BMRB Entry 34660

Name: Solution structure of Zipcode binding protein 1 (ZBP1) KH3(DD)KH4 domains in complex with N6-Methyladenosine containing RNA
Published: 2024-01-31

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PDB ID: 7pjl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34660
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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:

Solution structure of Zipcode binding protein 1 (ZBP1) KH3(DD)KH4 domains in complex with N6-Methyladenosine containing RNA

Deposition date:

2021-08-24

Original release date:

2024-01-31

Authors:

Nicastro, G.; Abis, G.; Taylor, I.; Ramos, A.

Citation:

Citation: Nicastro, G.; Candel, A.; Uhl, M.; Oregioni, A.; Hollingworth, D.; Backofen, R.; Martin, S.; Ramos, A.. "Mechanism of b-actin mRNA Recognition by ZBP1." Cell Rep. 18, 1187-1199 (2017).
PubMed: 28147274

Assembly members:

Assembly members:
entity_1, polymer, 191 residues, 20613.498 Da.
entity_2, polymer, 7 residues, 2211.382 Da.

Natural source:

Natural source: Common Name: Chicken Taxonomy ID: 9031 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Gallus gallus

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAMGPSSVSGAAPFSSFMPP EQETVHVFIPAQAVGAIIGD DGQHIKQLSRFASASIKIAP PETPDSKVRMVVITGPPEAQ FKAQGRIYGKLKEENFFGPK EEVKLETHIRVPASAAGRVI GKGGKTVNELQNLTAAEVVV PRDQTPDENEQVIVKIIGHF YASQMAQRKIRDILAQVKQQ HQKGQSGQLQA
entity_2: UCGGXCU

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	439
1H chemical shifts	1033

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 191 residues - 20613.498 Da.

1

GLY

ALA

MET

GLY

PRO

SER

VAL

SER

GLY

2

ALA

PRO

PHE

SER

PHE

MET

PRO

3

GLU

GLN

GLU

THR

VAL

HIS

VAL

PHE

ILE

PRO

4

ALA

GLN

ALA

VAL

GLY

ALA

ILE

GLY

ASP

5

ASP

GLY

GLN

HIS

ILE

LYS

GLN

LEU

SER

ARG

6

PHE

ALA

SER

ALA

SER

ILE

LYS

ILE

ALA

PRO

7

PRO

GLU

THR

PRO

ASP

SER

LYS

VAL

ARG

MET

8

VAL

ILE

THR

GLY

PRO

GLU

ALA

GLN

9

PHE

LYS

ALA

GLN

GLY

ARG

ILE

TYR

GLY

LYS

10

LEU

LYS

GLU

ASN

PHE

GLY

PRO

LYS

11

GLU

VAL

LYS

LEU

GLU

THR

HIS

ILE

ARG

12

VAL

PRO

ALA

SER

ALA

GLY

ARG

VAL

ILE

13

GLY

LYS

GLY

LYS

THR

VAL

ASN

GLU

LEU

14

GLN

ASN

LEU

THR

ALA

GLU

VAL

15

PRO

ARG

ASP

GLN

THR

PRO

ASP

GLU

ASN

GLU

16

GLN

VAL

ILE

VAL

LYS

ILE

GLY

HIS

PHE

17

TYR

ALA

SER

GLN

MET

ALA

GLN

ARG

LYS

ILE

18

ARG

ASP

ILE

LEU

ALA

GLN

VAL

LYS

GLN

19

HIS

GLN

LYS

GLY

GLN

SER

GLY

GLN

LEU

GLN

20

ALA

Entity 2, unit_2 7 residues - 2211.382 Da.

1

U

C

G

6MZ

C

U

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 300 mM

sample_conditions_1: ionic strength: 0.02 Not defined; pH: 6.5; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - refinement, structure calculation

XEASY, Bartels et al. - chemical shift assignment, peak picking

NMR spectrometers:

Bruker 950 Avance 950 MHz
Bruker 800 Avance 800 MHz
Bruker 700 Avance 700 MHz