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- PDB-4mjs: crystal structure of a PB1 complex -

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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) / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C signaling / brown fat cell proliferation / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / positive regulation of protein transport / regulation of Ras protein signal transduction ...TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / VEGFR2 mediated cell proliferation / calcium,diacylglycerol-dependent serine/threonine kinase activity / protein kinase C signaling / brown fat cell proliferation / diacylglycerol-dependent, calcium-independent serine/threonine kinase activity / protein localization to perinuclear region of cytoplasm / protein targeting to vacuole involved in autophagy / positive regulation of protein transport / regulation of Ras protein signal transduction / Estrogen-stimulated signaling through PRKCZ / RHO GTPases Activate NADPH Oxidases / response to mitochondrial depolarisation / aggrephagy / myelin sheath abaxonal region / protein kinase C / negative regulation of toll-like receptor 4 signaling pathway / Lewy body / amphisome / diacylglycerol-dependent serine/threonine kinase activity / apical cortex / positive regulation of T-helper 2 cell differentiation / positive regulation of T-helper 2 cell cytokine production / regulation of protein complex stability / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / axon hillock / endosome organization / pexophagy / autophagy of mitochondrion / membraneless organelle assembly / vesicle transport along microtubule / phagophore assembly site / ubiquitin-modified protein reader activity / regulation of mitochondrion organization / membrane hyperpolarization / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / neuron projection extension / aggresome / endosomal transport / intracellular membraneless organelle / positive regulation of cell-matrix adhesion / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of ferroptosis / temperature homeostasis / cellular response to stress / establishment of cell polarity / positive regulation of interleukin-4 production / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / cell leading edge / autolysosome / microtubule organizing center / positive regulation of interleukin-10 production / molecular sequestering activity / membrane depolarization / immune system process / bicellular tight junction / positive regulation of excitatory postsynaptic potential / positive regulation of insulin receptor signaling pathway / long-term memory / positive regulation of synaptic transmission / potassium channel regulator activity / negative regulation of protein-containing complex assembly / phospholipase binding / mitophagy / energy homeostasis / stress fiber / sperm midpiece / 14-3-3 protein binding / signaling adaptor activity / inclusion body / negative regulation of protein ubiquitination / ionotropic glutamate receptor binding / positive regulation of autophagy / SH2 domain binding / p75NTR recruits signalling complexes / negative regulation of insulin receptor signaling pathway / NF-kB is activated and signals survival / Pexophagy / protein kinase C binding / autophagosome / NRIF signals cell death from the nucleus / protein sequestering activity / sarcomere / response to ischemia / ubiquitin binding / positive regulation of long-term synaptic potentiation / PINK1-PRKN Mediated Mitophagy / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / macroautophagy / P-body / protein catabolic process / molecular condensate scaffold activity / positive regulation of NF-kappaB transcription factor activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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