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- PDB-2kdi: Solution structure of a Ubiquitin/UIM fusion protein -

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Basic information

Entry
Database: PDB / ID: 2kdi
TitleSolution structure of a Ubiquitin/UIM fusion protein
ComponentsUbiquitin, Vacuolar protein sorting-associated protein 27 fusion protein
KeywordsSIGNALING PROTEIN / Ubiquitin / Ubiquitin Interacting Motif / UIM / protein domain interface / Endosome / Membrane / Metal-binding / Phosphoprotein / Zinc / Zinc-finger
Function / homology
Function and homology information


positive regulation of protein maturation / microlipophagy / ESCRT-0 complex / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling ...positive regulation of protein maturation / microlipophagy / ESCRT-0 complex / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / Pexophagy / Regulation of pyruvate metabolism / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / microautophagy / protein retention in Golgi apparatus / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / E3 ubiquitin ligases ubiquitinate target proteins / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / multivesicular body sorting pathway / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / protein targeting to vacuole / Translesion Synthesis by POLH / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Termination of translesion DNA synthesis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / phosphatidylinositol-3-phosphate binding / Negative regulators of DDX58/IFIH1 signaling / cellular response to nitrogen starvation / vacuolar membrane / K48-linked polyubiquitin modification-dependent protein binding / K63-linked polyubiquitin modification-dependent protein binding / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / Antigen processing: Ubiquitination & Proteasome degradation / protein secretion / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / Ub-specific processing proteases / ubiquitin binding / modification-dependent protein catabolic process / protein tag activity / peroxisome / endosome / endosome membrane / protein ubiquitination / ribosome / structural constituent of ribosome / protein domain specific binding / translation / protein heterodimerization activity / ribonucleoprotein complex / ubiquitin protein ligase binding / protein-containing complex / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 ...: / Vacuolar protein sorting-associated protein 27, GAT-like domain / Hepatocyte growth factor-regulated tyrosine kinase substrate/VPS27 / VHS domain / VHS domain / VHS domain profile. / Domain present in VPS-27, Hrs and STAM / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / ENTH/VHS / Ubiquitin interaction motif / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger, FYVE/PHD-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Also encodes a ubiquitin protein / Polyubiquitin / Vacuolar protein sorting-associated protein 27
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics, energy minimization
Model detailslowest energy, model 1
AuthorsSgourakis, N.G. / Patel, M.M. / Garcia, A.E. / Makhatadze, G.I. / McCallum, S.A.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Conformational Dynamics and Structural Plasticity Play Critical Roles in the Ubiquitin Recognition of a UIM Domain.
Authors: Sgourakis, N.G. / Patel, M.M. / Garcia, A.E. / Makhatadze, G.I. / McCallum, S.A.
#1: Journal: To be Published
Title: Folding cooperativity and dynamics of a Ubiquitin/UIM fusion protein by NMR, DSC, CD, fluorescence experiments and MD simulations
Authors: Patel, M.M. / Sgourakis, N.G. / Streicher, W.W. / McCallum, S.A. / Garcia, A.E. / Makhatadze, G.I.
History
DepositionJan 9, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein


Theoretical massNumber of molelcules
Total (without water)12,8671
Polymers12,8671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin, Vacuolar protein sorting-associated protein 27 fusion protein / Golgi retention defective protein 11


Mass: 12867.400 Da / Num. of mol.: 1 / Fragment: UIM 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCRG_04109, SCRG_05320,VPS27, DID7, GRD11, SSV17, VPL23, VPT27, YNR006W, N2038
Production host: Escherichia coli (E. coli)
References: UniProt: B3LRG8, UniProt: P40343, UniProt: P0CG63*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(COCA)CB
1413D HN(CA)CB
1523D 1H-15N NOESY
1613D 1H-13C NOESY
1713D (H)CCH-COSY
1813D HNCO
1913D H(CCO)NH
11032D HN-IPAP
11123D 1H-15N TOCSY
11213D (H)CCH-TOCSY
11313D (H)C(CCO)NH-TOCSY
11432D 1H-15N HSQC
11522D HN-IPAP

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Sample preparation

Details
Solution-IDContentsSolvent system
11.24 mM [U-100% 13C; U-100% 15N] Ubiquitin/UIM fusion protein-1, 3 mM sodium azide-2, 20 mM sodium phosphate-3, 50 mM sodium chloride-4, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [U-100% 15N] Ubiquitin/UIM fusion protein-5, 3 mM sodium azide-6, 20 mM sodium phosphate-7, 50 mM sodium chloride-8, 95% H2O/5% D2O95% H2O/5% D2O
30.5 mM [U-100% 15N] Ubiquitin/UIM fusion protein-9, 3 mM sodium azide-10, 20 mM sodium phosphate-11, 50 mM sodium chloride-12, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.24 mMUbiquitin/UIM fusion protein-1[U-100% 13C; U-100% 15N]1
3 mMsodium azide-21
20 mMsodium phosphate-31
50 mMsodium chloride-41
1.1 mMUbiquitin/UIM fusion protein-5[U-100% 15N]2
3 mMsodium azide-62
20 mMsodium phosphate-72
50 mMsodium chloride-82
0.5 mMUbiquitin/UIM fusion protein-9[U-100% 15N]3
3 mMsodium azide-103
20 mMsodium phosphate-113
50 mMsodium chloride-123
Sample conditionsIonic strength: 0.103 / pH: 6 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichprocessing
Sparky3.111Goddardpeak picking
Sparky3.111Goddardchemical shift assignment
Sparky3.111Goddarddata analysis
X-PLOR2.18Brungergeometry optimization
X-PLOR2.18Brungerstructure solution
X-PLOR2.18Brungerrefinement
X-PLOR2.18Brungerdata analysis
TALOS2003.027.13.05Cornilescu, Delaglio and Baxdata analysis
TALOS2003.027.13.05Cornilescu, Delaglio and Baxstructure solution
PALESMarkus Zweckstetter and Ad Baxdata analysis
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics, energy minimization
Software ordinal: 1
NMR constraintsNOE constraints total: 2252 / NOE intraresidue total count: 452 / NOE long range total count: 830 / NOE medium range total count: 394 / NOE sequential total count: 576 / Hydrogen bond constraints total count: 49 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 79 / Protein psi angle constraints total count: 79
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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