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- PDB-2knb: Solution NMR structure of the parkin Ubl domain in complex with t... -

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Basic information

Entry
Database: PDB / ID: 2knb
TitleSolution NMR structure of the parkin Ubl domain in complex with the endophilin-A1 SH3 domain
Components
  • E3 ubiquitin-protein ligase parkin
  • Endophilin-A1
KeywordsPROTEIN BINDING / Ubl / SH3 / parkin / endophilin / Cell junction / Cell membrane / Cell projection / Endoplasmic reticulum / Ligase / Membrane / Metal-binding / Nucleus / Postsynaptic cell membrane / S-nitrosylation / Synapse / Ubl conjugation pathway / Zinc-finger / Endocytosis / Lipid-binding / Phosphoprotein / SH3 domain
Function / homology
Function and homology information


Negative regulation of MET activity / Josephin domain DUBs / membrane bending / Regulation of necroptotic cell death / Aggrephagy / EGFR downregulation / positive regulation of membrane tubulation / PINK1-PRKN Mediated Mitophagy / cellular response to L-glutamine / lipid tube assembly ...Negative regulation of MET activity / Josephin domain DUBs / membrane bending / Regulation of necroptotic cell death / Aggrephagy / EGFR downregulation / positive regulation of membrane tubulation / PINK1-PRKN Mediated Mitophagy / cellular response to L-glutamine / lipid tube assembly / positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / membrane tubulation / postsynaptic actin cytoskeleton organization / vesicle scission / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / regulation of clathrin-dependent endocytosis / basal dendrite / response to curcumin / negative regulation of exosomal secretion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / Retrograde neurotrophin signalling / cellular response to hydrogen sulfide / type 2 mitophagy / negative regulation of blood-brain barrier permeability / Lysosome Vesicle Biogenesis / negative regulation of actin filament bundle assembly / dendrite extension / regulation of receptor internalization / Golgi Associated Vesicle Biogenesis / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / MHC class II antigen presentation / positive regulation of protein linear polyubiquitination / negative regulation by host of viral genome replication / positive regulation of mitophagy / RBR-type E3 ubiquitin transferase / mitochondrial fragmentation involved in apoptotic process / F-box domain binding / positive regulation of mitochondrial fusion / mitochondrion localization / photoreceptor ribbon synapse / regulation of cellular response to oxidative stress / negative regulation of excitatory postsynaptic potential / Recycling pathway of L1 / regulation of dopamine metabolic process / Cargo recognition for clathrin-mediated endocytosis / regulation of neurotransmitter secretion / Clathrin-mediated endocytosis / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / dopaminergic synapse / positive regulation of dendrite extension / protein K6-linked ubiquitination / positive regulation of protein localization to membrane / cellular response to L-glutamate / autophagy of mitochondrion / norepinephrine metabolic process / cellular response to toxic substance / positive regulation of type 2 mitophagy / protein localization to mitochondrion / positive regulation of proteasomal protein catabolic process / synaptic transmission, dopaminergic / negative regulation of JNK cascade / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of synaptic transmission, glutamatergic / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / aggresome assembly / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / positive regulation of mitochondrial membrane potential / aggresome / regulation of reactive oxygen species metabolic process / response to corticosterone / positive regulation of mitochondrial fission / positive regulation of ATP biosynthetic process / response to muscle activity / dopamine uptake involved in synaptic transmission / intracellular vesicle / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / startle response / dopamine metabolic process / phospholipase binding / regulation of synaptic vesicle endocytosis / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / positive regulation of insulin secretion involved in cellular response to glucose stimulus / synaptic vesicle endocytosis / protein K63-linked ubiquitination / negative regulation of mitochondrial fission / protein monoubiquitination / regulation of protein ubiquitination
Similarity search - Function
Endophilin-A, SH3 domain / : / 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 ...Endophilin-A, SH3 domain / : / 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 / BAR domain / BAR domain profile. / BAR / : / BAR domain / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / AH/BAR domain superfamily / SH3 Domains / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Endophilin-A1 / E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsTrempe, J. / Guennadi, K. / Edna, C.M. / Kalle, G.
CitationJournal: Mol.Cell / Year: 2009
Title: SH3 domains from a subset of BAR proteins define a Ubl-binding domain and implicate parkin in synaptic ubiquitination.
Authors: Trempe, J.F. / Chen, C.X. / Grenier, K. / Camacho, E.M. / Kozlov, G. / McPherson, P.S. / Gehring, K. / Fon, E.A.
History
DepositionAug 20, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase parkin
B: Endophilin-A1


