BMRB Entry 19540

Name: haddock model of MyT1 F4F5 - DNA complex
Published: 2013-11-04

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PDB ID: 2mf8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19540
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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:

haddock model of MyT1 F4F5 - DNA complex

Deposition date:

2013-10-08

Original release date:

2013-11-04

Authors:

Gamsjaeger, Roland; O'Connell, Mitchell; Cubeddu, Liza; Shepherd, Nicholas; Lowry, Jason; Kwan, Ann; Vandevenne, Marylene; Swanton, Michael; Matthews, Jacqueline; Mackay, Joel

Citation:

Citation: Gamsjaeger, Roland; Cubeddu, Mitchell; Shepherd, Liza; Lowry, Nicholas; Kwan, Jason; Vandevenne, Ann; Swanton, Marylene; Matthews, Michael; Mackay, Jacqueline. "A structural analysis of DNA binding by myelin transcription factor 1 double zinc fingers." J. Biol. Chem. 288, 35180-35191 (2013).
PubMed: 24097990

Assembly members:

Assembly members:
entity_1, polymer, 93 residues, 65.380 Da.
DNA_26_mer, polymer, 26 residues, Formula weight is not available
entity_ZN, non-polymer, 65.409 Da.

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 Vector: pGEX-6P

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPLGSFDIKKELLTCPTPGC DGSGHITGNYASHRSLSGCP LADKSLRNLMAAHSADLKCP TPGCDGSGHITGNYASHRSL SGCPRAKKSGLRV
DNA_26_mer: ACCGAAAGTTCACGTGAACT TTCGGT

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	115
15N chemical shifts	51
1H chemical shifts	51

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Myelin transcription factor 1	1
2	DNA (26-MER)	2
3	ZINC ION_1	3
4	ZINC ION_2	3

Entities:

Entity 1, Myelin transcription factor 1 93 residues - 65.380 Da.

1

GLY

PRO

LEU

GLY

SER

PHE

ASP

ILE

LYS

2

GLU

LEU

THR

CYS

PRO

THR

PRO

GLY

CYS

3

ASP

GLY

SER

GLY

HIS

ILE

THR

GLY

ASN

TYR

4

ALA

SER

HIS

ARG

SER

LEU

SER

GLY

CYS

PRO

5

LEU

ALA

ASP

LYS

SER

LEU

ARG

ASN

LEU

MET

6

ALA

HIS

SER

ALA

ASP

LEU

LYS

CYS

PRO

7

THR

PRO

GLY

CYS

ASP

GLY

SER

GLY

HIS

ILE

8

THR

GLY

ASN

TYR

ALA

SER

HIS

ARG

SER

LEU

9

SER

GLY

CYS

PRO

ARG

ALA

LYS

SER

GLY

10

LEU

ARG

VAL

Entity 2, DNA (26-MER) 26 residues - Formula weight is not available

1

DA

DC

DG

DA

DG

DT

2

DC

DA

DC

DG

DT

DG

DA

DC

DT

3

DT

DC

DG

DT

Entity 3, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: Myelin transcription factor 1, [U-13C; U-15N], 0.2 – 1.0 mM; DNA (26-MER)0.2 – 1.0 mM; phosphate 10 mM; NaCl 50 mM; DTT 1 mM

sample_conditions_1: ionic strength: 60 mM; pH: 7.2; 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-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

HADDOCK, Alexandre Bonvin - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz