BMRB Entry 30276

Name: Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin
Published: 2017-05-15

Click here to enlarge.

PDB ID: 5vf0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30276
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
NMR-STAR v2.1 text file (deprecated)
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title: Solution NMR structure of human RAD18 (198-240) in complex with ubiquitin PubMed: 28506460

Deposition date: 2017-04-06 Original release date: 2017-05-15

Authors: Hu, Q.; Botuyan, M.; Mer, G.

Citation: Hu, Qi; Botuyan, Maria Victoria; Cui, Gaofeng; Zhao, Debiao; Mer, Georges. "Mechanisms of Ubiquitin-Nucleosome Recognition and Regulation of 53BP1 Chromatin Recruitment by RNF168/169 and RAD18" Mol. Cell 66, 473-487.e9 (2017).

Assembly members:
entity_1, polymer, 76 residues, 8576.831 Da.
entity_2, polymer, 46 residues, 5225.018 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: MQIFVKTLTGKTITLEVEPS DTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG
entity_2: GHMQVTKVDCPVCGVNIPES HINKHLDSCLSREEKKESLR SSVHKR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	391
15N chemical shifts	109
1H chemical shifts	835

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2
3	entity_3	3

Entities:

Entity 1, entity_1 76 residues - 8576.831 Da.

1

MET

GLN

ILE

PHE

VAL

LYS

THR

LEU

THR

GLY

2

LYS

THR

ILE

THR

LEU

GLU

VAL

GLU

PRO

SER

3

ASP

THR

ILE

GLU

ASN

VAL

LYS

ALA

LYS

ILE

4

GLN

ASP

LYS

GLU

GLY

ILE

PRO

ASP

GLN

5

GLN

ARG

LEU

ILE

PHE

ALA

GLY

LYS

GLN

LEU

6

GLU

ASP

GLY

ARG

THR

LEU

SER

ASP

TYR

ASN

7

ILE

GLN

LYS

GLU

SER

THR

LEU

HIS

LEU

VAL

8

LEU

ARG

LEU

ARG

GLY

Entity 2, entity_2 46 residues - 5225.018 Da.

1

GLY

HIS

MET

GLN

VAL

THR

LYS

VAL

ASP

CYS

2

PRO

VAL

CYS

GLY

VAL

ASN

ILE

PRO

GLU

SER

3

HIS

ILE

ASN

LYS

HIS

LEU

ASP

SER

CYS

LEU

4

SER

ARG

GLU

LYS

GLU

SER

LEU

ARG

5

SER

VAL

HIS

LYS

ARG

Entity 3, entity_3 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: KCl 50 mM; MES-Bis-TRIS 25 mM; RAD18, [U-100% 13C; U-100% 15N], 0.6 mM; Ubiquitin 3 mM; ZnCl2 10 uM

sample_2: KCl 50 mM; MES-Bis-TRIS 25 mM; RAD18 3 mM; Ubiquitin, [U-100% 13C; U-100% 15N], 0.6 mM; ZnCl2 10 uM

sample_3: KCl 50 mM; MES-Bis-TRIS 25 mM; RAD18, [U-15N], 0.9 mM; ZnCl2 10 uM

sample_4: KCl 50 mM; MES-Bis-TRIS 25 mM; RAD18, [U-100% 13C; U-100% 15N], 0.9 mM; ZnCl2 10 uM

sample_5: Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture 5%; KCl 50 mM; MES-Bis-TRIS 25 mM; RAD18, [U-100% 15N], 0.2 mM; Ubiquitin 1.0 mM; ZnCl2 10 uM

sample_6: Alkyl-polyethylene glycol (C12E5)/n-hexanol mixture 5%; KCl 50 mM; MES-Bis-TRIS 25 mM; RAD18 1.0 mM; Ubiquitin, [U-100% 15N], 0.2 mM; ZnCl2 10 uM

sample_conditions_1: ionic strength: 50 mM; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 15N/13C-FILTERED EDITED NOESY	sample_1	isotropic	sample_conditions_1
3D 15N/13C-FILTERED EDITED NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-15N IPAP HSQC	sample_5	anisotropic	sample_conditions_1
2D 1H-15N IPAP HSQC	sample_6	anisotropic	sample_conditions_1

Software:

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

TOPSPIN, Bruker Biospin - collection

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker Avance III 700 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts