BMRB Entry 50236

Name: WT1-KTS RNA complex
Published: 2021-03-01

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PDB ID: 6wlh
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50236
MolProbity Validation Chart

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

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Title:

WT1-KTS RNA complex

Deposition date:

2020-04-14

Original release date:

2021-03-01

Authors:

Nishikawa, Tadateru; Wojciak, Jonathan; Dyson, Helen Jane; Wright, Peter

Citation:

Citation: Nishikawa, Tadateru; Wojciak, Jonathan; Dyson, Helen Jane; Wright, Peter. "RNA Binding by the KTS Splice Variants of Wilms' Tumor Suppressor Protein WT1" Biochemistry 59, 3889-3901 (2020).
PubMed: 32955251

Assembly members:

Assembly members:
entity_1, polymer, 117 residues, Formula weight is not available
entity_2, polymer, 29 residues, Formula weight is not available
entity_ZN, non-polymer, 65.409 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 Vector: pWT1-4-

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: EKRPFMCAYPGCNKRYFKLS HLQMHSRKHTGEKPYQCDFK DCERRFSRSDQLKRHQRRHT GVKPFQCKTCQRKFSRSDHL KTHTRTHTGEKPFSCRWPSC QKKFARSDELVRHHNMH
entity_2: GGGCCACCAACGACAUUGAU AUGGUGCCC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
- assigned_chemical_shifts_2

Data type	Count
13C chemical shifts	473
15N chemical shifts	109
1H chemical shifts	264

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	protein	1
2	RNA	2
3	ZN, 1	3
4	ZN, 2	3
5	ZN, 3	3

Entities:

Entity 1, protein 117 residues - Formula weight is not available

1

GLU

LYS

ARG

PRO

PHE

MET

CYS

ALA

TYR

PRO

2

GLY

CYS

ASN

LYS

ARG

TYR

PHE

LYS

LEU

SER

3

HIS

LEU

GLN

MET

HIS

SER

ARG

LYS

HIS

THR

4

GLY

GLU

LYS

PRO

TYR

GLN

CYS

ASP

PHE

LYS

5

ASP

CYS

GLU

ARG

PHE

SER

ARG

SER

ASP

6

GLN

LEU

LYS

ARG

HIS

GLN

ARG

HIS

THR

7

GLY

VAL

LYS

PRO

PHE

GLN

CYS

LYS

THR

CYS

8

GLN

ARG

LYS

PHE

SER

ARG

SER

ASP

HIS

LEU

9

LYS

THR

HIS

THR

ARG

THR

HIS

THR

GLY

GLU

10

LYS

PRO

PHE

SER

CYS

ARG

TRP

PRO

SER

CYS

11

GLN

LYS

PHE

ALA

ARG

SER

ASP

GLU

LEU

12

VAL

ARG

HIS

ASN

MET

HIS

Entity 2, RNA 29 residues - Formula weight is not available

1

G

C

A

C

A

2

C

G

A

C

A

U

G

A

U

3

A

U

G

U

G

C

Entity 3, ZN, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: WT1(-KTS), [U-100% 13C; U-100% 15N; U-90% 2H], 0.55 ± 0.1 mM; aptamer RNA 0.55 ± 0.1 mM; TRIS, [U-100% 2H], 10 ± 0.1 mM; potassium chloride 350 ± 0.5 mM; DTT 10 ± 0.1 mM; ZnSO4 5 ± 0.1 uM; sodium azide 2 ± 0.1 mM

sample_2: WT1(-KTS), [U-100% 13C; U-100% 15N; U-65% 2H], 0.55 ± 0.1 mM; aptamer RNA 0.55 ± 0.1 mM; TRIS, [U-100% 2H], 10 ± 0.1 mM; potassium chloride 350 ± 0.5 mM; DTT 10 ± 0.1 mM; ZnSO4 5 ± 0.1 uM; sodium azide 2 ± 0.1 mM

sample_3: WT1(-KTS) 0.55 ± 0.1 mM; aptamer RNA, [U-99% 13C; U-99% 15N], 0.55 ± 0.1 mM; TRIS, [U-100% 2H], 10 ± 0.1 mM; potassium chloride 350 ± 0.5 mM; DTT 10 ± 0.1 mM; ZnSO4 5 ± 0.1 uM; sodium azide 2 ± 0.1 mM

sample_4: WT1(-KTS) 0.55 ± 0.1 mM; aptamer RNA, [U-100% 15N], 0.55 ± 0.1 mM; TRIS, [U-100% 2H], 10 ± 0.1 mM; potassium chloride 350 ± 0.5 mM; DTT 10 ± 0.1 mM; ZnSO4 5 ± 0.1 uM; sodium azide 2 ± 0.1 mM

sample_conditions_1: ionic strength: 350 mM; pH: 7.1; pressure: 1 atm; temperature: 310 K

sample_conditions_2: ionic strength: 350 mM; pH: 7.1; pressure: 1 atm; temperature: 280 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HMQC	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_3	isotropic	sample_conditions_1
3D HMQC-NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_3	isotropic	sample_conditions_1
2D 13C[F1,F2]filtered NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_4	isotropic	sample_conditions_2

Software:

NMRPipe - processing

NMRView - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Bruker Avance 900 MHz
Bruker Avance 750 MHz
Bruker Avance 500 MHz
Bruker DRX 800 MHz
Bruker DRX 600 MHz

UNP	P19544
AlphaFold	Q8IYZ5