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- PDB-5vey: Solution NMR structure of histone H2A-H2B mono-ubiquitylated at H... -

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Basic information

Entry
Database: PDB / ID: 5vey
TitleSolution NMR structure of histone H2A-H2B mono-ubiquitylated at H2A Lys15 in complex with RNF169 (653-708)
Components
  • E3 ubiquitin-protein ligase RNF169
  • Histone H2B type 1-J,Histone H2A type 1-B/E
  • Polyubiquitin-B
KeywordsTRANSFERASE / STRUCTURAL PROTEIN / SIGNALING PROTEIN / Nucleosome / Ubiquitin / Ubiquitin ligase / Complex
Function / homology
Function and homology information


negative regulation of double-strand break repair / ubiquitin-modified histone reader activity / symbiont entry into host cell via disruption of host cell glycocalyx / K63-linked polyubiquitin modification-dependent protein binding / symbiont entry into host cell via disruption of host cell envelope / virus tail / negative regulation of tumor necrosis factor-mediated signaling pathway / protein localization to CENP-A containing chromatin / nucleosome binding / Replacement of protamines by nucleosomes in the male pronucleus ...negative regulation of double-strand break repair / ubiquitin-modified histone reader activity / symbiont entry into host cell via disruption of host cell glycocalyx / K63-linked polyubiquitin modification-dependent protein binding / symbiont entry into host cell via disruption of host cell envelope / virus tail / negative regulation of tumor necrosis factor-mediated signaling pathway / protein localization to CENP-A containing chromatin / nucleosome binding / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / double-strand break repair via homologous recombination / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / RING-type E3 ubiquitin transferase / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / UCH proteinases / HCMV Early Events / ubiquitin-protein transferase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nucleosome / site of double-strand break / heterochromatin formation / double-strand break repair / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nucleosome assembly / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium / Estrogen-dependent gene expression / killing of cells of another organism / Ub-specific processing proteases / protein ubiquitination / defense response to Gram-positive bacterium / nuclear body / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / DNA damage response / nucleolus / extracellular space / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Histone, subunit A / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Histone, subunit A / Zinc finger, C3HC4 type (RING finger) / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...: / Histone, subunit A / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Histone, subunit A / Zinc finger, C3HC4 type (RING finger) / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Tail fiber / E3 ubiquitin-protein ligase RNF169
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHu, Q. / Botuyan, M.V. / Cui, G. / Mer, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM116829 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA132878 United States
