[English] 日本語
Yorodumi
- PDB-4mjs: crystal structure of a PB1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mjs
Titlecrystal structure of a PB1 complex
Components
  • Protein kinase C zeta type
  • Sequestosome-1
KeywordsTRANSFERASE/PROTEIN BINDING / PB1 domain / PB1 heterodimer and protein interaction / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / protein kinase C signaling / VEGFR2 mediated cell proliferation / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / Estrogen-stimulated signaling through PRKCZ / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity ...TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / protein kinase C signaling / VEGFR2 mediated cell proliferation / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / Estrogen-stimulated signaling through PRKCZ / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C / RHO GTPases Activate NADPH Oxidases / response to mitochondrial depolarisation / diacylglycerol-dependent serine/threonine kinase activity / aggrephagy / negative regulation of toll-like receptor 4 signaling pathway / amphisome / positive regulation of T-helper 2 cell differentiation / myelin sheath abaxonal region / positive regulation of protein transport / positive regulation of T-helper 2 cell cytokine production / apical cortex / regulation of protein complex stability / endosome organization / positive regulation of interleukin-13 production / vesicle transport along microtubule / positive regulation of interleukin-5 production / axon hillock / autophagy of mitochondrion / pexophagy / membraneless organelle assembly / membrane hyperpolarization / phagophore assembly site / ubiquitin-modified protein reader activity / regulation of mitochondrion organization / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / aggresome / endosomal transport / neuron projection extension / negative regulation of ferroptosis / intracellular membraneless organelle / positive regulation of cell-matrix adhesion / K63-linked polyubiquitin modification-dependent protein binding / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / temperature homeostasis / cellular response to stress / establishment of cell polarity / positive regulation of interleukin-4 production / cell leading edge / phospholipase binding / microtubule organizing center / autolysosome / positive regulation of interleukin-10 production / molecular sequestering activity / positive regulation of excitatory postsynaptic potential / membrane depolarization / immune system process / long-term memory / bicellular tight junction / positive regulation of synaptic transmission / potassium channel regulator activity / negative regulation of protein-containing complex assembly / positive regulation of insulin receptor signaling pathway / mitophagy / stress fiber / energy homeostasis / inclusion body / ionotropic glutamate receptor binding / positive regulation of autophagy / signaling adaptor activity / 14-3-3 protein binding / sperm midpiece / negative regulation of protein ubiquitination / negative regulation of insulin receptor signaling pathway / p75NTR recruits signalling complexes / SH2 domain binding / protein sequestering activity / NF-kB is activated and signals survival / autophagosome / Pexophagy / NRIF signals cell death from the nucleus / sarcomere / protein kinase C binding / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / protein localization to plasma membrane / PINK1-PRKN Mediated Mitophagy / positive regulation of protein localization to plasma membrane / macroautophagy / P-body / molecular condensate scaffold activity / protein catabolic process / Schaffer collateral - CA1 synapse / PML body / receptor tyrosine kinase binding / autophagy / microtubule cytoskeleton organization
Similarity search - Function
: / Protein kinase C / Protein kinase C, PB1 domain / Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain ...: / Protein kinase C / Protein kinase C, PB1 domain / Sequestosome-1, UBA domain / Sequestosome-1, PB1 domain / : / UBA domain / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Diacylglycerol/phorbol-ester binding / 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. / Phorbol esters/diacylglycerol binding domain (C1 domain) / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Protein kinase C zeta type / Sequestosome-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRen, J. / Wang, Z.X. / Wu, J.W.
CitationJournal: Sci China Life Sci / Year: 2014
Title: Structural and biochemical insights into the homotypic PB1-PB1 complex between PKC zeta and p62
Authors: Ren, J. / Wang, J. / Wang, Z.X. / Wu, J.W.
History
DepositionSep 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Protein kinase C zeta type
B: Sequestosome-1
C: Protein kinase C zeta type
D: Sequestosome-1
E: Protein kinase C zeta type
F: Sequestosome-1
G: Protein kinase C zeta type
H: Sequestosome-1
I: Protein kinase C zeta type
J: Sequestosome-1
K: Protein kinase C zeta type
L: Sequestosome-1
M: Protein kinase C zeta type
N: Sequestosome-1
O: Protein kinase C zeta type
P: Sequestosome-1
Q: Protein kinase C zeta type
R: Sequestosome-1
S: Protein kinase C zeta type
T: Sequestosome-1
U: Protein kinase C zeta type
V: Sequestosome-1
W: Protein kinase C zeta type
X: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,20728
Polymers261,95824
Non-polymers2484
Water7,152397
1
A: Protein kinase C zeta type
B: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein kinase C zeta type
D: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Protein kinase C zeta type
F: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Protein kinase C zeta type
H: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8923
Polymers21,8302
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Protein kinase C zeta type
J: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Protein kinase C zeta type
L: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: Protein kinase C zeta type
N: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8923
Polymers21,8302
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: Protein kinase C zeta type
P: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8923
Polymers21,8302
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
Q: Protein kinase C zeta type
R: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S: Protein kinase C zeta type
T: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
U: Protein kinase C zeta type
V: Sequestosome-1