Theoretical massNumber of molelcules
Total (without water)17,1312
Polymers17,1312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 9149.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Park2, Prkn / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21 DE3
References: UniProt: Q9JK66, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Endophilin-A1 / Endophilin-1 / SH3 domain-containing GRB2-like protein 2 / SH3 domain protein 2A / SH3p4


Mass: 7981.790 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sh3gl2, Sh3d2a, Sh3p4 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21 DE3 / References: UniProt: O35179

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D CBCA(CO)NH
1233D HN(CA)CB
1343D CBCA(CO)NH
1443D HN(CA)CB
1532D 1H-15N HSQC
1642D 1H-15N HSQC
1713D (H)CCH-COSY
1823D (H)CCH-COSY
1913D 1H-13C NOESY
11023D 1H-13C NOESY
11112D 1H-13C HSQC
11222D 1H-13C HSQC
11352D 1H-15N IPAP-HSQC
11462D 1H-15N IPAP-HSQC
11552D 1H-15N IPAP-HSQC
11662D 1H-15N IPAP-HSQC
11713D 1H-13C NOESY coupled
11823D 1H-13C NOESY coupled

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM [U-99% 13C; U-99% 15N] Ubl, 1.2 mM SH3, 100% D2O100% D2O
21.2 mM [U-99% 13C; U-99% 15N] SH3, 1.2 mM Ubl, 100% D2O100% D2O
30.8 mM [U-99% 13C; U-99% 15N] Ubl, 1.6 mM SH3, 95% H2O/5% D2O95% H2O/5% D2O
40.8 mM [U-99% 13C; U-99% 15N] SH3, 1.6 mM Ubl, 95% H2O/5% D2O95% H2O/5% D2O
50.8 mM [U-99% 15N] Ubl, 1.6 mM SH3, 95% H2O/5% D2O95% H2O/5% D2O
60.8 mM [U-99% 15N] SH3, 1.6 mM Ubl, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMUbl[U-99% 13C; U-99% 15N]1
1.2 mMSH31
1.2 mMSH3[U-99% 13C; U-99% 15N]2
1.2 mMUbl2
0.8 mMUbl[U-99% 13C; U-99% 15N]3
1.6 mMSH33
0.8 mMSH3[U-99% 13C; U-99% 15N]4
1.6 mMUbl4
0.8 mMUbl[U-99% 15N]5
1.6 mMSH35
0.8 mMSH3[U-99% 15N]6
1.6 mMUbl6
Sample conditionsIonic strength: 50 / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.5Delaglio, F. et al.processing
Sparky3.115Goddard, T. et al.chemical shift assignment
Sparky3.115Goddard, T. et al.peak picking
CNS1.2Brunger, A. et al.structure solution
CNS1.2Brunger, A. et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: HADDOCK used to dock Ubl and SH3 crystal structures using intermolecular NOEs and RDCs
NMR constraintsNOE constraints total: 64 / NOE intraresidue total count: 6 / NOE long range total count: 36 / NOE medium range total count: 2 / NOE sequential total count: 20 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 1 / Protein phi angle constraints total count: 71 / Protein psi angle constraints total count: 71
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å
NMR ensemble rmsDistance rms dev: 0.02 Å

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