BMRB Entry 30019

Name: NMR structure of UHRF1 Tandem Tudor Domains in a complex with Spacer peptide
Published: 2016-04-12

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PDB ID: 5iay
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30019
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of UHRF1 Tandem Tudor Domains in a complex with Spacer peptide

Deposition date:

2016-02-22

Original release date:

2016-04-12

Authors:

Fang, J.; Cheng, J.; Wang, J.; Zhang, Q.; Liu, M.; Gong, R.; Wang, P.; Zhang, X.; Feng, Y.; Lan, W.; Gong, Z.; Tang, C.; Wong, J.; Yang, H.; Cao, C.; Xu, Y.

Citation:

Citation: Fang, J.; Cheng, J.; Wang, J.; Zhang, Q.; Liu, M.; Gong, R.; Wang, P.; Zhang, X.; Feng, Y.; Lan, W.; Gong, Z.; Tang, C.; Wong, J.; Yang, H.; Cao, C.; Xu, Y.. "Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition" Nat. Commun. 7, .-. (2016).
PubMed: 27045799

Assembly members:

Assembly members:
E3 ubiquitin-protein ligase UHRF1, polymer, 152 residues, 17804.875 Da.
Spacer, polymer, 16 residues, 1606.849 Da.

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
E3 ubiquitin-protein ligase UHRF1: LYKVNEYVDARDTNMGAWFE AQVVRVTRKAPSRDEPCSST SRPALEEDVIYHVKYDDYPE NGVVQMNSRDVRARARTIIK WQDLEVGQVVMLNYNPDNPK ERGFWYDAEISRKRETRTAR ELYANVVLGDDSLNDCRIIF VDEVFKIERPGE
Spacer: TGKGKWKRKSAGGGPS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	421
15N chemical shifts	152
1H chemical shifts	951

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

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

Entities:

Entity 1, entity_1 152 residues - 17804.875 Da.

1

LEU

TYR

LYS

VAL

ASN

GLU

TYR

VAL

ASP

ALA

2

ARG

ASP

THR

ASN

MET

GLY

ALA

TRP

PHE

GLU

3

ALA

GLN

VAL

ARG

VAL

THR

ARG

LYS

ALA

4

PRO

SER

ARG

ASP

GLU

PRO

CYS

SER

THR

5

SER

ARG

PRO

ALA

LEU

GLU

ASP

VAL

ILE

6

TYR

HIS

VAL

LYS

TYR

ASP

TYR

PRO

GLU

7

ASN

GLY

VAL

GLN

MET

ASN

SER

ARG

ASP

8

VAL

ARG

ALA

ARG

ALA

ARG

THR

ILE

LYS

9

TRP

GLN

ASP

LEU

GLU

VAL

GLY

GLN

VAL

10

MET

LEU

ASN

TYR

ASN

PRO

ASP

ASN

PRO

LYS

11

GLU

ARG

GLY

PHE

TRP

TYR

ASP

ALA

GLU

ILE

12

SER

ARG

LYS

ARG

GLU

THR

ARG

THR

ALA

ARG

13

GLU

LEU

TYR

ALA

ASN

VAL

LEU

GLY

ASP

14

ASP

SER

LEU

ASN

ASP

CYS

ARG

ILE

PHE

15

VAL

ASP

GLU

VAL

PHE

LYS

ILE

GLU

ARG

PRO

16

GLY

GLU

Entity 2, entity_2 16 residues - 1606.849 Da.

1

THR

GLY

LYS

GLY

LYS

TRP

LYS

ARG

LYS

SER

2

ALA

GLY

PRO

SER

Samples:

sample_1: Spacer 1.2 mM; TTD, [U-13C; U-15N], 1.0 mM; H2O 90 mM; D2O 10 mM

sample_2: Spacer, [U-15N], 1.0 mM; TTD 1.0 mM; H2O 90 mM; D2O 10 mM

sample_conditions_1: pH: 7.4; temperature: 297.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
w2 x-filter TOCSY	sample_1	isotropic	sample_conditions_1
HBCBCGCDCEHE	sample_1	isotropic	sample_conditions_1
HBCBCGCDHD	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
MQ-CCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
13C-filer HSQC-NOESY	sample_1	isotropic	sample_conditions_1
w1,w2 x-filter NOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - chemical shift assignment, peak picking

TALOS, Cornilescu, Delaglio and Bax - data analysis

VNMR, Varian - collection

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

NMR spectrometers:

Varian INOVA 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks