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- PDB-3mtn: Usp21 in complex with a ubiquitin-based, USP21-specific inhibitor -

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Basic information

Entry
Database: PDB / ID: 3mtn
TitleUsp21 in complex with a ubiquitin-based, USP21-specific inhibitor
Components
  • UBIQUITIN VARIANT UBV.21.4
  • Ubiquitin carboxyl-terminal hydrolase 21
KeywordsHYDROLASE / UBIQUITIN-SPECIFIC PROTEASE ACTIVITY / UBIQUITIN BIOLOGY / STRUCTURAL GENOMICS CONSORTIUM / SGC / ACTIVATOR / CHROMATIN REGULATOR / NUCLEUS / PROTEASE / THIOL PROTEASE / TRANSCRIPTION / TRANSCRIPTION REGULATION / UBL CONJUGATION PATHWAY / ISOPEPTIDE BOND / PHOSPHOPROTEIN / INHIBITOR
Function / homology
Function and homology information


: / : / protein modification process => GO:0036211 / deNEDDylase activity / TNFR1-induced proapoptotic signaling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane ...: / : / protein modification process => GO:0036211 / deNEDDylase activity / TNFR1-induced proapoptotic signaling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / protein deubiquitination / 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) / 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 / cytosolic ribosome / 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 / cysteine-type peptidase activity / 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 / transcription initiation-coupled chromatin remodeling / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Regulation of BACH1 activity / Activated NOTCH1 Transmits Signal to the Nucleus / 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 / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / 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 / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / 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 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Negative regulation of FGFR3 signaling / Degradation of DVL / Fanconi Anemia Pathway
Similarity search - Function
: / 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. / Cysteine proteinases / Cathepsin B; Chain A ...: / 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. / Cysteine proteinases / Cathepsin B; Chain A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / 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 Complex / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / Ubiquitin-60S ribosomal protein L40 / Ubiquitin carboxyl-terminal hydrolase 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Li, Y. / Ernst, A. / Sidhu, S. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Li, Y. / Ernst, A. / Sidhu, S. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: Science / Year: 2013
Title: A strategy for modulation of enzymes in the ubiquitin system.
Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / ...Authors: Ernst, A. / Avvakumov, G. / Tong, J. / Fan, Y. / Zhao, Y. / Alberts, P. / Persaud, A. / Walker, J.R. / Neculai, A.M. / Neculai, D. / Vorobyov, A. / Garg, P. / Beatty, L. / Chan, P.K. / Juang, Y.C. / Landry, M.C. / Yeh, C. / Zeqiraj, E. / Karamboulas, K. / Allali-Hassani, A. / Vedadi, M. / Tyers, M. / Moffat, J. / Sicheri, F. / Pelletier, L. / Durocher, D. / Raught, B. / Rotin, D. / Yang, J. / Moran, M.F. / Dhe-Paganon, S. / Sidhu, S.S.
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 27, 2013Group: Database references
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_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 carboxyl-terminal hydrolase 21
B: UBIQUITIN VARIANT UBV.21.4
C: Ubiquitin carboxyl-terminal hydrolase 21
D: UBIQUITIN VARIANT UBV.21.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04312
Polymers102,5874
Non-polymers4578
Water77543
1
A: Ubiquitin carboxyl-terminal hydrolase 21
B: UBIQUITIN VARIANT UBV.21.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5577
Polymers51,2932
Non-polymers2645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-44 kcal/mol
Surface area17240 Å2
MethodPISA
2
C: Ubiquitin carboxyl-terminal hydrolase 21
D: UBIQUITIN VARIANT UBV.21.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4865
Polymers51,2932
Non-polymers1933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-30 kcal/mol
Surface area17310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.065, 58.235, 133.596
Angle α, β, γ (deg.)90.00, 121.19, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
/ NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Ubiquitin carboxyl-terminal hydrolase 21 / Ubiquitin thioesterase 21 / Ubiquitin-specific-processing protease 21 / Deubiquitinating enzyme 21


Mass: 41981.668 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN: UNP RESIDUES 209-562 / Mutation: T64G, P68H, L70V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PP1490, USP21, USP23 / Plasmid: PET28ALIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UK80, EC: 3.1.2.15
#2: Protein UBIQUITIN VARIANT UBV.21.4 / UBA80 / UBCEP1


Mass: 9311.595 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This is a triple mutant of ubiquitin. / Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA52, UBA80, UBB, UBC, UBCEP1, UBCEP2, UBQ / Plasmid: PET28ALIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P62988, UniProt: P0CG48*PLUS

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Non-polymers , 4 types, 51 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.16 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 11% PEG 4000, 0.1 M SODIUM CITRATE, 0.1 M AMMONIUM ACETATE, 5 MM TCEP, PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 28, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 31000 / Num. obs: 31000 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.112 / Net I/σ(I): 12.64
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.08 / Rsym value: 0.659 / % possible all: 95.4

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I3T

3i3t


Resolution: 2.7→19.61 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.874 / SU B: 30.542 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27291 1553 5 %RANDOM
Rwork0.2177 ---
obs0.22042 29294 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.866 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.02 Å2
2--0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6255 0 18 43 6316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226431
X-RAY DIFFRACTIONr_angle_refined_deg1.1971.968658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.07122.952315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.968151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1381564
X-RAY DIFFRACTIONr_chiral_restr0.0770.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214876
X-RAY DIFFRACTIONr_mcbond_it0.3761.53907
X-RAY DIFFRACTIONr_mcangle_it0.72426284
X-RAY DIFFRACTIONr_scbond_it1.02132524
X-RAY DIFFRACTIONr_scangle_it1.7354.52374
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2465medium positional0.330.5
22A607medium positional0.260.5
11B2465medium thermal0.332
22B607medium thermal0.252
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 98 -
Rwork0.344 2133 -
obs--99.51 %
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)
11.89730.14240.6611.4784-0.51532.9553-0.00820.278-0.0925-0.03810.0819-0.02860.0009-0.0004-0.07370.00920.00350.02670.1227-0.06960.1633-15.3829-13.5947.6249
25.5508-0.4055-2.53471.5466-0.69874.59660.040.52590.0596-0.3251-0.0463-0.2445-0.20210.01830.00630.1277-0.02550.02950.1816-0.03280.1538-5.8129-5.036633.7721
31.7921-0.34030.02931.78070.17463.40.11670.34660.1559-0.4022-0.1837-0.2180.1110.17080.06690.23270.07940.04710.16190.10530.193926.4371-14.435929.5102
43.5468-0.60510.53341.9118-0.9285.91560.25970.7142-0.1046-0.7592-0.47010.36580.6285-0.69560.21050.52580.1079-0.05380.4162-0.11830.207813.9494-23.032518.4534
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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