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- PDB-5zd0: Solution structure of human ubiquitin with three alanine mutation... -

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Basic information

Entry
Database: PDB / ID: 5zd0
TitleSolution structure of human ubiquitin with three alanine mutations in living eukaryotic cells by in-cell NMR spectroscopy
Componentsubiquitin
KeywordsCYTOSOLIC PROTEIN / regulatory protein / ubiquitination
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 / torsion angle dynamics
AuthorsTanaka, T. / Ikeya, T. / Kamoshida, H. / Mishima, M. / Shirakawa, M. / Guentert, P. / Ito, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST; JPMJCR13M3 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: High-Resolution Protein 3D Structure Determination in Living Eukaryotic Cells.
Authors: Tanaka, T. / Ikeya, T. / Kamoshida, H. / Suemoto, Y. / Mishima, M. / Shirakawa, M. / Guntert, P. / Ito, Y.
History
DepositionFeb 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ubiquitin


Theoretical massNumber of molelcules
Total (without water)8,4651
Polymers8,4651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 4400target function
RepresentativeModel #1target function

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Components

#1: Protein ubiquitin


Mass: 8464.617 Da / Num. of mol.: 1 / Mutation: L8A,I44A,V70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0CG47

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
211isotropic12D 1H-15N SOFAST-HMQC
121isotropic12D 1H-13C HSQC
231isotropic13D 1H-15N NOESY
141isotropic13D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 50 uM [U-100% 13C; U-100% 15N] human ubiquitin with three alanine mutations 1, 50 uM [U-100% 15N] human ubiquitin with three alanine mutations 2, 90% H2O/10% D2O
Label: UB3A_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 uMhuman ubiquitin with three alanine mutations 1[U-100% 13C; U-100% 15N]1
50 uMhuman ubiquitin with three alanine mutations 2[U-100% 15N]1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10 Not definedconditions_10AMBIENT atm300 K
20 Not definedconditions_20AMBIENT atm300 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
OPAL1.4Luginbuhl, Guntert, Billeter and Wuthrichrefinement
Azara2.8.1Boucherprocessing
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 4400 / Conformers submitted total number: 20

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