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- PDB-5ujn: Representative 2-conformer ensembles of K27-linked Ub2 from RDC data -

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Basic information

Entry
Database: PDB / ID: 5ujn
TitleRepresentative 2-conformer ensembles of K27-linked Ub2 from RDC data
ComponentsUbiquitin
KeywordsSIGNALING PROTEIN / diubiquitin / K27 / polyubiquitin chain
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 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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 1.2Jun 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 1.3Oct 30, 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: 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 area530 Å2
ΔGint1 kcal/mol
Surface area8030 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100000structures with the best agreement with RDC data
RepresentativeModel #20structures with best agreement with rdc data

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
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
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
122isotropic12D 1H-15N HSQC
131anisotropic12D 1H-15N HSQC
142anisotropic12D 1H-15N HSQC
151isotropic22D 1H-15N HSQC
162isotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution1150 uM [U-99% 15N] distal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O15N-labelled K27-Ub2 with the distal Ub 15N, and proximal Ub 14N. pH 6.8 20 mM NaPhosphate, 0.02% NaN3Distal K27-Ub295% H2O/5% D2O
solution2150 uM [U-99% 15N] proximal K27-Ub2, 20 mM NaPhosphate, 0.02 % NaN3, 95% H2O/5% D2O15N-labelled K27-Ub2 with the distal Ub 14N, and proximal Ub 15N. pH 6.8 20 mM NaPhosphate, 0.02% NaN3Proximal K27-Ub295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 uMdistal K27-Ub2[U-99% 15N]1
20 mMNaPhosphatenatural abundance1
0.02 %NaN3natural abundance1
150 uMproximal K27-Ub2[U-99% 15N]2
20 mMNaPhosphatenatural abundance2
0.02 %NaN3natural abundance2
Sample conditionsDetails: pH 6.8 20 mM NaPhospahte / Ionic strength: 20 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 296 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameDeveloperClassification
ARMORBerlin K, Castaneda, CA, Fushman Drefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: na / Software ordinal: 1
Details: Using ~100 RDC restraints, ARMOR was used to select 2-member ensembles of K27-Ub2 that are in best agreement with RDC data. This generated a total of 10 2-conformer ensembles for this entry.
NMR representativeSelection criteria: structures with best agreement with rdc data
NMR ensembleConformer selection criteria: structures with the best agreement with RDC data
Conformers calculated total number: 100000 / Conformers submitted total number: 20

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