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- PDB-6tuv: Crystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin -

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Basic information

Entry
Database: PDB / ID: 6tuv
TitleCrystal structure of Mindy1 in complex with Lys48 linked di-ubiquitin
Components
  • Polyubiquitin-C
  • Ubiquitin carboxyl-terminal hydrolase MINDY-1
KeywordsHYDROLASE / CYSTEINE PROTEASE / ISOPEPTIDASE AND UBIQUITIN BINDING
Function / homology
Function and homology information


cysteine-type carboxypeptidase activity / K48-linked deubiquitinase activity / K48-linked polyubiquitin modification-dependent protein binding / 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 ...cysteine-type carboxypeptidase activity / K48-linked deubiquitinase activity / K48-linked polyubiquitin modification-dependent protein binding / 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 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / 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 / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / 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
Similarity search - Function
MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family ...MINDY deubiquitinase / MINDY deubiquitinase domain / MINDY deubiquitinase / 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
Polyubiquitin-C / Ubiquitin carboxyl-terminal hydrolase MINDY-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å
AuthorsAbdul Rehman, S.A. / Kulathu, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_12016/6 United Kingdom
European Research Council (ERC)677623 United Kingdom
CitationJournal: Mol.Cell / Year: 2021
Title: Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.
Authors: Abdul Rehman, S.A. / Armstrong, L.A. / Lange, S.M. / Kristariyanto, Y.A. / Grawert, T.W. / Knebel, A. / Svergun, D.I. / Kulathu, Y.
History
DepositionJan 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 3, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase MINDY-1
H: Polyubiquitin-C
D: Polyubiquitin-C
L: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8335
Polymers57,7374
Non-polymers961
Water1,874104
1
A: Ubiquitin carboxyl-terminal hydrolase MINDY-1
H: Polyubiquitin-C
D: Polyubiquitin-C
hetero molecules


  • defined by author
  • Evidence: SAXS, Mindy1 and Mindy2 both are structurally identical. The SAXS measurements for Mindy2-Lys48 linked di-ubiquitin complex show it to be a dimer which consists of one molecule of Mindy2 ...Evidence: SAXS, Mindy1 and Mindy2 both are structurally identical. The SAXS measurements for Mindy2-Lys48 linked di-ubiquitin complex show it to be a dimer which consists of one molecule of Mindy2 and one polymer of ubiquitin (the individual chain of ubiquitin are covalently linked and are considered as a single molecule). This observation from MIndy2-Lys48 linked di-ubiquitin can be extrapolated onto Mindy1-Lys48 linked di-ubiquitin complex. Moreover, the structure-based mutational studies have validated the complex observed in the crystal structure.
  • 49.3 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)49,2564
Polymers49,1603
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)8,5771
Polymers8,5771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.862, 73.862, 202.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase MINDY-1 / Deubiquitinating enzyme MINDY-1 / Protein FAM63A


Mass: 32006.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MINDY1, FAM63A, KIAA1390 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N5J2, ubiquitinyl hydrolase 1
#2: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris-HCl, 200mM LiSO4.H2O, 30% PEG400 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.939274 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939274 Å / Relative weight: 1
ReflectionResolution: 2.16→41.81 Å / Num. obs: 31102 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Net I/σ(I): 13.9 / Num. measured all: 212300 / Scaling rejects: 908
Reflection shellResolution: 2.16→2.23 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2629 / CC1/2: 0.889 / Rpim(I) all: 0.378 / Rrim(I) all: 1.028 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JKN, 1UBQ

5jkn

1ubq


Resolution: 2.16→41.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.19 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.19
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1517 4.9 %RANDOM
Rwork0.2075 ---
obs0.2096 29517 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 161.11 Å2 / Biso mean: 49.244 Å2 / Biso min: 25.68 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å20 Å20 Å2
2--2.18 Å20 Å2
3----4.37 Å2
Refinement stepCycle: final / Resolution: 2.16→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3451 0 5 104 3560
Biso mean--58.2 48.14 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133516
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173263
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.644775
X-RAY DIFFRACTIONr_angle_other_deg1.2631.5757578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3195441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47324.099161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09615598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7791513
X-RAY DIFFRACTIONr_chiral_restr0.0650.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023867
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
LS refinement shellResolution: 2.16→2.216 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 112 -
Rwork0.278 2115 -
all-2227 -
obs--99.87 %

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