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- PDB-4hjk: U7Ub7 Disulfide variant -

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Basic information

Entry
Database: PDB / ID: 4hjk
TitleU7Ub7 Disulfide variant
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN/Inhibitor / USP7 / cytoplasmic / SIGNALING PROTEIN-Inhibitor complex
Function / homology
Function and homology information


Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression ...Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / 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 / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / Evasion by RSV of host interferon responses / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / 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 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling
Similarity search - Function
Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family ...Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / 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
PHOSPHATE ION / Ubiquitin-ribosomal protein eL40 fusion protein / Uncharacterized protein DKFZp434K0435
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.784 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 12, 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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8142
Polymers8,7191
Non-polymers951
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.197, 43.197, 79.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

21A-265-

HOH

31A-288-

HOH

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Components

#1: Protein Ubiquitin / / Protein DKFZp434K0435


Mass: 8718.974 Da / Num. of mol.: 1 / Fragment: UNP residues 87-162 / Mutation: T7C, I13N, I36Y, L69C, L71R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp434K0435, Ubiquitin / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UFQ0, UniProt: P62987*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 2.4M 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: Saturn 944 / Detector: CCD / Date: Feb 29, 2012
RadiationProtocol: SINGLE / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.78→43.197 Å / Num. all: 7483 / Num. obs: 7483 / % possible obs: 98.2 % / Redundancy: 12.8 % / Biso Wilson estimate: 12.5 Å2 / Rsym value: 0.095 / Net I/σ(I): 22.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.78-1.889.60.383293479750.38391.4
1.88-1.9913.40.2782.8133229940.27898.6
1.99-2.1313.50.1774.4129119590.17798.8
2.13-2.313.40.1465.3119428920.14699.3
2.3-2.5213.60.1226.3112968280.12299.5
2.52-2.8213.40.17.6104217750.199.8
2.82-3.2613.50.07110.491936820.07199.9
3.26-3.99130.0561377055930.056100
3.99-5.6412.60.04315.961094860.043100
5.64-43.19710.80.04814.132432990.04899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UBQ

1ubq


Resolution: 1.784→37.918 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.24 / Cross valid method: Random / σ(F): 1.37 / Phase error: 20.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 345 4.63 %
Rwork0.1835 --
obs0.1851 7457 97.73 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.903 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso max: 50.95 Å2 / Biso mean: 15.1537 Å2 / Biso min: 2.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.2088 Å20 Å2-0 Å2
2---0.2088 Å20 Å2
3---0.4177 Å2
Refinement stepCycle: LAST / Resolution: 1.784→37.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms609 0 5 88 702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012608
X-RAY DIFFRACTIONf_angle_d1.386815
X-RAY DIFFRACTIONf_chiral_restr0.09793
X-RAY DIFFRACTIONf_plane_restr0.006106
X-RAY DIFFRACTIONf_dihedral_angle_d17.355241
LS refinement shellResolution: 1.784→2.2476 Å / Total num. of bins used: 2
RfactorNum. reflection% reflection
Rfree0.229 166 -
Rwork0.1691 3391 -
all-3557 -
obs--96 %
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)
10.70970.11980.2050.645-0.22471.07990.0518-0.09250.05760.1697-0.0430.10520.0158-0.06540.01150.0992-0.0232-0.00960.04990.01180.05815.333-3.83797.0186
21.6962-1.04320.00912.62452.23142.93340.05920.04850.1313-0.081-0.0102-0.0778-0.11840.0827-0.03890.0452-0.0028-0.02070.04140.01420.07198.3494.30845.294
35.44730.7911-2.35471.67771.48853.31160.24740.115-0.0569-0.0051-0.0208-0.1155-0.1706-0.029-0.19320.08920.0138-0.00750.0589-0.0010.060514.24056.18939.9774
40.79840.4768-0.76373.99260.33561.53540.0612-0.25520.13550.03340.2229-0.3719-0.05570.2616-0.06330.05070.0071-0.01770.0884-0.0010.152718.8301-3.51625.3897
52.49620.9181-0.89762.1411-1.00022.29650.08310.1485-0.3485-0.0359-0.0665-0.35370.0879-0.00130.03190.0784-0.02010.0050.0702-0.01460.082911.8738-6.9215-1.7919
60.8717-0.4048-0.70791.58060.70762.14940.0936-0.14020.3217-0.07930.0198-0.2111-0.18250.32860.12640.0415-0.0168-0.03240.02720.02130.08715.2611-2.781312.9256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:22)A1 - 22
2X-RAY DIFFRACTION2chain 'A' and (resseq 23:34)A23 - 34
3X-RAY DIFFRACTION3chain 'A' and (resseq 35:39)A35 - 39
4X-RAY DIFFRACTION4chain 'A' and (resseq 40:49)A40 - 49
5X-RAY DIFFRACTION5chain 'A' and (resseq 50:65)A50 - 65
6X-RAY DIFFRACTION6chain 'A' and (resseq 66:73)A66 - 73

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