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- PDB-6rya: Structure of Dup1 mutant H67A:Ubiquitin complex -

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Basic information

Entry
Database: PDB / ID: 6rya
TitleStructure of Dup1 mutant H67A:Ubiquitin complex
Components
  • Polyubiquitin-C
  • Septation initiation protein
KeywordsCELL INVASION / Legionella pneumophila / deubiquitinase / Phosphoribose ubiquitination / TOXIN
Function / homology
Function and homology information


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 ...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 / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / 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 / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / 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 / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / 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 / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation / Negative regulation of NOTCH4 signaling / Negative regulation of FGFR1 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Vif-mediated degradation of APOBEC3G
Similarity search - Function
SidE, PDE domain / SidE phosphodiesterase (PDE) domain / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Septation initiation protein / Polyubiquitin-C
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsDonghyuk, S. / Ivan, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB1177 Germany
German Research FoundationSFB902 Germany
CitationJournal: Mol.Cell / Year: 2020
Title: Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB.
Authors: Shin, D. / Mukherjee, R. / Liu, Y. / Gonzalez, A. / Bonn, F. / Liu, Y. / Rogov, V.V. / Heinz, M. / Stolz, A. / Hummer, G. / Dotsch, V. / Luo, Z.Q. / Bhogaraju, S. / Dikic, I.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Septation initiation protein
B: Polyubiquitin-C
C: Septation initiation protein
D: Polyubiquitin-C
E: Septation initiation protein
F: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)143,0766
Polymers143,0766
Non-polymers00
Water00
1
A: Septation initiation protein
B: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)47,6922
Polymers47,6922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-8 kcal/mol
Surface area16660 Å2
MethodPISA
2
C: Septation initiation protein
D: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)47,6922
Polymers47,6922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-9 kcal/mol
Surface area16630 Å2
MethodPISA
3
E: Septation initiation protein
F: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)47,6922
Polymers47,6922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-9 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.328, 67.136, 182.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVALAA3 - 3101 - 308
21SERSERVALVALCC3 - 3101 - 308
12SERSERVALVALAA3 - 3101 - 308
22SERSERVALVALEE3 - 3101 - 308
13METMETGLYGLYBB1 - 761 - 76
23METMETGLYGLYDD1 - 761 - 76
14METMETGLYGLYBB1 - 761 - 76
24METMETGLYGLYFF1 - 761 - 76
15SERSERVALVALCC3 - 3101 - 308
25SERSERVALVALEE3 - 3101 - 308
16METMETGLYGLYDD1 - 761 - 76
26METMETGLYGLYFF1 - 761 - 76

NCS ensembles :
ID
6
1
2
3
4
5

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Components

#1: Protein Septation initiation protein


Mass: 39115.121 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Gene: D1H98_09620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A6VNK6
#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

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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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20 - 22.5 % PEG 3350/ PEG4000, 100 mM Tris-HCl pH 8.0, 100 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.176
11h,-k,-l20.169
11-1/2H-3/2K, -1/2H+1/2K, -L30.162
11-1/2H+3/2K, 1/2H+1/2K, -L40.167
111/2H-3/2K, -1/2H-1/2K, -L50.159
111/2H+3/2K, 1/2H-1/2K, -L60.167
ReflectionResolution: 2.21→49.07 Å / Num. obs: 68825 / % possible obs: 99.85 % / Redundancy: 2.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.08094 / Rpim(I) all: 0.05954 / Rrim(I) all: 0.101 / Net I/σ(I): 7.28
Reflection shellResolution: 2.21→2.289 Å / Rmerge(I) obs: 0.4521 / Num. unique obs: 7031 / CC1/2: 0.672 / Rpim(I) all: 0.3469 / Rrim(I) all: 0.5725

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B7P

6b7p


Resolution: 2.21→49.07 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.864 / SU B: 4.524 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28877 3328 4.9 %RANDOM
Rwork0.20878 ---
obs0.21265 65182 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.091 Å2
Baniso -1Baniso -2Baniso -3
1-15.11 Å20 Å24.34 Å2
2--0.96 Å2-0 Å2
3----16.07 Å2
Refinement stepCycle: LAST / Resolution: 2.21→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9222 0 0 0 9222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178758
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.64712774
X-RAY DIFFRACTIONr_angle_other_deg1.2191.57820294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75551152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70821.461534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76151653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9041575
X-RAY DIFFRACTIONr_chiral_restr0.0740.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022059
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.25.0874606
X-RAY DIFFRACTIONr_mcbond_other6.1975.0884604
X-RAY DIFFRACTIONr_mcangle_it8.8377.635751
X-RAY DIFFRACTIONr_mcangle_other8.8347.635751
X-RAY DIFFRACTIONr_scbond_it5.0325.134836
X-RAY DIFFRACTIONr_scbond_other5.0325.134836
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1277.6647016
X-RAY DIFFRACTIONr_long_range_B_refined14.52795.66538787
X-RAY DIFFRACTIONr_long_range_B_other14.52895.67238778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99610.13
12C99610.13
21A101080.11
22E101080.11
31B21160.14
32D21160.14
41B21380.14
42F21380.14
51C98820.13
52E98820.13
61D21580.14
62F21580.14
LS refinement shellResolution: 2.207→2.264 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 258 -
Rwork0.21 4565 -
obs--91.15 %

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