BMRB Entry 19230

Name: Solution structure of Hdm2 with engineered cyclotide
Published: 2013-07-29

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PDB ID: 2m86
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19230
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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:

Solution structure of Hdm2 with engineered cyclotide

Deposition date:

2013-05-07

Original release date:

2013-07-29

Authors:

Majumder, Subhabrata; Ji, Yanbin; Millard, Melissa; Borra, Radikha; Bi, Tao; Elnagar, Ahmed; Neamati, Nouri; Camarero, Julio

Citation:

Citation: Ji, Yanbin; Majumder, Subhabrata; Millard, Melissa; Borra, Radhika; Bi, Tao; Elnagar, Ahmed; Neamati, Nouri; Shekhtman, Alexander; Camarero, Julio. "In Vivo Activation of the p53 Tumor Suppressor Pathway by an Engineered Cyclotide." J. Am. Chem. Soc. 135, 11623-11633 (2013).
PubMed: 23848581

Assembly members:

Assembly members:
Hdm2, polymer, 51 residues, 5291.016 Da.
MCo-PMI, polymer, 83 residues, 9814.753 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: pTXB1

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Hdm2: SGSGASKAPTSFAEYWNLLS AGGVCPKILQRCRRDSDCPG ACICRGNGYCG
MCo-PMI: LVRPKPLLLKLLKSVGAQKD TYTMKEVLFYLGQYIMTKRL YDEKQQHIVYCSNDLLGDLF GVPSFSVKEHRKIYTMIYRN LVV

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	147
15N chemical shifts	121
1H chemical shifts	581

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Hdm2	1
2	MCo-PMI	2

Entities:

Entity 1, Hdm2 51 residues - 5291.016 Da.

This is an engineered cyclotide based on MCoTI-I., cyclic-pseudo-peptide

1

SER

GLY

SER

GLY

ALA

SER

LYS

ALA

PRO

THR

2

SER

PHE

ALA

GLU

TYR

TRP

ASN

LEU

SER

3

ALA

GLY

VAL

CYS

PRO

LYS

ILE

LEU

GLN

4

ARG

CYS

ARG

ASP

SER

ASP

CYS

PRO

GLY

5

ALA

CYS

ILE

CYS

ARG

GLY

ASN

GLY

TYR

CYS

6

GLY

Entity 2, MCo-PMI 83 residues - 9814.753 Da.

1

LEU

VAL

ARG

PRO

LYS

PRO

LEU

LYS

2

LEU

LYS

SER

VAL

GLY

ALA

GLN

LYS

ASP

3

THR

TYR

THR

MET

LYS

GLU

VAL

LEU

PHE

TYR

4

LEU

GLY

GLN

TYR

ILE

MET

THR

LYS

ARG

LEU

5

TYR

ASP

GLU

LYS

GLN

HIS

ILE

VAL

TYR

6

CYS

SER

ASN

ASP

LEU

GLY

ASP

LEU

PHE

7

GLY

VAL

PRO

SER

PHE

SER

VAL

LYS

GLU

HIS

8

ARG

LYS

ILE

TYR

THR

MET

ILE

TYR

ARG

ASN

9

LEU

VAL

Samples:

sample_1: MCo-PMI 0.2 mM; Hdm2, [U-99% 13C; U-99% 15N], 0.2 mM; H2O 90%; D2O 10%

sample_2: MCo-PMI, [U-99% 15N], 0.2 mM; Hdm2 0.2 mM; H2O 90%; D2O 10%

Sample_3: MCo-PMI 0.2 mM; Hdm2 0.2 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.133 M; pH: 6.5; pressure: 1 atm; temperature: 300 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	Sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

CHRMM v36, CHARMM-Karplus M. - refinement

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

NMR spectrometers:

Bruker Avance 700 MHz

PDB	2M86 1RV1 1T4E 1T4F 1YCR 1Z1M 2AXI 2GV2 2LZG 2M86 2RUH 3EQS 3G03 3IUX 3IWY 3JZK 3JZR 3JZS 3LBK 3LBL 3LNJ 3LNZ 3TJ2 3TPX 3TU1 3V3B 3VBG 3VZV 3W69 4DIJ 4ERE 4ERF 4HBM 4HFZ 4HG7 4JV7 4JV9 4JVE 4JVR 4JWR 4MDN 4MDQ 4OAS 4OBA 4OCC 4ODE 4ODF 4OGN 4OGT 4OGV 4OQ3 4QO4 4UMN 4WT2
BMRB	15945 18755 2410 6612
DBJ	BAB11975 BAC78209 BAF83030 BAJ17752
EMBL	CAA78055 CAD23251 CAD36959 CAH89564 CAP16708
GB	AAA60568 AAF28866 AAF67833 AAG42840 AAG42841
PRF	1814460A
REF	NP_001003103 NP_001009346 NP_001092577 NP_001098773 NP_001124685
SP	P56950 P56951 Q00987 Q7YRZ8
TPG	DAA29805
AlphaFold	P56950 P56951 Q00987 Q7YRZ8