BMRB Entry 31098

Name: Solution structure of the zinc finger repeat domain of BCL11A (ZnF456)
Published: 2024-07-17

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PDB ID: 8tho
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31098
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:

Solution structure of the zinc finger repeat domain of BCL11A (ZnF456)

Deposition date:

2023-07-17

Original release date:

2024-07-17

Authors:

Viennet, T.; Yin, M.; Orkin, S.; Arthanari, H.

Citation:

Citation: Viennet, T.; Yin, M.; Jayaraj, A.; Kim, W.; Sun, Z.-Y.J.; Seo, H.-S.; Dhe-Paganon, S.; Orkin, S.; Arthanari, H.. "Structural and dynamic investigation of DNA-binding by BCL11A reveals a specific role for ZnF6" .

Assembly members:

Assembly members:
entity_1, polymer, 100 residues, 11703.447 Da.
entity_ZN, non-polymer, 65.409 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SEGRRSDTCEYCGKVFKNCS NLTVHRRSHTGERPYKCELC NYACAQSSKLTRHMKTHGQV GKDVYKCEICKMPFSVYSTL EKHMKKWHSDRVLNNDIKTE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	311
15N chemical shifts	97
1H chemical shifts	551

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
3	unit_3	2
4	unit_4	2

Entities:

Entity 1, unit_1 100 residues - 11703.447 Da.

1	SER	GLU	GLY	ARG	ARG	SER	ASP	THR	CYS	GLU
2	TYR	CYS	GLY	LYS	VAL	PHE	LYS	ASN	CYS	SER
3	ASN	LEU	THR	VAL	HIS	ARG	ARG	SER	HIS	THR
4	GLY	GLU	ARG	PRO	TYR	LYS	CYS	GLU	LEU	CYS
5	ASN	TYR	ALA	CYS	ALA	GLN	SER	SER	LYS	LEU
6	THR	ARG	HIS	MET	LYS	THR	HIS	GLY	GLN	VAL
7	GLY	LYS	ASP	VAL	TYR	LYS	CYS	GLU	ILE	CYS
8	LYS	MET	PRO	PHE	SER	VAL	TYR	SER	THR	LEU
9	GLU	LYS	HIS	MET	LYS	LYS	TRP	HIS	SER	ASP
10	ARG	VAL	LEU	ASN	ASN	ASP	ILE	LYS	THR	GLU

Entity 2, unit_2 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: sodium chloride 137 mM; potassium chloride 2.7 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; dithiothreitol 1 mM

sample_conditions_1: ionic strength: 163 mM; pH: 6.0; 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 aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment

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

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman - refinement

NMR spectrometers:

Bruker AVANCE III HD 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	SER	GLU	GLY	ARG	ARG	SER	ASP	THR	CYS	GLU
2	TYR	CYS	GLY	LYS	VAL	PHE	LYS	ASN	CYS	SER
3	ASN	LEU	THR	VAL	HIS	ARG	ARG	SER	HIS	THR
4	GLY	GLU	ARG	PRO	TYR	LYS	CYS	GLU	LEU	CYS
5	ASN	TYR	ALA	CYS	ALA	GLN	SER	SER	LYS	LEU
6	THR	ARG	HIS	MET	LYS	THR	HIS	GLY	GLN	VAL
7	GLY	LYS	ASP	VAL	TYR	LYS	CYS	GLU	ILE	CYS
8	LYS	MET	PRO	PHE	SER	VAL	TYR	SER	THR	LEU
9	GLU	LYS	HIS	MET	LYS	LYS	TRP	HIS	SER	ASP
10	ARG	VAL	LEU	ASN	ASN	ASP	ILE	LYS	THR	GLU

1	SER	GLU	GLY	ARG	ARG	SER	ASP	THR	CYS	GLU
2	TYR	CYS	GLY	LYS	VAL	PHE	LYS	ASN	CYS	SER
3	ASN	LEU	THR	VAL	HIS	ARG	ARG	SER	HIS	THR
4	GLY	GLU	ARG	PRO	TYR	LYS	CYS	GLU	LEU	CYS
5	ASN	TYR	ALA	CYS	ALA	GLN	SER	SER	LYS	LEU
6	THR	ARG	HIS	MET	LYS	THR	HIS	GLY	GLN	VAL
7	GLY	LYS	ASP	VAL	TYR	LYS	CYS	GLU	ILE	CYS
8	LYS	MET	PRO	PHE	SER	VAL	TYR	SER	THR	LEU
9	GLU	LYS	HIS	MET	LYS	LYS	TRP	HIS	SER	ASP
10	ARG	VAL	LEU	ASN	ASN	ASP	ILE	LYS	THR	GLU

1	SER	GLU	GLY	ARG	ARG	SER	ASP	THR	CYS	GLU
2	TYR	CYS	GLY	LYS	VAL	PHE	LYS	ASN	CYS	SER
3	ASN	LEU	THR	VAL	HIS	ARG	ARG	SER	HIS	THR
4	GLY	GLU	ARG	PRO	TYR	LYS	CYS	GLU	LEU	CYS
5	ASN	TYR	ALA	CYS	ALA	GLN	SER	SER	LYS	LEU
6	THR	ARG	HIS	MET	LYS	THR	HIS	GLY	GLN	VAL
7	GLY	LYS	ASP	VAL	TYR	LYS	CYS	GLU	ILE	CYS
8	LYS	MET	PRO	PHE	SER	VAL	TYR	SER	THR	LEU
9	GLU	LYS	HIS	MET	LYS	LYS	TRP	HIS	SER	ASP
10	ARG	VAL	LEU	ASN	ASN	ASP	ILE	LYS	THR	GLU