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- PDB-4nql: The crystal structure of the DUB domain of AMSH orthologue, Sst2 ... -

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Basic information

Entry
Database: PDB / ID: 4nql
TitleThe crystal structure of the DUB domain of AMSH orthologue, Sst2 from S. pombe, in complex with lysine 63-linked diubiquitin
Components
  • (Ubiquitin) x 2
  • AMSH-like protease sst2
KeywordsHYDROLASE/PROTEIN BINDING / JAMM domain / Zinc metalloprotease / protein complex / AMSH / heix-beta-helix sandwich / hydrolase / metal binding / K63-linked diubiquitin / Helix-beta-helix sandwich / Deubiquitinase / Ubiquitin / Hse1 / cytosol / endosome / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


Metalloprotease DUBs / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription ...Metalloprotease DUBs / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / cytoplasm to vacuole targeting by the NVT pathway / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of innate immune responses to cytosolic DNA / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / Dual Incision in GG-NER / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TNFR1-induced NF-kappa-B signaling pathway / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / Dual incision in TC-NER / Inactivation of CSF3 (G-CSF) signaling / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Oncogene Induced Senescence / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Regulation of TNFR1 signaling / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / IKK complex recruitment mediated by RIP1 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Degradation of AXIN / Asymmetric localization of PCP proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Regulation of RUNX3 expression and activity / Deactivation of the beta-catenin transactivating complex / Regulation of RAS by GAPs / Ovarian tumor domain proteases / Regulation of PTEN stability and activity / Cyclin D associated events in G1
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRonau, J.A. / Shrestha, R.K. / Das, C.
CitationJournal: Biochemistry / Year: 2014
Title: Insights into the mechanism of deubiquitination by JAMM deubiquitinases from cocrystal structures of the enzyme with the substrate and product.
Authors: Shrestha, R.K. / Ronau, J.A. / Davies, C.W. / Guenette, R.G. / Strieter, E.R. / Paul, L.N. / Das, C.
History
DepositionNov 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.2Jan 10, 2024Group: Derived calculations / Category: struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMSH-like protease sst2
B: Ubiquitin
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,45811
Polymers41,9583
Non-polymers5008
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.489, 56.740, 135.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein AMSH-like protease sst2 / Suppressor of ste12 deletion protein 2


Mass: 24660.975 Da / Num. of mol.: 1 / Fragment: UNP residues 221-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC19B12.10, sst2 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein Ubiquitin / Ubiquitin / Ubiquitin-related 1 / Ubiquitin-related 2


Mass: 8604.845 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: K63R mutation / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubc / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P0CG50
#3: Protein Ubiquitin / Ubiquitin / Ubiquitin-related 1 / Ubiquitin-related 2


Mass: 8691.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: D77 Mutant / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ubc / Plasmid: pET26B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P0CG50

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Non-polymers , 3 types, 56 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.26 Å3/Da / Density % sol: 45.59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→60 Å / Num. all: 17629 / Num. obs: 17629 / % possible obs: 100 % / Observed criterion σ(F): 4.1 / Observed criterion σ(I): 4.1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value
2.3-2.346.70.5494.18640.549
2.34-2.386.80.5064.58640.506
2.38-2.436.80.45858610.458

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model generated from PDB Entries 4MSQ (Sst2) and 2ZNV (diubiquitin)

4msq

2znv


Resolution: 2.3→46.47 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.002 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26333 889 5.1 %RANDOM
Rwork0.21344 ---
all0.21344 16697 --
obs0.21587 16689 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.916 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 29 48 2470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192461
X-RAY DIFFRACTIONr_bond_other_d0.0010.022459
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9743320
X-RAY DIFFRACTIONr_angle_other_deg0.6683.0015656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5735307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02624.42195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51115430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9961511
X-RAY DIFFRACTIONr_chiral_restr0.0640.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02521
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 73 -
Rwork0.202 1206 -
obs--99.61 %
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)
11.3737-0.2382-0.01271.1197-0.13091.16410.028-0.1243-0.00070.0337-0.05140.0457-0.0035-0.00350.02340.0027-0.00990.00240.07580.02130.035921.22157.866723.3868
210.4275-1.8975-6.64133.50491.35728.1659-0.2421-0.2783-0.03820.36070.08540.11690.10360.3160.15670.0542-0.0072-0.02780.11130.02440.101741.6812.455114.1186
316.35130.55130.54668.738-3.3397.9025-0.03080.6104-0.6640.02790.2222-0.0808-0.19180.153-0.19140.03940.02360.02350.0603-0.01840.047242.755112.2860.4536
42.54931.0463-0.386811.95850.14474.5924-0.137-0.01520.00130.0316-0.0998-0.37840.22850.05450.23680.0188-0.0060.01250.0788-0.00310.046334.18477.90397.4452
56.55210.01070.65272.4213-0.082310.74790.13470.04760.2663-0.0188-0.05540.1564-0.428-0.2762-0.07930.02480.02280.02360.03830.03610.098937.636621.17232.9758
616.27673.3775-2.8641.9014-0.73191.58950.24360.10050.40640.1117-0.10210.08-0.0420.0703-0.14150.02850.0011-0.01010.05320.02220.049134.072814.781611.275
717.656-2.56030.01689.7192-3.67832.08410.71571.3621-0.9917-0.6016-0.4930.7030.55380.0978-0.22280.27190.0453-0.08230.3501-0.16350.28114.0234-3.71045.9265
83.2203-0.1493-2.20831.53841.78053.37130.16590.2981-1.47120.6488-0.4033-0.23410.4054-0.29270.23740.6331-0.1951-0.3940.49330.00291.5712-3.3371-10.53878.721
92.58451.1842.214713.4395-4.42624.43550.6634-0.1669-1.10090.27930.41350.66080.5062-0.4084-1.07690.2488-0.0284-0.22220.4167-0.03710.97021.8642-5.496412.2012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A248 - 434
2X-RAY DIFFRACTION2B1 - 15
3X-RAY DIFFRACTION3B16 - 25
4X-RAY DIFFRACTION4B26 - 43
5X-RAY DIFFRACTION5B44 - 61
6X-RAY DIFFRACTION6B62 - 76
7X-RAY DIFFRACTION7C1 - 23
8X-RAY DIFFRACTION8C24 - 54
9X-RAY DIFFRACTION9C55 - 69

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