[English] 日本語
Yorodumi
- PDB-3b0f: Crystal structure of the UBA domain of p62 and its interaction wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3b0f
TitleCrystal structure of the UBA domain of p62 and its interaction with ubiquitin
ComponentsSequestosome-1
KeywordsPROTEIN BINDING / Ubiquitin / Autophagy
Function / homology
Function and homology information


Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / negative regulation of toll-like receptor 4 signaling pathway ...Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / negative regulation of toll-like receptor 4 signaling pathway / non-membrane-bounded organelle assembly / aggrephagy / response to mitochondrial depolarisation / amphisome / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / pexophagy / endosome organization / regulation of protein complex stability / phagophore assembly site / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / autolysosome / temperature homeostasis / intracellular non-membrane-bounded organelle / immune system process / mitophagy / autophagosome / signaling adaptor activity / positive regulation of autophagy / energy homeostasis / inclusion body / negative regulation of protein ubiquitination / sperm midpiece / ionotropic glutamate receptor binding / molecular condensate scaffold activity / SH2 domain binding / sarcomere / protein sequestering activity / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / P-body / transcription coregulator activity / positive regulation of protein localization to plasma membrane / macroautophagy / protein catabolic process / PML body / autophagy / cellular response to reactive oxygen species / protein import into nucleus / protein-macromolecule adaptor activity / late endosome / signaling receptor activity / transcription by RNA polymerase II / cell differentiation / positive regulation of protein phosphorylation / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / mitochondrion / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Ubiquitin associated domain / Zinc finger ZZ-type signature. / Zinc-binding domain, present in Dystrophin, CREB-binding protein. ...Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / UBA domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Ubiquitin associated domain / Zinc finger ZZ-type signature. / 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. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsIsogai, S. / Morimoto, D. / Arita, K. / Unzai, S. / Tenno, T. / Hasegawa, J. / Sou, Y. / Komatsu, M. / Tanaka, K. / Shirakawa, M. / Tochio, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of the ubiquitin-associated (UBA) domain of p62 and its interaction with ubiquitin.
Authors: Isogai, S. / Morimoto, D. / Arita, K. / Unzai, S. / Tenno, T. / Hasegawa, J. / Sou, Y.S. / Komatsu, M. / Tanaka, K. / Shirakawa, M. / Tochio, H.
History
DepositionJun 9, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 13, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / reflns / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sequestosome-1
B: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7313
Polymers11,6352
Non-polymers961
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-6 kcal/mol
Surface area4670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.967, 72.967, 32.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Sequestosome-1 / STONE14 / Ubiquitin-binding protein p62


Mass: 5817.500 Da / Num. of mol.: 2 / Fragment: UBA domain (UNP RESIDUES 391-438)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sqstm1, A170, STAP / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64337
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 1.86 Å3/Da / Density % sol: 33.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100mM Citrate buffer pH5.0, 1.8M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-5A20.97928, 0.97909, 0.96405, 0.98317
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJan 25, 2008
ADSC QUANTUM 3152CCDJan 25, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Numerical link type Si(111) double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Numerical link type Si(111) double crystal monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979281
30.979091
40.964051
50.983171
ReflectionResolution: 1.4→51.57 Å / Num. all: 17371 / Num. obs: 17371 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 11 % / Rmerge(I) obs: 0.356 / % possible all: 82.5

-
Processing

Software
NameVersionClassification
SERGUIdata collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.283 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20054 888 5.1 %RANDOM
Rwork0.17011 ---
all0.17167 17323 --
obs0.17167 16435 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.036 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 5 77 760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021873
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9781207
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3265125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19525.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54415166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.295157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02697
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4181.5529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0242872
X-RAY DIFFRACTIONr_scbond_it3.0273344
X-RAY DIFFRACTIONr_scangle_it4.1794.5327
X-RAY DIFFRACTIONr_rigid_bond_restr1.73873
X-RAY DIFFRACTIONr_sphericity_free6.591377
X-RAY DIFFRACTIONr_sphericity_bonded3.0523843
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 69 -
Rwork0.225 994 -
obs--82.28 %
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)
13.09160.433-1.10059.58922.05453.03360.072-0.10360.10720.1439-0.09540.0055-0.16460.13760.02340.0478-0.00910.01870.06120.00720.07589.5626-9.8215-2.1438
26.66391.7954-1.49285.20761.27633.1244-0.02080.14650.023-0.06870.04890.18690.0508-0.058-0.0280.03720.01020.00250.05770.01590.05868.3705-19.2525-6.9589
34.2482-5.63420.936710.3815-0.49552.3570.1740.2319-0.2868-0.3664-0.00070.267-0.03790.0302-0.17330.0504-0.018-0.00070.10570.00270.11740.4333-16.6996-10.9963
43.2031-0.02370.40760.91470.35973.6067-0.0362-0.0843-0.0371-0.0080.1010.05110.04660.1015-0.06480.03860.00410.01690.05870.00240.0825-0.9434-12.6891-1.9173
54.0391-0.56870.05559.8003-0.61541.6031-0.0142-0.2599-0.09250.16980.113-0.2324-0.0614-0.0503-0.09880.01450.0172-0.00060.08260.02470.06474.1736-16.78693.0215
610.51770.85595.64535.72170.20278.64640.1028-0.2046-0.793-0.1395-0.0722-0.38680.43510.1649-0.03060.03990.00790.01150.03390.05060.1581-1.5268-24.80380.0779
77.70330.40112.08141.655-3.2977.6598-0.0385-0.05480.26650.18910.22460.1355-0.4132-0.5037-0.18610.12980.03850.00330.1295-0.00140.0218-21.716-17.2429-8.5714
85.4191-3.38380.73586.7334-1.39523.15920.0055-0.0382-0.0301-0.10830.1292-0.0372-0.00190.0251-0.13470.0525-0.00920.01420.0406-0.02080.039-16.0787-22.3364-3.1311
92.29182.0215-1.59216.85411.09232.33710.0081-0.24720.09610.06040.0752-0.00510.04880.29-0.08330.02840.0154-0.02390.157-0.06040.0907-9.2174-17.6592-0.7467
105.04421.93032.97082.34593.87716.4823-0.29510.11010.6445-0.11710.08570.0943-0.16110.08310.20940.0682-0.0206-0.01980.0583-0.01440.1906-10.6423-14.8478-11.1535
1110.10040.48051.21425.16571.20730.4354-0.18080.2492-0.2626-0.27180.15430.0621-0.09430.0620.02650.0616-0.01550.01130.0652-0.02360.0849-11.0229-23.4824-11.7292
129.70241.8052.52387.68511.53728.393-0.108-0.1124-0.72860.23440.0217-0.19350.24110.09670.08620.02620.01050.02970.0475-0.02010.1272-3.6847-25.7337-8.449
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 15
2X-RAY DIFFRACTION2A16 - 21
3X-RAY DIFFRACTION3A22 - 27
4X-RAY DIFFRACTION4A28 - 37
5X-RAY DIFFRACTION5A38 - 45
6X-RAY DIFFRACTION6A46 - 50
7X-RAY DIFFRACTION7B8 - 13
8X-RAY DIFFRACTION8B14 - 20
9X-RAY DIFFRACTION9B21 - 31
10X-RAY DIFFRACTION10B32 - 39
11X-RAY DIFFRACTION11B40 - 45
12X-RAY DIFFRACTION12B46 - 50

+
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