[English] 日本語
Yorodumi
- PDB-1elk: VHS domain of TOM1 protein from H. sapiens -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1elk
TitleVHS domain of TOM1 protein from H. sapiens
ComponentsTARGET OF MYB1
KeywordsENDOCYTOSIS/EXOCYTOSIS / Superhelix of helices / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / clathrin heavy chain binding / autophagosome-lysosome fusion / phosphatidylinositol-5-phosphate binding / positive regulation of autophagosome maturation / azurophil granule membrane / endosomal transport / clathrin binding ...myosin VI binding / substrate localization to autophagosome / regulation of endosome organization / clathrin heavy chain binding / autophagosome-lysosome fusion / phosphatidylinositol-5-phosphate binding / positive regulation of autophagosome maturation / azurophil granule membrane / endosomal transport / clathrin binding / polyubiquitin modification-dependent protein binding / specific granule membrane / ubiquitin binding / endocytosis / protein transport / early endosome membrane / early endosome / endosome membrane / endosome / Neutrophil degranulation / signal transduction / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Target of Myb protein 1 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 ...Target of Myb protein 1 / GAT domain / GAT domain superfamily / GAT domain / GAT domain profile. / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Target of Myb1 membrane trafficking protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsMisra, S. / Beach, B. / Hurley, J.H.
Citation
Journal: Biochemistry / Year: 2000
Title: Structure of the VHS domain of human Tom1 (target of myb 1): insights into interactions with proteins and membranes
Authors: Misra, S. / Beach, B. / Hurley, J.H.
#1: Journal: FEBS Lett. / Year: 1998
Title: VHS domain marks a group of proteins involved in endocytosis and vesicular trafficking.
Authors: Lohi, O. / Lehto, V.P.
History
DepositionMar 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TARGET OF MYB1
B: TARGET OF MYB1


Theoretical massNumber of molelcules
Total (without water)34,9682
Polymers34,9682
Non-polymers00
Water6,792377
1
A: TARGET OF MYB1


Theoretical massNumber of molelcules
Total (without water)17,4841
Polymers17,4841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TARGET OF MYB1


Theoretical massNumber of molelcules
Total (without water)17,4841
Polymers17,4841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.07, 52.86, 73.22
Angle α, β, γ (deg.)90.0, 99.75, 90.0
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly unknown; dimer within asymmetric unit is likely nonbiological

-
Components

#1: Protein TARGET OF MYB1


Mass: 17484.029 Da / Num. of mol.: 2 / Fragment: VHS DOMAIN / Mutation: M1G; C-TERMINAL CLONING ARTIFACT GAM
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Plasmid details: PARALLEL PHIS2 (SHEFFIELD P, GARRARD S, DEREWENDA Z.,PROTEIN EXPR PURIF. 1999, 15(1):34-99
Plasmid: PHIS2 / Production host: Escherichia coli (E. coli) / References: UniProt: O60784
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%PEG8000, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mM1dropNaCl
220 mMTris-HCl1drop
30.1 mMEDTA1drop
410 mMdithiothreitol1drop
512-18 mg/mlprotain1drop
620 %PEG80001reservoir
7100 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9793
DetectorType: ADSC / Detector: CCD / Date: Nov 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. all: 49338 / Num. obs: 49338 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.36 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.276 / % possible all: 94.8
Reflection
*PLUS
Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 94.8 % / Num. unique obs: 4775 / Mean I/σ(I) obs: 6.3

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9refinement
CNS0.9phasing
RefinementResolution: 1.5→15.67 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 4722 Random
Rwork0.193 --
all0.201 48257 -
obs0.201 48257 -
Refinement stepCycle: LAST / Resolution: 1.5→15.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 0 377 2787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_torsion_impr_deg1.38
X-RAY DIFFRACTIONc_torsion_deg21.2
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / % reflection Rfree: 10 % / Rfactor obs: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.38
LS refinement shell
*PLUS
Rfactor Rfree: 0.214 / Rfactor obs: 0.174

+
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://pdbjlvh1.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