CitationJournal: Mol. Cell / Year: 2017
Title: Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18.
Authors: Hu, Q. / Botuyan, M.V. / Cui, G. / Zhao, D. / Mer, G.
History
DepositionApr 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 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: Histone H2B type 1-J,Histone H2A type 1-B/E
B: Polyubiquitin-B
C: E3 ubiquitin-protein ligase RNF169


Theoretical massNumber of molelcules
Total (without water)37,2533
Polymers37,2533
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, isothermal titration calorimetry, SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1

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Components

#1: Protein Histone H2B type 1-J,Histone H2A type 1-B/E / Histone H2B.1 / Histone H2B.r / H2B/r / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 21658.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR, HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06899, UniProt: P04908
#2: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#3: Protein E3 ubiquitin-protein ligase RNF169 / RING finger protein 169 / RING-type E3 ubiquitin transferase RNF169


Mass: 7016.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF169, KIAA1991 / Plasmid: pTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8NCN4, RING-type E3 ubiquitin transferase
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 TROSY 1H-15N HSQC
122isotropic12D TROSY 1H-15N HSQC
133isotropic12D TROSY 1H-15N HSQC
144isotropic122D TROSY 1H-15N HSQC
155isotropic12D TROSY 1H-15N HSQC
166isotropic12D TROSY 1H-15N HSQC
177isotropic12D TROSY 1H-15N HSQC
188isotropic12D TROSY 1H-15N HSQC
199isotropic12D TROSY 1H-15N HSQC
11010isotropic12D TROSY 1H-15N HSQC
11111isotropic12D TROSY 1H-15N HSQC
11212isotropic12D TROSY 1H-15N HSQC
11313isotropic12D TROSY 1H-15N HSQC
11414isotropic12D TROSY 1H-15N HSQC
11515isotropic12D TROSY 1H-15N HSQC
11616isotropic12D TROSY 1H-15N HSQC
11717isotropic12D TROSY 1H-15N HSQC
11818isotropic12D TROSY 1H-15N HSQC
11919isotropic12D TROSY 1H-15N HSQC
12020isotropic12D TROSY 1H-15N HSQC
12121isotropic12D TROSY 1H-15N HSQC
12222isotropic12D TROSY 1H-15N HSQC
22323isotropic12D 1H-15N HSQC
22424isotropic12D 1H-15N HSQC
22525isotropic12D 1H-15N HSQC
22626isotropic12D 1H-15N HSQC
22727isotropic12D 1H-15N HSQC
22828isotropic12D 1H-15N HSQC
22929isotropic12D 1H-15N HSQC
23030isotropic12D 1H-15N HSQC
13131isotropic12D TROSY 1H-15N HSQC
13232isotropic12D TROSY 1H-15N HSQC
13333isotropic12D TROSY 1H-15N HSQC
13434isotropic12D TROSY 1H-15N HSQC
13535isotropic12D TROSY 1H-15N HSQC
13636isotropic12D TROSY 1H-15N HSQC
13737isotropic12D TROSY 1H-15N HSQC
13838isotropic12D TROSY 1H-15N HSQC
13939isotropic12D TROSY 1H-15N HSQC
14040isotropic12D TROSY 1H-15N HSQC
14141isotropic12D TROSY 1H-15N HSQC
1421isotropic12D 1H-13C HMQC
1431isotropic12D 1H-13C HSQC
1441isotropic13D TROSY HNCO
1451isotropic13D TROSY HNCA
1461isotropic13D TROSY HN(CO)CA
1471isotropic13D TROSY HN(CA)CB
1481isotropic13D TROSY HN(COCA)CB
1493isotropic13D HBHA(CO)NH
1503isotropic13D (H)CC(CO)NH
1513isotropic13D CCCH-TOCSY
1523isotropic13D 1H-15N NOESY
