BMRB Entry 11469

Name: Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice
Published: 2012-08-13

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PDB ID: 2rsd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11469
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of the plant homeodomain (PHD) of the E3 SUMO ligase Siz1 from rice

Deposition date:

2012-01-11

Original release date:

2012-08-13

Authors:

Shindo, Heisaburo; Tsuchiya, Wataru; Suzuki, Rintaro; Yamazaki, Toshimasa

Citation:

Citation: Shindo, Heisaburo; Suzuki, Rintaro; Tsuchiya, Wataru; Taichi, Misako; Nishiuchi, Yuji; Yamazaki, Toshimasa. "PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2" FEBS Lett. 586, 1783-1789 (2012).
PubMed: 22626555

Assembly members:

Assembly members:
entity_1, polymer, 68 residues, 7671.758 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Oryza sativa subsp. japonica Taxonomy ID: 39947 Superkingdom: Eukaryota Kingdom: Viridiplantae Genus/species: Oryza Oryza sativa

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-4T-3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSDSFQPEAKVRCICSSTMV NDSMIQCEDQRCQVWQHLNC VLIPDKPGESAEVPPVFYCE LCRLSRAD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	308
15N chemical shifts	72
1H chemical shifts	460

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	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, entity_1 68 residues - 7671.758 Da.

Residues 105-106 represent a non-native sequence from affinity tag.

1

GLY

SER

ASP

SER

PHE

GLN

PRO

GLU

ALA

LYS

2

VAL

ARG

CYS

ILE

CYS

SER

THR

MET

VAL

3

ASN

ASP

SER

MET

ILE

GLN

CYS

GLU

ASP

GLN

4

ARG

CYS

GLN

VAL

TRP

GLN

HIS

LEU

ASN

CYS

5

VAL

LEU

ILE

PRO

ASP

LYS

PRO

GLY

GLU

SER

6

ALA

GLU

VAL

PRO

VAL

PHE

TYR

CYS

GLU

7

LEU

CYS

ARG

LEU

SER

ARG

ALA

ASP

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: OsSiz1-PHD, [U-13C; U-15N], 0.5 – 1.0 mM; ZINC ION1.0 – 2.0 mM; sodium chloride 100 mM; potassium phosphate 10 mM; DTT 5 mM; H2O 92%; D2O 8%

sample_2: OsSiz1-PHD, [U-13C; U-15N], 0.5 – 1.0 mM; ZINC ION1.0 – 2.0 mM; sodium chloride 100 mM; potassium phosphate 10 mM; DTT 5 mM; D2O 100%

sample_conditions_1: pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HCABGCO	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 15N-separated NOESY-HSQC	sample_1	isotropic	sample_conditions_1
3D 13C/15N-separated NOESY-HSQC	sample_1	isotropic	sample_conditions_1
4D 13C/13C-separated NOESY-HSQC	sample_2	isotropic	sample_conditions_1

Software:

xwinnmr v3.1, Bruker Biospin - collection

NMRPipe vreleased at Feb 10, 2006, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.113, Goddard - chemical shift assignment, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

TALOS+ v1.01F, Shen, Delaglio, Cornilescu and Bax - data analysis

AQUA v3.2, Rullmann, Doreleijers and Kaptein - data analysis

ProcheckNMR v3.5.4, Laskowski and MacArthur - data analysis

NMR spectrometers:

Bruker DMX 750 MHz

PDB	2RSD
DBJ	BAF16431 BAG97182 BAS92058
GB	AAT39226 EEC78434 EEE62174
REF	NP_001054517
SP	Q6L4L4
AlphaFold	Q6L4L4