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- PDB-5ujl: Representative 1-conformer ensembles of K27-linked Ub2 from RDC data -

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Basic information

Entry
Database: PDB / ID: 5ujl
TitleRepresentative 1-conformer ensembles of K27-linked Ub2 from RDC data
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN / diubiquitin / K27-linkage / post-translational modification
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 / na
AuthorsCastaneda, C.A. / Fushman, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM065334 United States
CitationJournal: Structure / Year: 2016
Title: Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins.
Authors: Castaneda, C.A. / Dixon, E.K. / Walker, O. / Chaturvedi, A. / Nakasone, M.A. / Curtis, J.E. / Reed, M.R. / Krueger, S. / Cropp, T.A. / Fushman, D.
History
DepositionJan 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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 1.4May 15, 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1542
Polymers17,1542
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area220 Å2
ΔGint2 kcal/mol
Surface area8010 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)2 / 2structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / 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
111isotropic22D 1H-15N HSQC
122isotropic22D 1H-15N HSQC
131isotropic12D 1H-15N HSQC
142isotropic12D 1H-15N HSQC
251anisotropic22D 1H-15N HSQC
262anisotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is 15N-labelled Proximal Ub is not enriched, 95% H2O/5% D2OpH 6.8 20 mM NaPhosphate, 0.02% NaN3 K27-linked Ub2 (covalent linkage between K27 side chain and C-terminus of distal Ub) Distal Ub is 15N-labelled Proximal Ub is not enriched15N_distal_K27-Ub295% H2O/5% D2O
solution2150 uM [U-99% 15N] K27-diubiquitin, Distal Ub is not enriched Proximal Ub is 15N-labelled, 95% H2O/5% D2OpH 6.8 20 mM NaPhosphate, 0.02% NaN3 K27-linked Ub2 (covalent linkage between K27 side chain and C-terminus of distal Ub) Distal Ub is not enriched Proximal Ub is 15N-labelled15N_proximal_K27-Ub295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 uMK27-diubiquitin, Distal Ub is 15N-labelled Proximal Ub is not enriched[U-99% 15N]1
150 uMK27-diubiquitin, Distal Ub is not enriched Proximal Ub is 15N-labelled[U-99% 15N]2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1pH 6.8 20 mM NaPhosphate, 0.02% NaN320 mMstandard6.81 atm296 K
2pH 6.8 20 mM NaPhosphate, 0.02% NaN3 5% C12E5/hexanol mixture20 mManisotropic media6.81 atm296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameVersionDeveloperClassification
ARMOR1.1Berlin K, Castaneda CA, Fushman D.refinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: na / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 2 / Conformers submitted total number: 2

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