[English] 日本語
Yorodumi
- PDB-1eyh: CRYSTAL STRUCTURE OF THE EPSIN N-TERMINAL HOMOLOGY (ENTH) DOMAIN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eyh
TitleCRYSTAL STRUCTURE OF THE EPSIN N-TERMINAL HOMOLOGY (ENTH) DOMAIN AT 1.56 ANGSTROM RESOLUTION
ComponentsEPSIN
KeywordsCELL CYCLE / SUPERHELIX OF HELICES
Function / homology
Function and homology information


positive regulation of clathrin coat assembly / EGFR downregulation / negative regulation of sprouting angiogenesis / clathrin vesicle coat / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / membrane fission / molecular sequestering activity ...positive regulation of clathrin coat assembly / EGFR downregulation / negative regulation of sprouting angiogenesis / clathrin vesicle coat / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / membrane fission / molecular sequestering activity / clathrin binding / embryonic organ development / clathrin-coated pit / Notch signaling pathway / female pregnancy / Schaffer collateral - CA1 synapse / terminal bouton / phospholipid binding / endocytosis / presynapse / presynaptic membrane / postsynapse / postsynaptic membrane / in utero embryonic development / transmembrane transporter binding / endosome / nucleus / plasma membrane / cytosol
Similarity search - Function
ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.56 Å
AuthorsFremont, D.H.
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF THE EPSIN N-TERMINAL HOMOLOGY (ENTH) DOMAIN AT 1.56 ANGSTROM RESOLUTION
Authors: FREMONT, D.H.
History
DepositionMay 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EPSIN


Theoretical massNumber of molelcules
Total (without water)16,7801
Polymers16,7801
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.885, 49.885, 99.333
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-184-

HOH

-
Components

#1: Protein EPSIN


Mass: 16780.031 Da / Num. of mol.: 1 / Fragment: ENTH DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O88339
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, 100mM Tris-HCl pH 8.5, 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 20K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.56→20 Å / Num. all: 21042 / Num. obs: 21042 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 42.3
Reflection shellResolution: 1.56→1.61 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.394 / Num. unique all: 1708 / % possible all: 98.4

-
Processing

Software
NameClassification
CNSrefinement
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 1.56→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 711895.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 963 4.7 %RANDOM
Rwork0.199 ---
all0.21 21006 --
obs0.201 20355 96.6 %-
Displacement parametersBiso mean: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å22.27 Å20 Å2
2---1.52 Å20 Å2
3---3.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-20 Å
Luzzati sigma a0.14 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 0 195 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_deg1
X-RAY DIFFRACTIONo_dihedral_angle_d17.7
X-RAY DIFFRACTIONo_improper_angle_d0.68
X-RAY DIFFRACTIONo_mcbond_it1.631.5
X-RAY DIFFRACTIONo_mcangle_it2.312
X-RAY DIFFRACTIONo_scbond_it3.542
X-RAY DIFFRACTIONo_scangle_it5.362.5
LS refinement shellResolution: 1.56→1.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 149 4.8 %
Rwork0.384 2929 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

+
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