BMRB Entry 11569

Name: Chemical Shift Assignments for MIP and MDM2 in bound state
Published: 2015-06-02

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PDB ID: 2ruh
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11569
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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:

Chemical Shift Assignments for MIP and MDM2 in bound state

Deposition date:

2014-06-03

Original release date:

2015-06-02

Authors:

Nagata, Takashi; Shirakawa, Kie; Kobayashi, Naohiro; Shiheido, Hidekazu; Horisawa, Kenichi; Katahira, Masato; Doi, Nobuhide; Yanagawa, Hiroshi

Citation:

Citation: Nagata, Takashi; Shirakawa, Kie; Kobayashi, Naohiro; Shiheido, Hidekazu; Horisawa, Kenichi; Katahira, Masato; Doi, Nobuhide; Yanagawa, Hiroshi. "Structural Basis for Inhibition of the MDM2:p53 Interaction by an Optimized MDM2-Binding Peptide Selected with mRNA Display" Plos One 9, e109163-e109163 (2014).
PubMed: 25275651

Assembly members:

Assembly members:
MIP-MDM2, polymer, 131 residues, 15031.517 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: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MIP-MDM2: MPRFWEYWLRLMEGGGENLY FQGMSVPTDGAVTTSQIPAS EQETLVRPKPLLLKLLKSVG AQKDTYTMKEVLFYLGQYIM TKRLYDEKQQHIVYCSNDLL GDLFGVPSFSVKEHRKIYTM MASMTGGQQMG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	575
15N chemical shifts	115
1H chemical shifts	863

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity	1

Entities:

Entity 1, entity 131 residues - 15031.517 Da.

Residues -11Met to 1Glu corresponds to 0Met to 12Glu of MIP peptide, residues 2Gly to 10Gln represents TEV cleavage sequence, residues 11Gly to 108Met corresponds to MDM2, and residues M109 to 119Gly represents T7tag."

1

MET

PRO

ARG

PHE

TRP

GLU

TYR

TRP

LEU

ARG

2

LEU

MET

GLU

GLY

GLU

ASN

LEU

TYR

3

PHE

GLN

GLY

MET

SER

VAL

PRO

THR

ASP

GLY

4

ALA

VAL

THR

SER

GLN

ILE

PRO

ALA

SER

5

GLU

GLN

GLU

THR

LEU

VAL

ARG

PRO

LYS

PRO

6

LEU

LYS

LEU

LYS

SER

VAL

GLY

7

ALA

GLN

LYS

ASP

THR

TYR

THR

MET

LYS

GLU

8

VAL

LEU

PHE

TYR

LEU

GLY

GLN

TYR

ILE

MET

9

THR

LYS

ARG

LEU

TYR

ASP

GLU

LYS

GLN

10

HIS

ILE

VAL

TYR

CYS

SER

ASN

ASP

LEU

11

GLY

ASP

LEU

PHE

GLY

VAL

PRO

SER

PHE

SER

12

VAL

LYS

GLU

HIS

ARG

LYS

ILE

TYR

THR

MET

13

MET

ALA

SER

MET

THR

GLY

GLN

MET

14

GLY

Samples:

sample_1: MIP-MDM2 fusion, [U-100% 13C; U-100% 15N], 300 uM; TRIS 20 mM; sodium chloride 300 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 160 mM; pH: 7.6; 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_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(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 HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	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	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1

Software:

AMBER v12, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA v2.0.14, Guntert, Mumenthaler and Wuthrich - structure solution

Kujira v0.984, Naohiro Kobayashi - chemical shift assignment

NMRView, Johnson, One Moon Scientific - chemical shift assignment

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

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

SPARKY, Goddard - chemical shift assignment

CHIMERA, UCSF - data analysis

NMR spectrometers:

Bruker DRX 600 MHz

BMRB	18755 18876 2410
PDB	1RV1 1T4E 1T4F 1YCR 1Z1M 2AXI 2GV2 2LZG 2M86 2MPS 2RUH 3EQS 3G03 3IUX 3IWY 3JZK 3JZR 3JZS 3LBK 3LBL 3LNJ 3LNZ 3TJ2 3TPX 3TU1 3V3B 3VBG 3VZV 3W69 4DIJ 4ERE 4ERF 4HBM 4JV7 4JV9 4JVE 4JVR 4JWR 4MDN 4MDQ 4OAS 4OBA 4OCC 4ODE 4ODF 4OGN 4OGT 4OGV 4OQ3 4QO4 4QOC 4UMN 4WT2 4ZYC 4ZYF 4ZYI
DBJ	BAF83030 BAJ17752
EMBL	CAA78055 CAD23251 CAD36959 CAH89564 CAP16708
GB	AAA60568 AAI48523 AAI52385 AAI52391 AAI53118
PRF	1814460A
REF	NP_001124685 NP_001138809 NP_001138811 NP_001253331 NP_002383
SP	Q00987
AlphaFold	Q00987