[English] 日本語
Yorodumi
- PDB-5yph: p62/SQSTM1 ZZ domain with Ile-peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yph
Titlep62/SQSTM1 ZZ domain with Ile-peptide
Components78 kDa glucose-regulated protein,Sequestosome-1
KeywordsSIGNALING PROTEIN / Complex / p62/SQSTM1 / ZZ domain / Autophagy / N-end rule
Function / homology
Function and homology information


regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / maintenance of protein localization in endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response ...regulation of protein folding in endoplasmic reticulum / regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / cerebellum structural organization / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / maintenance of protein localization in endoplasmic reticulum / negative regulation of IRE1-mediated unfolded protein response / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / IRE1alpha activates chaperones / cerebellar Purkinje cell layer development / Lewy body / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / response to mitochondrial depolarisation / aggrephagy / endoplasmic reticulum chaperone complex / amphisome / negative regulation of toll-like receptor 4 signaling pathway / PERK regulates gene expression / protein folding in endoplasmic reticulum / pexophagy / regulation of protein complex stability / autophagy of mitochondrion / endosome organization / molecular sequestering activity / non-membrane-bounded organelle assembly / misfolded protein binding / post-translational protein targeting to membrane, translocation / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / ubiquitin-modified protein reader activity / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / endosomal transport / temperature homeostasis / immune system process / ER overload response / non-chaperonin molecular chaperone ATPase / mitophagy / chaperone cofactor-dependent protein refolding / endoplasmic reticulum-Golgi intermediate compartment / Regulation of HSF1-mediated heat shock response / autophagosome / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / cellular response to glucose starvation / positive regulation of autophagy / signaling adaptor activity / energy homeostasis / ERAD pathway / endoplasmic reticulum unfolded protein response / protein folding chaperone / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / protein sequestering activity / heat shock protein binding / p75NTR recruits signalling complexes / substantia nigra development / PINK1-PRKN Mediated Mitophagy / Pexophagy / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / response to endoplasmic reticulum stress / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of protein ubiquitination / positive regulation of long-term synaptic potentiation / response to ischemia / protein kinase C binding / macroautophagy / positive regulation of protein localization to plasma membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / ionotropic glutamate receptor binding / P-body / protein catabolic process / protein localization / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / unfolded protein binding / melanosome / late endosome / Platelet degranulation
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Endoplasmic reticulum targeting sequence. / Ubiquitin associated domain ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / Endoplasmic reticulum chaperone BIP, nucleotide-binding domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Endoplasmic reticulum targeting sequence. / Ubiquitin associated domain / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Zinc finger ZZ-type signature. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / UBA-like superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Endoplasmic reticulum chaperone BiP / Sequestosome-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.629 Å
AuthorsKwon, D.H. / Kim, L. / Song, H.K.
CitationJournal: Nat Commun / Year: 2018
Title: Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter.
Authors: Kwon, D.H. / Park, O.H. / Kim, L. / Jung, Y.O. / Park, Y. / Jeong, H. / Hyun, J. / Kim, Y.K. / Song, H.K.
History
DepositionNov 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 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: 78 kDa glucose-regulated protein,Sequestosome-1
B: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2006
Polymers12,9392
Non-polymers2624
Water2,108117
1
A: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6003
Polymers6,4691
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 78 kDa glucose-regulated protein,Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6003
Polymers6,4691
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.658, 33.381, 35.019
Angle α, β, γ (deg.)90.00, 103.61, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 78 kDa glucose-regulated protein,Sequestosome-1 / GRP-78 / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck ...GRP-78 / EBI3-associated protein of 60 kDa / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62


Mass: 6469.278 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA5, GRP78, SQSTM1, ORCA, OSIL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11021, UniProt: Q13501
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIle (-3 position) is synthetic residue generated by special enzyme

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity % sol: 16.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: sodium phosphate, potassium phosphate, MgCl2

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.629→17.91 Å / Num. obs: 9011 / % possible obs: 94 % / Redundancy: 3.3 % / Net I/σ(I): 34.7

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YP7

5yp7


Resolution: 1.629→17.909 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18
RfactorNum. reflection% reflection
Rfree0.187 912 10.12 %
Rwork0.1469 --
obs0.1511 9011 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.629→17.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms747 0 4 117 868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011762
X-RAY DIFFRACTIONf_angle_d1.3051030
X-RAY DIFFRACTIONf_dihedral_angle_d6.252458
X-RAY DIFFRACTIONf_chiral_restr0.073112
X-RAY DIFFRACTIONf_plane_restr0.011137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.629-1.71480.19061220.11861067X-RAY DIFFRACTION89
1.7148-1.82210.18131210.13031126X-RAY DIFFRACTION92
1.8221-1.96270.18151240.13191138X-RAY DIFFRACTION93
1.9627-2.15990.21911330.1371155X-RAY DIFFRACTION94
2.1599-2.47170.20251350.1491172X-RAY DIFFRACTION96
2.4717-3.11140.19021380.1541190X-RAY DIFFRACTION97
3.1114-17.90960.16741390.15951251X-RAY DIFFRACTION98

+
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