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- PDB-5gg4: Crystal structure of USP7 with RNF169 peptide -

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Basic information

Entry
Database: PDB / ID: 5gg4
TitleCrystal structure of USP7 with RNF169 peptide
Components
  • Peptide from E3 ubiquitin-protein ligase RNF169
  • Ubiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE/LIGASE / HYDROLASE-LIGASE complex
Function / homology
Function and homology information


negative regulation of double-strand break repair / regulation of telomere capping / positive regulation of DNA demethylation / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity ...negative regulation of double-strand break repair / regulation of telomere capping / positive regulation of DNA demethylation / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosome binding / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / regulation of protein stability / regulation of circadian rhythm / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / rhythmic process / double-strand break repair / Regulation of TP53 Degradation / p53 binding / site of double-strand break / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / protein ubiquitination / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / DNA damage response / nucleolus / protein-containing complex / proteolysis / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. ...Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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. / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Papain-like cysteine peptidase superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF169 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsJiang, Y. / Gong, Q.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Dual-utility NLS drives RNF169-dependent DNA damage responses.
Authors: An, L. / Jiang, Y. / Ng, H.H. / Man, E.P. / Chen, J. / Khoo, U.S. / Gong, Q. / Huen, M.S.
History
DepositionJun 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 8, 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

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Ubiquitin carboxyl-terminal hydrolase 7
E: Peptide from E3 ubiquitin-protein ligase RNF169
F: Peptide from E3 ubiquitin-protein ligase RNF169
G: Peptide from E3 ubiquitin-protein ligase RNF169
H: Peptide from E3 ubiquitin-protein ligase RNF169


Theoretical massNumber of molelcules
Total (without water)162,1048
Polymers162,1048
Non-polymers00
Water0
1
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
E: Peptide from E3 ubiquitin-protein ligase RNF169
F: Peptide from E3 ubiquitin-protein ligase RNF169


Theoretical massNumber of molelcules
Total (without water)81,0524
Polymers81,0524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ubiquitin carboxyl-terminal hydrolase 7
D: Ubiquitin carboxyl-terminal hydrolase 7
G: Peptide from E3 ubiquitin-protein ligase RNF169
H: Peptide from E3 ubiquitin-protein ligase RNF169


Theoretical massNumber of molelcules
Total (without water)81,0524
Polymers81,0524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)162.195, 99.965, 124.299
Angle α, β, γ (deg.)90.000, 95.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 38869.043 Da / Num. of mol.: 4 / Fragment: UNP residues 560-890
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Plasmid: pET28aSUMO
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide
Peptide from E3 ubiquitin-protein ligase RNF169 / / RING finger protein 169


Mass: 1657.000 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q8NCN4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.2M sodium chloride, 6% w/v PEG 8000, 0.1M Sodium cacodylate, pH 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 3.1→46.965 Å / Num. obs: 35693 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.115 / Net I/av σ(I): 10 / Net I/σ(I): 3.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.1-3.153.60.6791100
3.15-3.213.50.551100
3.21-3.273.60.5161100
3.27-3.343.70.4111100
3.34-3.414.10.3541100
3.41-3.494.10.2841100
3.49-3.584.10.2391100
3.58-3.6840.202199.9
3.68-3.7840.1751100
3.78-3.9140.1481100
3.91-4.0440.126199.9
4.04-4.213.90.111100
4.21-4.43.80.1011100
4.4-4.633.50.087199.9
4.63-4.923.60.081199.9
4.92-5.340.085199.9
5.3-5.8340.089199.9
5.83-6.6740.092199.8
6.67-8.43.70.082199.8
8.4-503.70.074199.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WPH

4wph


Resolution: 3.11→46.965 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.878 / SU B: 19.351 / SU ML: 0.336 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1783 5 %RANDOM
Rwork0.2259 ---
obs0.228 33903 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 177.17 Å2 / Biso mean: 78.44 Å2 / Biso min: 45 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0.08 Å2
2---0.14 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 3.11→46.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8632 0 0 0 8632
Num. residues----1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0198825
X-RAY DIFFRACTIONr_bond_other_d0.0010.027916
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.96212019
X-RAY DIFFRACTIONr_angle_other_deg0.738318123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06651118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28524.596396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.231151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9011539
X-RAY DIFFRACTIONr_chiral_restr0.0590.21361
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021993
X-RAY DIFFRACTIONr_mcbond_it3.068.3874511
X-RAY DIFFRACTIONr_mcbond_other3.0588.3864510
X-RAY DIFFRACTIONr_mcangle_it5.25212.5655616
LS refinement shellResolution: 3.106→3.187 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 120 -
Rwork0.296 2379 -
all-2499 -
obs--93.74 %

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