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- PDB-5jqs: Crystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5jqs
TitleCrystal structure of deubiquitinase MINDY-1 in complex with Ubiquitin
Components
  • Protein FAM63A
  • Ubiquitin-40S ribosomal protein S27a
KeywordsHYDROLASE / Cysteine protease / isopeptidase and Ubiquitin binding
Function / homology
Function and homology information


cysteine-type carboxypeptidase activity / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling ...cysteine-type carboxypeptidase activity / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Negative regulation of FLT3 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of pyruvate metabolism / SCF-beta-TrCP mediated degradation of Emi1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Ovarian tumor domain proteases / Cyclin D associated events in G1 / Regulation of BACH1 activity / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Formation of Incision Complex in GG-NER / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Inactivation of CSF3 (G-CSF) signaling / Termination of translesion DNA synthesis / Iron uptake and transport / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex
Similarity search - Function
MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site ...MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / 1,4-DIETHYLENE DIOXIDE / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin carboxyl-terminal hydrolase MINDY-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsAbdul Rehman, S.A. / Kulathu, Y.
CitationJournal: Mol.Cell / Year: 2016
Title: MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes.
Authors: Abdul Rehman, S.A. / Kristariyanto, Y.A. / Choi, S.Y. / Nkosi, P.J. / Weidlich, S. / Labib, K. / Hofmann, K. / Kulathu, Y.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Feb 7, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein FAM63A
D: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0848
Polymers40,6152
Non-polymers4696
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-35 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.336, 82.336, 332.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Protein FAM63A


Mass: 32038.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM63A, KIAA1390 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N5J2
#2: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell: Erythrocytes / Gene: RPS27A, UBA80, UBCEP1 / Production host: Bos taurus (domestic cattle) / References: UniProt: P62992

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Non-polymers , 5 types, 59 molecules

#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 4 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100mM MES, 10% Dioxane and 1.6 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 10, 2015
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.65→48.63 Å / Num. obs: 20518 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.1
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 10 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKN

5jkn


Resolution: 2.65→48.63 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2309 1076 5.27 %
Rwork0.2053 --
obs0.2067 20406 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 26 53 2588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083166
X-RAY DIFFRACTIONf_angle_d1.1044309
X-RAY DIFFRACTIONf_dihedral_angle_d14.6591130
X-RAY DIFFRACTIONf_chiral_restr0.046510
X-RAY DIFFRACTIONf_plane_restr0.005547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.77060.32321220.26922334X-RAY DIFFRACTION100
2.7706-2.91670.27431290.23762357X-RAY DIFFRACTION100
2.9167-3.09940.34161240.23422362X-RAY DIFFRACTION100
3.0994-3.33860.29211330.22822369X-RAY DIFFRACTION100
3.3386-3.67450.21371290.19632391X-RAY DIFFRACTION100
3.6745-4.20590.2031610.16852404X-RAY DIFFRACTION100
4.2059-5.2980.18681410.16912456X-RAY DIFFRACTION100
5.298-48.6380.22791370.23122657X-RAY DIFFRACTION99

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