1533isotropic13D 1H-13C NOESY-HSQC
1544isotropic13D HBHA(CO)NH
1554isotropic13D (H)CC(CO)NH
1564isotropic13D CCCH-TOCSY
1574isotropic13D 1H-15N NOESY
1584isotropic13D 1H-13C NOESY-HSQC
1595isotropic13D 1H-15N NOESY
1605isotropic13D 1H-13C NOESY-HSQC
1617isotropic13D TROSY HNCO
1627isotropic13D TROSY HNCA
1637isotropic13D TROSY HN(CO)CA
1647isotropic13D TROSY HN(CA)CB
1657isotropic13D TROSY HN(COCA)CB
1668isotropic13D HBHA(CO)NH
1678isotropic13D (H)CC(CO)NH
1688isotropic13D CCCH-TOCSY
1699isotropic13D HBHA(CO)NH
1709isotropic13D (H)CC(CO)NH
1719isotropic13D CCCH-TOCSY
1729isotropic13D 1H-15N NOESY
1739isotropic13D 1H-13C NOESY-HSQC
17410isotropic13D 1H-15N NOESY
1758isotropic13D 1H-13C NOESY-HSQC
1768isotropic113C-edited/filtered NOESY
1779isotropic113C-edited/filtered NOESY
1788isotropic115N-edited/filtered NOESY
1799isotropic115N-edited/filtered NOESY
1808isotropic13D 1H-13C NOESY aromatic
1819isotropic13D 1H-13C NOESY aromatic
18220isotropic12D 1H-13C HMQC
18321isotropic12D 1H-13C HMQC
18420isotropic13D 1H-13C NOESY-HMQC
18521isotropic13D 1H-13C NOESY-HMQC
18620isotropic13D 1H-13C NOESY-HSQC
18721isotropic13D 1H-13C NOESY-HSQC
18812isotropic13D 1H-13C NOESY
18913isotropic13D 1H-15N NOESY
19014isotropic13D 1H-15N NOESY
19115isotropic13D 1H-13C NOESY
116216isotropic13D 1H-15N NOESY
19216isotropic13D 1H-13C NOESY
19317isotropic13D 1H-15N NOESY
19418isotropic13D 1H-15N NOESY
116118isotropic13D 1H-13C NOESY-HSQC
19519isotropic13D 1H-13C NOESY
19622isotropic13D 1H-13C NOESY-HMQC
29723isotropic13D CBCA(CO)NH
29823isotropic13D HN(CA)CB
29923isotropic13D HNCO
210023isotropic13D HN(CA)CO
210123isotropic13D HBHA(CO)NH
211523isotropic13D (H)CC(CO)NH
210223isotropic13D CCCH-TOCSY
210323isotropic13D 1H-15N NOESY
210423isotropic13D 1H-13C NOESY-HSQC
210523isotropic113C-edited/filtered NOESY
210624isotropic13D CBCA(CO)NH
210724isotropic13D HN(CA)CB
210824isotropic13D HNCO
210924isotropic13D HN(CA)CO
211024isotropic13D HBHA(CO)NH
211624isotropic13D (H)CC(CO)NH
211124isotropic13D CCCH-TOCSY
211224isotropic13D 1H-15N NOESY
211324isotropic13D 1H-13C NOESY-HSQC
211424isotropic113C-edited/filtered NOESY
211729isotropic13D CBCA(CO)NH
211829isotropic13D HN(CA)CB
211929isotropic13D HNCO
212029isotropic13D HN(CA)CO
212129isotropic13D HBHA(CO)NH
212229isotropic13D (H)CC(CO)NH
212329isotropic13D CCCH-TOCSY
212429isotropic13D 1H-15N NOESY
212529isotropic13D 1H-13C NOESY-HSQC
212629isotropic113C-edited/filtered NOESY
212730isotropic13D CBCA(CO)NH
212830isotropic13D HN(CA)CB
212930isotropic13D HNCO
213030isotropic13D HN(CA)CO
213130isotropic13D HBHA(CO)NH
213230isotropic13D (H)CC(CO)NH
213330isotropic13D CCCH-TOCSY
213430isotropic13D 1H-15N NOESY
213530isotropic13D 1H-13C NOESY-HSQC
213630isotropic113C-edited/filtered NOESY
213725isotropic13D CBCA(CO)NH
213825isotropic13D HN(CA)CB
213925isotropic13D HNCO
214025isotropic13D HN(CA)CO
214125isotropic13D HBHA(CO)NH
214225isotropic13D (H)CC(CO)NH
214325isotropic13D CCCH-TOCSY
214425isotropic13D 1H-15N NOESY
214525isotropic13D 1H-13C NOESY-HSQC
214627isotropic13D CBCA(CO)NH
214727isotropic13D HN(CA)CB
214827isotropic13D HNCO
214927isotropic13D HN(CA)CO
215027isotropic13D HBHA(CO)NH
215127isotropic13D (H)CC(CO)NH
