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- PDB-7xed: Crystal Structure of OsCIE1-Ubox and OsUBC8 complex -

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Basic information

Entry
Database: PDB / ID: 7xed
TitleCrystal Structure of OsCIE1-Ubox and OsUBC8 complex
Components
  • U-box domain-containing protein 12
  • UBC core domain-containing protein
KeywordsTRANSFERASE / complex / ubiquitination / Ubox / ligase / PLANT PROTEIN
Function / homology
Function and homology information


RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / ATP binding / nucleus / cytoplasm
Similarity search - Function
PUB10-like, N-terminal domain / PUB protein, U-box domain, plant / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo ...PUB10-like, N-terminal domain / PUB protein, U-box domain, plant / U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
UBC core domain-containing protein / U-box domain-containing protein 12
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, Y. / Yu, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesYSBR-011 China
CitationJournal: Nature / Year: 2024
Title: Release of a ubiquitin brake activates OsCERK1-triggered immunity in rice.
Authors: Wang, G. / Chen, X. / Yu, C. / Shi, X. / Lan, W. / Gao, C. / Yang, J. / Dai, H. / Zhang, X. / Zhang, H. / Zhao, B. / Xie, Q. / Yu, N. / He, Z. / Zhang, Y. / Wang, E.
History
DepositionMar 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBC core domain-containing protein
C: U-box domain-containing protein 12
B: UBC core domain-containing protein
D: U-box domain-containing protein 12


Theoretical massNumber of molelcules
Total (without water)50,9854
Polymers50,9854
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, OsCIE1-Ubox dimmer can bind two OsUBC8 monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.290, 132.550, 47.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein UBC core domain-containing protein


Mass: 16540.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: OsJ_21490 / Production host: Escherichia coli (E. coli) / References: UniProt: A3BC59
#2: Protein U-box domain-containing protein 12 / Plant U-box protein 12 / OsPUB12 / RING-type E3 ubiquitin transferase PUB12


Mass: 8952.272 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: PUB12, Os06g0102700, LOC_Os06g01304, OSJNBa0075G19.19-1
Production host: Escherichia coli (E. coli)
References: UniProt: Q5VRH9, RING-type E3 ubiquitin transferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 0.3M Calcium acetate, 20% PEG 3350, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 21, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→66.28 Å / Num. obs: 19672 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 75.07 Å2 / CC1/2: 0.992 / Net I/σ(I): 9.8
Reflection shellResolution: 2.5→2.57 Å / Num. unique obs: 1418 / CC1/2: 0.341 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OXQ

2oxq


Resolution: 2.5→43.64 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1969 10.01 %
Rwork0.2311 17703 -
obs0.2329 19672 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.35 Å2 / Biso mean: 81.4838 Å2 / Biso min: 46.23 Å2
Refinement stepCycle: final / Resolution: 2.5→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 0 26 3467
Biso mean---82.39 -
Num. residues----454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.560.44111370.433212331370100
2.56-2.630.43721400.407412651405100
2.63-2.710.38381350.368112121347100
2.71-2.80.28741390.327312491388100
2.8-2.90.35451360.32812301366100
2.9-3.010.39061420.346112761418100
3.01-3.150.36161380.301112351373100
3.15-3.320.30531400.275512561396100
3.32-3.520.29781390.260112511390100
3.52-3.790.27291410.242312701411100
3.8-4.180.2521410.219212681409100
4.18-4.780.21091430.197612831426100
4.78-6.020.21991440.197213011445100
6.02-43.640.17631540.1761374152899

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