[English] 日本語
Yorodumi
- PDB-5wf9: Tepsin tENTH domain 1-153 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wf9
TitleTepsin tENTH domain 1-153
ComponentsAP-4 complex accessory subunit Tepsin
KeywordsPROTEIN TRANSPORT / protein trafficking
Function / homology
Function and homology information


coated vesicle membrane / organelle membrane / trans-Golgi network membrane / intracellular membrane-bounded organelle / protein-containing complex binding / cytosol / cytoplasm
Similarity search - Function
Tepsin, ENTH/VHS domain / AP-4 complex accessory subunit Tepsin / ENTH domain / ENTH domain / ENTH/VHS
Similarity search - Domain/homology
AP-4 complex accessory subunit Tepsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArchuleta, T.L. / Jackson, L.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119525 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)T32MH65215-12 United States
CitationJournal: Traffic / Year: 2017
Title: Structure and evolution of ENTH and VHS/ENTH-like domains in tepsin.
Authors: Archuleta, T.L. / Frazier, M.N. / Monken, A.E. / Kendall, A.K. / Harp, J. / McCoy, A.J. / Creanza, N. / Jackson, L.P.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AP-4 complex accessory subunit Tepsin


Theoretical massNumber of molelcules
Total (without water)16,8661
Polymers16,8661
Non-polymers00
Water99155
1
A: AP-4 complex accessory subunit Tepsin

A: AP-4 complex accessory subunit Tepsin

A: AP-4 complex accessory subunit Tepsin

A: AP-4 complex accessory subunit Tepsin


Theoretical massNumber of molelcules
Total (without water)67,4664
Polymers67,4664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area4780 Å2
ΔGint-29 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.180, 90.180, 42.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

-
Components

#1: Protein AP-4 complex accessory subunit Tepsin / ENTH domain-containing protein 2 / Epsin for AP-4 / Tetra-epsin


Mass: 16866.463 Da / Num. of mol.: 1 / Fragment: UNP residues 1-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEPSIN, C17orf56, ENTHD2 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q96N21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 150mM MES monohydrate pH 6.0, 15% (w/v) PEG6000.

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→63.8 Å / Num. obs: 16739 / % possible obs: 98.9 % / Redundancy: 26.8 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.02 / Net I/σ(I): 24.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.905 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1518 / CC1/2: 0.534 / Rpim(I) all: 0.462 / % possible all: 91.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFB

5wfb


Resolution: 1.8→45.09 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 837 5 %
Rwork0.1891 --
obs0.1907 16732 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 0 55 1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041033
X-RAY DIFFRACTIONf_angle_d0.6451398
X-RAY DIFFRACTIONf_dihedral_angle_d9.071625
X-RAY DIFFRACTIONf_chiral_restr0.036157
X-RAY DIFFRACTIONf_plane_restr0.004179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.27161300.24922468X-RAY DIFFRACTION94
1.9128-2.06050.2311380.18962611X-RAY DIFFRACTION100
2.0605-2.26790.17941390.16032637X-RAY DIFFRACTION100
2.2679-2.5960.19711390.15832645X-RAY DIFFRACTION100
2.596-3.27050.21061420.17712704X-RAY DIFFRACTION100
3.2705-45.10410.23381490.20472831X-RAY DIFFRACTION100

+
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