215227isotropic13D CCCH-TOCSY
215328isotropic13D CBCA(CO)NH
215428isotropic13D HN(CA)CB
215528isotropic13D HNCO
215628isotropic13D HN(CA)CO
215728isotropic13D HBHA(CO)NH
215828isotropic13D (H)CC(CO)NH
215928isotropic13D CCCH-TOCSY
216028isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDLabelSolvent system
solution1Sample_190% H2O/10% D2O
solution2Sample_290% H2O/10% D2O
solution3Sample_390% H2O/10% D2O
solution4Sample_490% H2O/10% D2O
solution5Sample_590% H2O/10% D2O
solution6Sample_690% H2O/10% D2O
solution7Sample_790% H2O/10% D2O
solution8Sample_890% H2O/10% D2O
solution9Sample_990% H2O/10% D2O
solution10Sample_1090% H2O/10% D2O
solution11Sample_1190% H2O/10% D2O
solution12Sample_1290% H2O/10% D2O
solution13Sample_1390% H2O/10% D2O
solution14Sample_1490% H2O/10% D2O
solution15Sample_1590% H2O/10% D2O
solution16Sample_1690% H2O/10% D2O
solution17Sample_1790% H2O/10% D2O
solution18Sample_1890% H2O/10% D2O
solution19Sample_1990% H2O/10% D2O
solution20Sample_2090% H2O/10% D2O
solution21Sample_2190% H2O/10% D2O
solution22Sample_2290% H2O/10% D2O
solution23Sample_2390% H2O/10% D2O
solution24Sample_2490% H2O/10% D2O
solution25Sample_2590% H2O/10% D2O
solution26Sample_2690% H2O/10% D2O
solution27Sample_2790% H2O/10% D2O
solution28Sample_2890% H2O/10% D2O
solution29Sample_2990% H2O/10% D2O
solution30Sample_3090% H2O/10% D2O
solution31Sample_3190% H2O/10% D2O
solution32Sample_3290% H2O/10% D2O
solution33Sample_3390% H2O/10% D2O
solution34Sample_3490% H2O/10% D2O
solution35Sample_3590% H2O/10% D2O
solution36Sample_3690% H2O/10% D2O
solution37Sample_3790% H2O/10% D2O
solution38Sample_3890% H2O/10% D2O
solution39Sample_3990% H2O/10% D2O
solution40Sample_4090% H2O/10% D2O
solution41Sample_4190% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMH2A-H2B100% 2H; 13C; 15N1
25 mMMES-Bis-TRISnatural abundance1
50 mMKClnatural abundance1
4 mMEDTAnatural abundance1
1 mMH2A-H2B100% 2H, 15N2
25 mMMES-Bis-TRISnatural abundance2
50 mMKClnatural abundance2
4 mMEDTAnatural abundance2
1 mMH2A-H2B70% 2H, 13C, 15N3
25 mMMES-Bis-TRISnatural abundance3
50 mMKClnatural abundance3
4 mMEDTAnatural abundance3
1 mMH2A-H2B30% 2H; 13C; 15N4
25 mMMES-Bis-TRISnatural abundance4
50 mMKClnatural abundance4
4 mMEDTAnatural abundance4
1 mMH2A-H2B13C; 15N5
25 mMMES-Bis-TRISnatural abundance5
50 mMKClnatural abundance5
4 mMEDTAnatural abundance5
1 mMH2A-H2B15N6
25 mMMES-Bis-TRISnatural abundance6
50 mMKClnatural abundance6
4 mMEDTAnatural abundance6
0.8 mMH2A-H2B100% 2H; 13C; 15N7
8 mMRNF169 (688-704)natural abundance7
25 mMMES-Bis-TRISnatural abundance7
50 mMKClnatural abundance7
4 mMEDTAnatural abundance7
0.8 mMH2A-H2B70% 2H; 13C; 15N8
8 mMRNF169 (688-704)natural abundance8
25 mMMES-Bis-TRISnatural abundance8
50 mMKClnatural abundance8
4 mMEDTAnatural abundance8
0.8 mMH2A-H2B30% 2H; 13C; 15N9
8 mMRNF169 (688-704)natural abundance9
25 mMMES-Bis-TRISnatural abundance9
50 mMKClnatural abundance9
4 mMEDTAnatural abundance9
0.8 mMH2A-H2B13C; 15N10
8 mMRNF169 (688-704)natural abundance10
25 mMMES-Bis-TRISnatural abundance10
50 mMKClnatural abundance10
4 mMEDTAnatural abundance10
0.8 mMH2A-H2B100% 2H; 13C; 15N11
0.8 mMH2A K15-linked ubiquitinnatural abundance11
2.4 mMRNF169 (653-708)natural abundance11
