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- PDB-6djx: Crystal Structure of pParkin-pUb-UbcH7 complex -

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Basic information

Entry
Database: PDB / ID: 6djx
TitleCrystal Structure of pParkin-pUb-UbcH7 complex
Components
  • RBR-type E3 ubiquitin transferase,RBR-type E3 ubiquitin transferase
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 L3
KeywordsTRANSFERASE / Ubiquitin / E3 ligase / E2 conjugating enzyme / phosphorylation / mitophagy / Parkinson disease
Function / homology
Function and homology information


positive regulation of metabolic process / 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 ...positive regulation of metabolic process / 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 / Formation of Incision Complex in GG-NER / 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 / Termination of translesion DNA synthesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Ovarian tumor domain proteases / Cyclin D associated events in G1 / Negative regulators of DDX58/IFIH1 signaling / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Inactivation of CSF3 (G-CSF) signaling / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / DNA Damage Recognition in GG-NER
Similarity search - Function
E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / : / : / : / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / IBR domain / E3 ubiquitin ligase RBR family ...E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / : / : / : / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / IBR domain / E3 ubiquitin ligase RBR family / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / 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 / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin / Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin-conjugating enzyme E2 L3
Similarity search - Component
Biological speciesBactrocera dorsalis (oriental fruit fly)
Homo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.801 Å
AuthorsSauve, V. / Sung, G. / Trempe, J.F. / Gehring, K.
Funding support Canada, United States, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-125924 Canada
Michael J. Fox Foundation12144 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Mechanism of parkin activation by phosphorylation.
Authors: Sauve, V. / Sung, G. / Soya, N. / Kozlov, G. / Blaimschein, N. / Miotto, L.S. / Trempe, J.F. / Lukacs, G.L. / Gehring, K.
History
DepositionMay 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RBR-type E3 ubiquitin transferase,RBR-type E3 ubiquitin transferase
B: Ubiquitin
C: Ubiquitin-conjugating enzyme E2 L3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1229
Polymers75,7293
Non-polymers3926
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-28 kcal/mol
Surface area30660 Å2
Unit cell
Length a, b, c (Å)135.669, 135.669, 87.993
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RBR-type E3 ubiquitin transferase,RBR-type E3 ubiquitin transferase / Parkin


Mass: 48745.352 Da / Num. of mol.: 1 / Fragment: UNP residues 29-109,155-496 / Mutation: C463A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bactrocera dorsalis (oriental fruit fly)
Gene: PRKN2 / Plasmid: pGEX-6p1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A034W4L8, RBR-type E3 ubiquitin transferase
#2: Protein Ubiquitin


Mass: 8656.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P62992
#3: Protein Ubiquitin-conjugating enzyme E2 L3 / E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin- ...E2 ubiquitin-conjugating enzyme L3 / L-UBC / UbcH7 / Ubiquitin carrier protein L3 / Ubiquitin-conjugating enzyme E2-F1 / Ubiquitin-protein ligase L3


Mass: 18327.082 Da / Num. of mol.: 1 / Mutation: C86K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2L3, UBCE7, UBCH7 / Plasmid: pGEX-6p1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P68036, E2 ubiquitin-conjugating enzyme
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M HEPES, pH 6.5, 6% isopropanol, 50 mM magnesium chloride, 5% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.238 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.238 Å / Relative weight: 1
ReflectionResolution: 4.8→48.84 Å / Num. obs: 4791 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 233.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible allRpim(I) allRrim(I) all
4.8-4.9710.10.6214.34670.879100
10.73-48.867.60.0464680.99999.10.0170.049

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASER2.8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 5N2W & 1C4Z

5n2w

1c4z


Resolution: 4.801→48.858 Å / SU ML: 0.76 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 38.24
RfactorNum. reflection% reflection
Rfree0.2898 239 5 %
Rwork0.2569 --
obs0.2585 4778 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 545.59 Å2 / Biso mean: 299.5883 Å2 / Biso min: 192.96 Å2
Refinement stepCycle: final / Resolution: 4.801→48.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 6 0 4346
Biso mean--311.84 --
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044458
X-RAY DIFFRACTIONf_angle_d0.7656026
X-RAY DIFFRACTIONf_chiral_restr0.03650
X-RAY DIFFRACTIONf_plane_restr0.004782
X-RAY DIFFRACTIONf_dihedral_angle_d10.9451703
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.8015-5.49550.37591490.329328132962100
5.4955-6.92060.35571510.333427932944100
6.9206-48.86080.25181510.21662773292499
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)
11.56451.27080.51067.00890.13620.04970.0687-0.2982-0.0021-1.06980.13820.26420.0479-0.3646-0.00022.76020.1104-0.18992.81130.27882.491641.61916.59697.5346
21.07741.767-1.29332.7109-0.18870.954-0.1707-0.65320.8365-0.8344-0.149-0.4981-1.1533-3.2031-0.00154.09251.02720.62513.2162-0.58413.276828.89133.742931.6824
33.18083.1704-1.47635.31043.4169.47950.19671.6699-0.41921.1190.6553-0.1772-0.2367-1.07570.00071.99760.04060.08972.52120.02152.481328.865811.347622.9891
43.06353.0601-0.31358.2726-4.04683.29170.03320.2561-0.0996-0.4224-0.57860.0629-0.04190.6508-0.00012.18870.09630.15472.59380.15742.345870.058539.29963.9774
52.88961.8844-0.48333.7517-2.71840.4931-0.8695-0.5550.4706-1.3363-0.6949-0.9362.14310.7158-0.0014.1126-0.12340.36482.0511-0.25142.254939.4551-23.63136.363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resid 172 through 363 ) or (resid 1001 through 1004))A0
2X-RAY DIFFRACTION2chain 'A' and ((resid 364 through 410 ) or (resid 1005 through 1006))A0
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 74 )B1 - 74
4X-RAY DIFFRACTION4chain 'C' and (resid 0 through 152 )C0 - 152
5X-RAY DIFFRACTION5chain 'A' and (resid 25 through 102 )A25 - 102

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