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- PDB-4jjq: Crystal structure of usp7-ntd with an e2 enzyme -

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Basic information

Entry
Database: PDB / ID: 4jjq
TitleCrystal structure of usp7-ntd with an e2 enzyme
Components
  • Ubiquitin carboxyl-terminal hydrolase 7
  • Ubiquitin-conjugating enzyme E2 E1
KeywordsHYDROLASE / DEUBIQUITINATING ENZYME / TRAF domain / UbE2E1
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / regulation of telomere capping / regulation of establishment of protein localization to telomere / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / monoubiquitinated protein deubiquitination / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of retrograde transport, endosome to Golgi ...ISG15 transferase activity / ISG15-protein conjugation / regulation of telomere capping / regulation of establishment of protein localization to telomere / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / monoubiquitinated protein deubiquitination / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of retrograde transport, endosome to Golgi / Phosphorylation of the APC/C / deubiquitinase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / E2 ubiquitin-conjugating enzyme / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / protein deubiquitination / protein monoubiquitination / ubiquitin ligase complex / negative regulation of gluconeogenesis / protein K48-linked ubiquitination / transcription-coupled nucleotide-excision repair / negative regulation of TORC1 signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / regulation of circadian rhythm / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / PML body / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / CDK-mediated phosphorylation and removal of Cdc6 / ISG15 antiviral mechanism / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / protein polyubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / Separation of Sister Chromatids / p53 binding / rhythmic process / Regulation of TP53 Degradation / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / chromosome / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / protein ubiquitination / nuclear body / cysteine-type endopeptidase activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / proteolysis / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
MATH domain / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain ...MATH domain / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / 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. / 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 / Papain-like cysteine peptidase superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 E1 / Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSaridakis, V.
CitationJournal: J. Biol. Chem. / Year: 2013
Title: Ubiquitin-specific protease 7 is a regulator of ubiquitin-conjugating enzyme UbE2E1.
Authors: Sarkari, F. / Wheaton, K. / La Delfa, A. / Mohamed, M. / Shaikh, F. / Khatun, R. / Arrowsmith, C.H. / Frappier, L. / Saridakis, V. / Sheng, Y.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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-conjugating enzyme E2 E1


Theoretical massNumber of molelcules
Total (without water)19,4572
Polymers19,4572
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-3 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.901, 69.901, 45.733
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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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: 18472.488 Da / Num. of mol.: 1 / Fragment: USP7-NTD, UNP RESIDUES 54-205 / Mutation: A156D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAUSP, USP7, USP7/HAUSP / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Protein/peptide Ubiquitin-conjugating enzyme E2 E1 / UbcH6 / Ubiquitin carrier protein E1 / Ubiquitin-protein ligase E1


Mass: 984.945 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-14 / Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P51965, ubiquitin-protein ligase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.91 Å3/Da / Density % sol: 57.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 % PEG 4000, 0.1 M TRIS PH 8.5 AND 0.2 M LITHIUM SULFATE , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 17000 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 6.7 Å2 / Rsym value: 0.133 / Net I/σ(I): 29

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Processing

Software
NameClassification
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YY6

1yy6


Resolution: 1.95→49.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 89284.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1188 7.8 %RANDOM
Rwork0.197 ---
obs0.197 15267 93.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.24 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.95→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1157 0 0 75 1232
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.241 172 7.4 %
Rwork0.204 2148 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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