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Basic information

Entry
Database: PDB / ID: 4hk2
TitleU7Ub25.2540
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN/Inhibitor / Computationally designed ubiquitin / USP7 / SIGNALING PROTEIN-Inhibitor complex
Function / homology
Function and homology information


Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex ...Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Hh mutants are degraded by ERAD / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / EGFR downregulation / Termination of translesion DNA synthesis / Degradation of GLI1 by the proteasome / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Iron uptake and transport / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Assembly Of The HIV Virion
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsMurray, J.M. / Rouge, L.
CitationJournal: to be published
Title: Potent and selective inhibitors of USP7/HAUSP activity by protein conformational stabilization
Authors: Zhang, Y. / Zhou, L. / Rouge, L. / Phillips, A.H. / Lam, C. / Liu, P. / Sandoval, W. / Helgason, E. / Murray, J.M. / Wertz, I. / Corn, J.E.
History
DepositionOct 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Ubiquitin
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7375
Polymers35,6414
Non-polymers961
Water4,414245
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0062
Polymers8,9101
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,9101
Polymers8,9101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,9101
Polymers8,9101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,9101
Polymers8,9101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.782, 85.782, 54.457
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-259-

HOH

21D-149-

HOH

31D-159-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq -1:71 )
21chain B and (resseq -1:71 )
31chain C and (resseq -1:71 )
41chain D and (resseq -1:71 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: -1 - 71 / Label seq-ID: 1 - 73

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A' and (resseq -1:71 )AA
2chain 'B' and (resseq -1:71 )BB
3chain 'C' and (resseq -1:71 )CC
4chain 'D' and (resseq -1:71 )DD

NCS oper:
IDCodeMatrixVector
1given(-0.507993, 0.861338, 0.006303), (-0.861243, -0.507788, -0.020304), (-0.014288, -0.015743, 0.999774)-21.835699, 37.702599, -17.564301
2given(-0.536987, -0.84359, -0.00057), (-0.84346, 0.536892, 0.017935), (-0.014824, 0.010111, -0.999839)41.870602, -1.71126, 17.821301
3given(-0.517835, -0.855471, 0.003907), (-0.853849, 0.517124, 0.059358), (-0.0528, 0.027401, -0.998229)21.998899, 36.684601, 18.6633

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Components

#1: Protein
Ubiquitin


Mass: 8910.185 Da / Num. of mol.: 4 / Mutation: T7F, L8R, I13Y, R42W, Q49R, L69G, L71R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC, Ubiquitin / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG48
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.4 M AmSO4 and 0.1M Citric acid pH 4.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2012
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→43.9 Å / Num. obs: 45185 / % possible obs: 98.7 % / Redundancy: 7 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 34.9
Reflection shellResolution: 1.4→1.405 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / Num. unique all: 402 / % possible all: 88

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
PHENIXdev_982refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ubq

1ubq


Resolution: 1.4→28.079 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.13 / σ(F): 1.35 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 2257 5 %random
Rwork0.1966 ---
obs0.1989 45124 98.61 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.924 Å2 / ksol: 0.556 e/Å3
Displacement parametersBiso max: 61.62 Å2 / Biso mean: 19.0583 Å2 / Biso min: 5.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.0596 Å2-0 Å20 Å2
2---0.0596 Å2-0 Å2
3---0.1191 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 5 245 2673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0292484
X-RAY DIFFRACTIONf_angle_d1.9593338
X-RAY DIFFRACTIONf_chiral_restr0.117369
X-RAY DIFFRACTIONf_plane_restr0.008428
X-RAY DIFFRACTIONf_dihedral_angle_d15.665984
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A575X-RAY DIFFRACTIONPOSITIONAL0.938
12B575X-RAY DIFFRACTIONPOSITIONAL0.938
13C580X-RAY DIFFRACTIONPOSITIONAL0.61
14D575X-RAY DIFFRACTIONPOSITIONAL0.794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.43040.27511410.22062443258491
1.4304-1.46370.32211450.21862521266695
1.4637-1.50030.28461530.21232641279499
1.5003-1.54090.23561450.194426902835100
1.5409-1.58620.27931580.194926822840100
1.5862-1.63740.27781150.196527202835100
1.6374-1.69590.29121410.194727002841100
1.6959-1.76380.23491510.201826742825100
1.7638-1.84410.23881180.190527282846100
1.8441-1.94130.23321370.180227212858100
1.9413-2.06290.21241520.181626962848100
2.0629-2.22210.21561280.175927252853100
2.2221-2.44560.20091490.176727202869100
2.4456-2.79920.20731550.197427252880100
2.7992-3.52560.21091370.183927592896100
3.5256-28.0790.27971320.23442722285494

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