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- PDB-5xk5: Relaxed state of S65-phosphorylated ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5xk5
TitleRelaxed state of S65-phosphorylated ubiquitin
ComponentsPolyubiquitin-B
KeywordsCELL CYCLE / pH-sensitive ubiquitin conformational switch
Function / homologysymbiont entry into host cell via disruption of host cell glycocalyx / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / symbiont entry into host cell via disruption of host cell envelope / virus tail / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family / Tail fiber
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsXu, D. / Zhou, G. / Qin, L.Y. / Ran, M.L. / Zhang, C.L. / Liu, K. / Liu, Z. / Zhang, W.P. / Tang, C.
Funding support China, 6items
OrganizationGrant numberCountry
the Chinese Ministry of Science and Technology2013CB910200 China
the Chinese Ministry of Science and Technology2016YFA0501200 China
the National Natural Science Foundation of China31225007 China
the National Natural Science Foundation of China31500595 China
the National Natural Science Foundation of China31400735 China
the National Natural Science Foundation of China31400644 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch
Authors: Dong, X. / Gong, Z. / Lu, Y.B. / Liu, K. / Qin, L.Y. / Ran, M.L. / Zhang, C.L. / Liu, Z. / Zhang, W.P. / Tang, C.
History
DepositionMay 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)8,6571
Polymers8,6571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5130 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 160structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Polyubiquitin-B


Mass: 8656.811 Da / Num. of mol.: 1 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0CG47
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic23D CBCA(CO)NH
131isotropic23D HNCA
141isotropic23D 1H-15N NOESY
151isotropic23D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-98% 13C; U-98% 15N] relaxed pUb, 90% H2O/10% D2O
Label: 13C 15N relaxed / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: relaxed pUb / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 150 mM / Label: buffer 1 / pH: 7.4 / Pressure: 760 mmHg / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNMRCCPNchemical shift assignment
CcpNMRCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 160 / Conformers submitted total number: 30

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