Theoretical massNumber of molelcules
Total (without water)21,8302
Polymers21,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
W: Protein kinase C zeta type
X: Sequestosome-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8923
Polymers21,8302
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.715, 135.681, 259.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Protein kinase C zeta type / nPKC-zeta


Mass: 10287.679 Da / Num. of mol.: 12 / Fragment: PB1 domain, UNP residues 15-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pkcz, Prkcz / Plasmid: PGEX4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09217, protein kinase C
#2: Protein
Sequestosome-1 / EBI3-associated protein of 60 kDa / EBIAP / p60 / Phosphotyrosine-independent ligand for the Lck ...EBI3-associated protein of 60 kDa / EBIAP / p60 / Phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa / Ubiquitin-binding protein p62


Mass: 11542.182 Da / Num. of mol.: 12 / Fragment: PB1 domain, UNP residues 3-102 / Mutation: D69A,D71R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORCA, OSIL, SQSTM1 / Plasmid: PACYCduet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13501
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 8% PEG8000, 0.4M MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 105540 / Num. obs: 105401 / % possible obs: 100 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5 / Redundancy: 7.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 22.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 4.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WMH

1wmh


Resolution: 2.5→39.534 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 5264 5 %
Rwork0.2378 --
obs0.2402 105316 99.91 %
all-105540 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.28 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1569 Å2-0 Å20 Å2
2---1.5123 Å2-0 Å2
3---4.0658 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16410 0 16 397 16823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916736
X-RAY DIFFRACTIONf_angle_d1.222511
X-RAY DIFFRACTIONf_dihedral_angle_d17.1376270
X-RAY DIFFRACTIONf_chiral_restr0.0782499
X-RAY DIFFRACTIONf_plane_restr0.0052882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.38131650.27413315X-RAY DIFFRACTION100
2.5284-2.55820.31731660.26573275X-RAY DIFFRACTION100
2.5582-2.58930.34891730.26073334X-RAY DIFFRACTION100
2.5893-2.62210.33071850.26213262X-RAY DIFFRACTION100
2.6221-2.65660.35571810.27153294X-RAY DIFFRACTION100
2.6566-2.6930.33091980.27213282X-RAY DIFFRACTION100
2.693-2.73150.36581500.28273319X-RAY DIFFRACTION100
2.7315-2.77220.34021920.28073322X-RAY DIFFRACTION100
2.7722-2.81550.30071480.26353297X-RAY DIFFRACTION100
2.8155-2.86170.34271900.27033289X-RAY DIFFRACTION100
2.8617-2.9110.33691870.26753273X-RAY DIFFRACTION100
2.911-2.96390.31191760.26093347X-RAY DIFFRACTION100
2.9639-3.02090.32871640.24933308X-RAY DIFFRACTION100
3.0209-3.08250.30511870.25873314X-RAY DIFFRACTION100
3.0825-3.14950.34491590.25783320X-RAY DIFFRACTION100
3.1495-3.22280.32351700.25723296X-RAY DIFFRACTION100
3.2228-3.30330.27841640.24593354X-RAY DIFFRACTION100
3.3033-3.39260.32221660.24893341X-RAY DIFFRACTION100
3.3926-3.49240.28681680.24373288X-RAY DIFFRACTION100
3.4924-3.6050.32391890.25293341X-RAY DIFFRACTION100
3.605-3.73380.25331720.2363348X-RAY DIFFRACTION100
3.7338-3.88320.28171610.21713354X-RAY DIFFRACTION100
3.8832-4.05970.26361730.21533342X-RAY DIFFRACTION100
4.0597-4.27350.25461820.2053352X-RAY DIFFRACTION100
4.2735-4.54090.24511690.18713367X-RAY DIFFRACTION100
4.5409-4.89090.21961870.18673354X-RAY DIFFRACTION100
4.8909-5.3820.23921830.20863395X-RAY DIFFRACTION100
5.382-6.15830.30291860.27213405X-RAY DIFFRACTION100
6.1583-7.74920.26491890.26743424X-RAY DIFFRACTION100
7.7492-39.53850.2771840.23233540X-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://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