BMRB Entry 25855

Name: Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the RNA target UCGGACU
Published: 2017-01-19

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PDB ID: 2n8m
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25855
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:

Zipcode-binding-protein-1 KH3(DD)KH4 domains in complex with the RNA target UCGGACU

Deposition date:

2015-10-21

Original release date:

2017-01-19

Authors:

Nicastro, Giuseppe; Ramos, Andres; Candel, Adela; Hollingworth, David

Citation:

Citation: Hollingworth, David; Candel, Adela; Nicastro, Giuseppe; Martin, Stephen; Briata, Paola; Gherzi, Roberto; Ramos, Andres. "KH domains with impaired nucleic acid binding as a tool for functional analysis." Nucleic Acids Res. 40, 6873-6886 (2012).
PubMed: 22547390

Assembly members:

Assembly members:
entity_1, polymer, 191 residues, 20613.682 Da.
entity_2, polymer, 8 residues, Formula weight is not available

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GAMGPSSVSGAAPFSSFMPP EQETVHVFIPAQAVGAIIGK KGQHIKQLSRFASASIKIAP PETPDSKVRMVVITGPPEAQ FKAQGRIYGKLKEENFFGPK EEVKLETHIRVPASAAGRVI GKGGKTVNELQNLTAAEVVV PRDQTPDENEQVIVKIIGHF YASQMAQRKIRDILAQVKQQ HQKGQSGQLQA
entity_2: UCGGACU

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	403
1H chemical shifts	941

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_1 191 residues - 20613.682 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

LYS

5

LYS

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, entity_2 8 residues - Formula weight is not available

1

U

C

G

A

C

U

Samples:

sample_1: entity_1, [U-100% 13C; U-100% 15N], 0.3 mM; entity_2 0.3 mM; phosphate buffer 20 mM; potassium phosphate 20 mM

sample_conditions_1: ionic strength: 0.02 M; 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-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

XEASY, Bartels et al. - chemical shift assignment

ARIA, Linge, O'Donoghue and Nilges - structure solution

NMR spectrometers:

Varian INOVA 800 MHz
Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 950 MHz