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- PDB-5ngf: Crystal structure of USP7 in complex with the covalent inhibitor,... -

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Basic information

Entry
Database: PDB / ID: 5ngf
TitleCrystal structure of USP7 in complex with the covalent inhibitor, FT827
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / Deubiquitination
Function / homology
Function and homology information


regulation of telomere capping / histone H2B deubiquitinase activity / histone H2A deubiquitinase activity / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / peptidase complex / regulation of retrograde transport, endosome to Golgi / DNA alkylation repair / deubiquitinase activity / protein K48-linked deubiquitination ...regulation of telomere capping / histone H2B deubiquitinase activity / histone H2A deubiquitinase activity / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / peptidase complex / regulation of retrograde transport, endosome to Golgi / DNA alkylation repair / deubiquitinase activity / protein K48-linked deubiquitination / K48-linked deubiquitinase activity / regulation of tumor necrosis factor-mediated signaling pathway / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / protein K63-linked deubiquitination / negative regulation of gluconeogenesis / protein deubiquitination / ubiquitin ligase complex / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of TORC1 signaling / regulation of signal transduction by p53 class mediator / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of protein stability / antiviral innate immune response / PML body / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / p53 binding / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of TP53 Degradation / nuclear body / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / protein stabilization / protein ubiquitination / Ub-specific processing proteases / chromosome / cysteine-type endopeptidase activity / protein-containing complex / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / 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. ...ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / 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. / Single Sheet / Papain-like cysteine peptidase superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-8WN / Ubiquitin C-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsKrajewski, W.W. / Turnbull, A.P. / Ioannidis, S. / Kessler, B.M. / Komander, D.
CitationJournal: Nature / Year: 2017
Title: Molecular basis of USP7 inhibition by selective small-molecule inhibitors.
Authors: Turnbull, A.P. / Ioannidis, S. / Krajewski, W.W. / Pinto-Fernandez, A. / Heride, C. / Martin, A.C.L. / Tonkin, L.M. / Townsend, E.C. / Buker, S.M. / Lancia, D.R. / Caravella, J.A. / Toms, A. ...Authors: Turnbull, A.P. / Ioannidis, S. / Krajewski, W.W. / Pinto-Fernandez, A. / Heride, C. / Martin, A.C.L. / Tonkin, L.M. / Townsend, E.C. / Buker, S.M. / Lancia, D.R. / Caravella, J.A. / Toms, A.V. / Charlton, T.M. / Lahdenranta, J. / Wilker, E. / Follows, B.C. / Evans, N.J. / Stead, L. / Alli, C. / Zarayskiy, V.V. / Talbot, A.C. / Buckmelter, A.J. / Wang, M. / McKinnon, C.L. / Saab, F. / McGouran, J.F. / Century, H. / Gersch, M. / Pittman, M.S. / Marshall, C.G. / Raynham, T.M. / Simcox, M. / Stewart, L.M.D. / McLoughlin, S.B. / Escobedo, J.A. / Bair, K.W. / Dinsmore, C.J. / Hammonds, T.R. / Kim, S. / Urbe, S. / Clague, M.J. / Kessler, B.M. / Komander, D.
History
DepositionMar 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 1, 2017Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 17, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4605
Polymers82,2972
Non-polymers1,1633
Water32418
1
A: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7613
Polymers41,1481
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6992
Polymers41,1481
Non-polymers5511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.810, 63.310, 65.660
Angle α, β, γ (deg.)105.05, 107.88, 113.03
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 209 - 554 / Label seq-ID: 4 - 349

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 41148.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-8WN / ~{N}-[2-[4-[4-[(1-methyl-4-oxidanylidene-pyrazolo[3,4-d]pyrimidin-5-yl)methyl]-4-oxidanyl-piperidin-1-yl]carbonylphenyl]phenyl]ethanesulfonamide


Mass: 550.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H30N6O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 % (w/v) PEG3350, 100 mM Bis-Tris propane pH 7.5, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.33→52.5 Å / Num. obs: 33087 / % possible obs: 97 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 10.9
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.588 / Num. measured obs: 6763 / Num. unique all: 2428 / CC1/2: 0.811 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NB8

1nb8


Resolution: 2.33→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 19.168 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.239 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 1471 4.4 %RANDOM
Rwork0.18802 ---
obs0.19081 31606 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.1 Å2-0.09 Å2
2---0.15 Å2-0.04 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.33→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5083 0 82 18 5183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195279
X-RAY DIFFRACTIONr_bond_other_d0.0040.024784
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9747164
X-RAY DIFFRACTIONr_angle_other_deg1.0183.00410942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655658
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.39524.522230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94115835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.041523
X-RAY DIFFRACTIONr_chiral_restr0.0920.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216022
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8365.3612650
X-RAY DIFFRACTIONr_mcbond_other3.8375.362649
X-RAY DIFFRACTIONr_mcangle_it5.2168.0363302
X-RAY DIFFRACTIONr_mcangle_other5.2158.0373303
X-RAY DIFFRACTIONr_scbond_it4.4845.6572629
X-RAY DIFFRACTIONr_scbond_other4.485.6572629
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3058.3523863
X-RAY DIFFRACTIONr_long_range_B_refined7.6342.6825630
X-RAY DIFFRACTIONr_long_range_B_other7.62942.6925631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18534 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 104 -
Rwork0.313 2317 -
obs--96.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3545-0.20410.84443.0834-1.10763.00280.21250.0888-0.09490.0264-0.1544-0.12180.03140.0084-0.05810.04320.032-0.00340.08720.0290.01954.5915-23.011221.2375
23.0887-0.06611.31772.3868-0.57422.8312-0.1636-0.23130.0943-0.06680.1630.10880.00090.00620.00060.08190.0675-0.02770.0826-0.0160.0133-26.5532-2.360137.2126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A209 - 554
2X-RAY DIFFRACTION2B209 - 554

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