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- PDB-6do5: KLHDC2 ubiquitin ligase in complex with USP1 C-end degron -

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Basic information

Entry
Database: PDB / ID: 6do5
TitleKLHDC2 ubiquitin ligase in complex with USP1 C-end degron
Components
  • Kelch domain-containing protein 2
  • USP1 C-END DEGRON
KeywordsLIGASE / kelch repeat / beta-propeller / degron / complex / substrate receptor / E3 / ubiquitin ligase
Function / homology
Function and homology information


positive regulation of error-prone translesion synthesis / monoubiquitinated protein deubiquitination / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / protein deubiquitination / ubiquitin ligase-substrate adaptor activity / regulation of DNA repair / response to UV / skeletal system development / Recognition of DNA damage by PCNA-containing replication complex ...positive regulation of error-prone translesion synthesis / monoubiquitinated protein deubiquitination / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / Cul2-RING ubiquitin ligase complex / protein deubiquitination / ubiquitin ligase-substrate adaptor activity / regulation of DNA repair / response to UV / skeletal system development / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / positive regulation of receptor signaling pathway via JAK-STAT / peptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear membrane / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein ubiquitination / cysteine-type endopeptidase activity / DNA repair / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin specific peptidase 1 / Galactose oxidase, central domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Kelch-type beta propeller / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 1 / Kelch domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsRusnac, D.V. / Lin, H.C. / Yen, H.C.S. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mol. Cell / Year: 2018
Title: Recognition of the Diglycine C-End Degron by CRL2KLHDC2Ubiquitin Ligase.
Authors: Rusnac, D.V. / Lin, H.C. / Canzani, D. / Tien, K.X. / Hinds, T.R. / Tsue, A.F. / Bush, M.F. / Yen, H.S. / Zheng, N.
History
DepositionJun 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kelch domain-containing protein 2
B: Kelch domain-containing protein 2
D: USP1 C-END DEGRON
C: USP1 C-END DEGRON


Theoretical massNumber of molelcules
Total (without water)83,7604
Polymers83,7604
Non-polymers00
Water2,306128
1
A: Kelch domain-containing protein 2
C: USP1 C-END DEGRON


Theoretical massNumber of molelcules
Total (without water)41,8802
Polymers41,8802
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-3 kcal/mol
Surface area13470 Å2
MethodPISA
2
B: Kelch domain-containing protein 2
D: USP1 C-END DEGRON


Theoretical massNumber of molelcules
Total (without water)41,8802
Polymers41,8802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-2 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.496, 87.086, 88.322
Angle α, β, γ (deg.)90.000, 104.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kelch domain-containing protein 2 / Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor- ...Hepatocellular carcinoma-associated antigen 33 / Host cell factor homolog LCP / Host cell factor-like protein 1 / HCLP-1


Mass: 41351.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLHDC2, HCA33 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y2U9
#2: Protein/peptide USP1 C-END DEGRON


Mass: 528.644 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O94782*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 0.03M MgCl2*6H2O, 0.03M CaCl2*2H2O, 0.05M Imidazole, 0.05M MES monohydrate, 12.5% v/v MPD, 12.5% PEG1000, 12.5% w/v PEG3350, pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 32634 / % possible obs: 98 % / Redundancy: 5.9 % / Biso Wilson estimate: 32.82 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.053 / Rrim(I) all: 0.13 / Χ2: 1.236 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.80.52713380.7140.2870.6040.54380.3
2.24-2.284.20.5314790.7390.2780.6020.54389.3
2.28-2.324.70.46515690.8340.2330.5220.52593.8
2.32-2.375.10.47315630.8010.2290.5270.56197.2
2.37-2.425.60.49316580.8060.2280.5440.56599.8
2.42-2.486.10.43616860.8770.1920.4770.567100
2.48-2.546.30.38616550.8990.1680.4220.608100
2.54-2.616.30.34216530.920.1480.3730.632100
2.61-2.696.30.29216330.9370.1260.3190.686100
2.69-2.776.40.2516840.9570.1080.2730.743100
2.77-2.876.30.20716350.9690.090.2260.836100
2.87-2.996.30.16916680.9750.0730.1850.954100
2.99-3.126.30.13816630.9810.060.1511.102100
3.12-3.296.30.11916640.9860.0520.131.234100
3.29-3.496.30.10816820.9890.0470.1181.641100
3.49-3.766.30.09616720.9890.0420.1052.046100
3.76-4.146.20.08816500.9910.0390.0972.49100
4.14-4.746.10.07516630.9930.0330.0822.97499.9
4.74-5.976.10.0716870.9940.0310.0762.414100
5.97-506.10.05517320.9970.0240.061.93299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VPJ
Resolution: 2.5→43.067 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.2525 1399 6.17 %
Rwork0.1996 --
obs0.2029 22666 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.12 Å2 / Biso mean: 32.64 Å2 / Biso min: 15.26 Å2
Refinement stepCycle: final / Resolution: 2.5→43.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5095 0 0 128 5223
Biso mean---33.65 -
Num. residues----647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135259
X-RAY DIFFRACTIONf_angle_d1.3037151
X-RAY DIFFRACTIONf_chiral_restr0.077735
X-RAY DIFFRACTIONf_plane_restr0.006913
X-RAY DIFFRACTIONf_dihedral_angle_d14.0031797
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.58940.29271400.215721232263
2.5894-2.6930.31031380.222220902228
2.693-2.81560.26191400.214421292269
2.8156-2.9640.28961430.21421292272
2.964-3.14960.2761350.199921032238
3.1496-3.39270.25121400.202121362276
3.3927-3.7340.23211400.193321152255
3.734-4.27390.23511380.187621162254
4.2739-5.3830.22471400.184721592299
5.383-43.07320.25431450.20821672312

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