25 mMMES-Bis-TRISnatural abundance11
50 mMKClnatural abundance11
4 mMEDTAnatural abundance11
0.8 mMH2A-H2B30% 2H; 13C; 15N12
0.8 mMH2A K15-linked ubiquitinnatural abundance12
2.4 mMRNF169 (653-708)natural abundance12
25 mMMES-Bis-TRISnatural abundance12
50 mMKClnatural abundance12
4 mMEDTAnatural abundance12
0.8 mMH2A-H2B30% 2H; 15N13
0.8 mMH2A K15-linked ubiquitinnatural abundance13
2.4 mMRNF169 (653-708)natural abundance13
25 mMMES-Bis-TRISnatural abundance13
50 mMKClnatural abundance13
4 mMEDTAnatural abundance13
0.8 mMH2A-H2B30% 2H; 15N14
0.8 mMH2A K15-linked ubiquitin100% 2H14
2.4 mMRNF169 (653-708)natural abundance14
25 mMMES-Bis-TRISnatural abundance14
50 mMKClnatural abundance14
4 mMEDTAnatural abundance14
0.8 mMH2A-H2B30% 2H; 13C; 15N15
0.8 mMH2A K15-linked ubiquitin100% 2H15
2.4 mMRNF169 (653-708)natural abundance15
25 mMMES-Bis-TRISnatural abundance15
50 mMKClnatural abundance15
4 mMEDTAnatural abundance15
0.8 mMH2B-H2B100% 2H16
0.8 mMH2A K15-linked ubiquitin13C; 15N16
2.4 mMRNF169 (653-708)natural abundance16
25 mMMES-Bis-TRISnatural abundance16
50 mMKClnatural abundance16
4 mMEDTAnatural abundance16
0.8 mMH2A-H2B100% 2H17
0.8 mMH2A K15-linked ubiquitin15N17
2.4 mMRNF169 (653-708)natural abundance17
25 mMMES-Bis-TRISnatural abundance17
50 mMKClnatural abundance17
4 mMEDTAnatural abundance17
1 mMH2A-H2B100% 2H18
1 mMH2A K15-linked ubiquitinnatural abundance18
0.3 mMRNF169 (653-708)13C; 15N18
25 mMMES-Bis-TRISnatural abundance18
50 mMKClnatural abundance18
4 mMEDTAnatural abundance18
1 mMH2A-H2B30% 2H19
1 mMH2A K15-linked ubiquitin100% 2H19
0.3 mMRNF169 (653-708)13C; 15N19
25 mMMES-Bis-TRISnatural abundance19
50 mMKClnatural abundance19
4 mMEDTAnatural abundance19
0.8 mMH2A-H2B100% 2H (13CH3/12CD3-Leu, Val, Ile); 15N20
0.8 mMH2A K15-linked ubiquitinnatural abundance20
2.4 mMRNF169 (653-708)natural abundance20
25 mMMES-Bis-TRISnatural abundance20
50 mMKClnatural abundance20
4 mMEDTAnatural abundance20
0.8 mMH2A-H2B100% 2H (13CH3/13CH3-Leu, Val); 15N21
0.8 mMH2A K15-linked ubiquitinnatural abundance21
2.4 mMRNF169 (653-708)natural abundance21
25 mMMES-Bis-TRISnatural abundance21
50 mMKClnatural abundance21
4 mMEDTAnatural abundance21
0.8 mMH2A-H2B100% 2H22
0.8 mMH2A K15-linked ubiquitin100% 2H (13CH3/12CD3-Leu, Val, Ile); 15N22
2.4 mMRNF169 (653-708)natural abundance22
25 mMMES-Bis-TRISnatural abundance22
50 mMKClnatural abundance22
4 mMEDTAnatural abundance22
1 mMUbiquitin13C; 15N23
6 mMRNF169 (653-708)natural abundance23
25 mMMES-Bis-TRISnatural abundance23
50 mMKClnatural abundance23
4 mMEDTAnatural abundance23
6 mMUbiquitinnatural abundance24
1 mMRNF169 (653-708)13C; 15N24
25 mMMES-Bis-TRISnatural abundance24
50 mMKClnatural abundance24
4 mMEDTAnatural abundance24
1 mMRNF169 (653-687)13C; 15N25
25 mMMES-Bis-TRISnatural abundance25
50 mMKClnatural abundance25
4 mMEDTAnatural abundance25
1 mMRNF169 (653-708)13C; 15N26
25 mMMES-Bis-TRISnatural abundance26
50 mMKClnatural abundance26
4 mMEDTAnatural abundance26
1 mMRNF169 (688-708)13C; 15N27
25 mMMES-Bis-TRISnatural abundance27
50 mMKClnatural abundance27
4 mMEDTAnatural abundance27
1 mMUbiquitin13C; 15N28
25 mMMES-Bis-TRISnatural abundance28
50 mMKClnatural abundance28
