauer, D.
History
DepositionJun 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UNC18
B: SYNTAXIN1


Theoretical massNumber of molelcules
Total (without water)103,9772
Polymers103,9772
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-19.8 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.200, 146.200, 214.861
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein UNC18


Mass: 71997.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MONOSIGA BREVICOLLIS (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9V0L3
#2: Protein SYNTAXIN1


Mass: 31979.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MONOSIGA BREVICOLLIS (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A9UTG5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.19 Å3/Da / Density % sol: 66.9 % / Description: NONE
Crystal growpH: 7
Details: 7.5% PEG-6000, 0.1 M TRIS-HCL PH 7.0, 4.25% MPD, 15% GLYCEROL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0385
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0385 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 34089 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.7 % / Biso Wilson estimate: 75.23 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C98

3c98


Resolution: 2.8→34.6 Å / SU ML: 0.39 / σ(F): 2.01 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 1726 5.1 %
Rwork0.1879 --
obs0.191 34041 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.777 Å2 / ksol: 0.286 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.8979 Å20 Å20 Å2
2---9.8979 Å20 Å2
3---19.7957 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6267 0 0 48 6315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076358
X-RAY DIFFRACTIONf_angle_d1.0698570
X-RAY DIFFRACTIONf_dihedral_angle_d18.0732421
X-RAY DIFFRACTIONf_chiral_restr0.075971
X-RAY DIFFRACTIONf_plane_restr0.0041120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.88240.30981410.27852641X-RAY DIFFRACTION100
2.8824-2.97540.33031560.23222617X-RAY DIFFRACTION100
2.9754-3.08170.28151320.21562634X-RAY DIFFRACTION100
3.0817-3.2050.26291520.20912656X-RAY DIFFRACTION100
3.205-3.35070.291400.20222645X-RAY DIFFRACTION100
3.3507-3.52720.2961460.20412656X-RAY DIFFRACTION100
3.5272-3.74790.23991510.18682664X-RAY DIFFRACTION100
3.7479-4.03690.25561460.17872671X-RAY DIFFRACTION100
4.0369-4.44240.2131260.15522716X-RAY DIFFRACTION100
4.4424-5.08350.22381440.15192721X-RAY DIFFRACTION100
5.0835-6.39810.23991450.18552760X-RAY DIFFRACTION100
6.3981-34.60480.2281470.17732934X-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)
11.5091-1.02160.00593.0537-0.11770.2119-0.28930.3242-0.2213-0.63320.33990.16340.7089-0.1265-0.00411.1601-0.56760.08410.5409-0.13240.32770.2382-65.10540.2208
23.17441.8773-0.13734.06711.1970.5992-0.28620.568-0.4413-1.02020.3814-0.16450.4123-0.3982-0.07070.8695-0.421-0.09370.67490.06140.3253-3.9215-38.8999-4.6076
32.31081.769-1.38992.5159-1.1663.09380.0364-0.01750.2099-0.03550.04790.14010.152-0.1378-0.050.3559-0.09980.05110.2519-0.07670.31934.9819-30.728920.7622
40.51560.09210.05643.3962-0.23111.8195-0.21790.14190.2476-0.42040.28120.42570.4662-0.4265-0.10020.4869-0.3095-0.10550.52550.13450.2938-6.7206-31.642.7672
50.73850.4948-0.22561.6338-0.01620.6068-0.44320.29750.2534-0.2093-0.29960.19060.3139-0.39650.17040.8619-0.3435-0.14280.5070.07960.4151-2.6289-75.10041.1768
62.973-0.9108-3.05211.38620.29441.6552-0.03020.5965-0.13360.15620.14840.1180.4596-0.18830.04090.9182-0.4738-0.10420.5790.00530.362-10.1169-69.059131.9884
71.8855-0.4993-1.09470.07270.37212.8673-0.36580.47050.5497-0.12290.5614-0.14791.289-0.510.05431.0731-0.51650.11080.56670.06360.6064-21.4294-61.356352.9882
81.3673-1.2993-2.17641.04071.54393.1048-0.639-0.0142-0.5866-0.16180.12390.61640.10150.1670.23590.8227-0.2905-0.06970.74990.07650.59858.4716-62.041619.413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 0:129)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 130:237)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 238:476)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 477:616)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 2:53)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 54:167)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 168:234)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 235:261)

+
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