4 mMEDTAnatural abundance28
1 mMUbiquitin13C; 15N29
6 mMRNF169 (653-687)natural abundance29
25 mMMES-Bis-TRISnatural abundance29
50 mMKClnatural abundance29
4 mMEDTAnatural abundance29
6 mMUbiquitinnatural abundance30
1 mMRNF169 (653-687)13C; 15N30
25 mMMES-Bis-TRISnatural abundance30
50 mMKClnatural abundance30
4 mMEDTAnatural abundance30
0.5 mMH2A-H2B_MTSL_H2A_G37100% 2H31
0.5 mMH2A K15-linked ubiquitin15N31
1.5 mMRNF169 (653-708)natural abundance31
25 mMMES-Bis-TRISnatural abundance31
50 mMKClnatural abundance31
4 mMEDTAnatural abundance31
0.5 mMH2A-H2B_MTSL_H2A_K74100% 2H32
0.5 mMH2A K15-linked ubiquitin15N32
1.5 mMRNF169 (653-708)natural abundance32
25 mMMES-Bis-TRISnatural abundance32
50 mMKClnatural abundance32
4 mMEDTAnatural abundance32
0.5 mMH2A-H2B_MTSL_H2B_S56100% 2H33
0.5 mMH2A K15-linked ubiquitin15N33
1.5 mMRNF169 (653-708)natural abundance33
25 mMMES-Bis-TRISnatural abundance33
50 mMKClnatural abundance33
4 mMEDTAnatural abundance33
0.5 mMH2A-H2B_MTSL_H2B_S87100% 2H34
0.5 mMH2A K15-linked ubiquitin15N34
1.5 mMRNF169 (653-708)natural abundance34
25 mMMES-Bis-TRISnatural abundance34
50 mMKClnatural abundance34
4 mMEDTAnatural abundance34
0.5 mMH2A-H2B_MTSL_H2B_S112100% 2H35
0.5 mMH2A K15-linked ubiquitin15N35
1.5 mMRNF169 (653-708)natural abundance35
25 mMMES-Bis-TRISnatural abundance35
50 mMKClnatural abundance35
4 mMEDTAnatural abundance35
0.5 mMH2A-H2B_MTSL_H2B_S123100% 2H36
0.5 mMH2A K15-linked ubiquitin15N36
1.5 mMRNF169 (653-708)natural abundance36
25 mMMES-Bis-TRISnatural abundance36
50 mMKClnatural abundance36
4 mMEDTAnatural abundance36
0.5 mMH2A-H2B100% 2H; 15N37
0.5 mMH2A K15-linked ubiquitin_MTSL_T9natural abundance37
1.5 mMRNF169 (653-708)natural abundance37
25 mMMES-Bis-TRISnatural abundance37
50 mMKClnatural abundance37
4 mMEDTAnatural abundance37
0.5 mMH2A-H2B100% 2H; 15N38
0.5 mMH2A K15-linked ubiquitin_MTSL_T14natural abundance38
1.5 mMRNF169 (653-708)natural abundance38
25 mMMES-Bis-TRISnatural abundance38
50 mMKClnatural abundance38
4 mMEDTAnatural abundance38
0.5 mMH2A-H2B100% 2H; 15N39
0.5 mMH2A K15-linked ubiquitin_MTSL_E34natural abundance39
1.5 mMRNF169 (653-708)natural abundance39
25 mMMES-Bis-TRISnatural abundance39
50 mMKClnatural abundance39
4 mMEDTAnatural abundance39
0.5 mMH2A-H2B100% 2H; 15N40
0.5 mMH2A K15-linked ubiquitin_MTSL_D39natural abundance40
1.5 mMRNF169 (653-708)natural abundance40
25 mMMES-Bis-TRISnatural abundance40
50 mMKClnatural abundance40
4 mMEDTAnatural abundance40
0.5 mMH2A-H2B100% 2H; 15N41
0.5 mMH2A K15-linked ubiquitin_MTSL_S57natural abundance41
1.5 mMRNF169 (653-708)natural abundance41
25 mMMES-Bis-TRISnatural abundance41
50 mMKClnatural abundance41
4 mMEDTAnatural abundance41
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mM KCl mMConditions_161 atm303 K
250 mM KCl mMConditions_261 atm298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSCHWIETERS, KUSZEWSKI, TJANDRA AND CLORErefinement
TopSpinstructure solution
NMRDrawstructure solution
NMRViewstructure solution
NMRPipestructure solution
Sparkystructure solution
TALOSstructure solution
X-PLOR NIHstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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