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BMRB: 34149

5O9B

Solution NMR structure of human GATA2 C-terminal zinc finger domain

Authors

Nurmohamed, S.S., Broadhurst, R.W., May, G., Enver, T.

Assembly

Endothelial transcription factor GATA-2

Entity

1. Endothelial transcription factor GATA-2, entity 1 (polymer, Thiol state: free and other bound), 68 monomers, 7685.667 Da Detail

MAHHHHHHSS GLEVLFQGPR RAGTCCANCQ TTTTTLWRRN ANGDPVCNAC GLYYKLHNVN RPLTMKKE

2. Endothelial transcription factor GATA-2, entity ZN (non-polymer), 65.409 Da

Total weight

7751.076 Da

Max. entity weight

7685.667 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS26:SG	2:ZN1:ZN
2	na	sing	1:CYS29:SG	2:ZN1:ZN
3	na	sing	1:CYS47:SG	2:ZN1:ZN
4	na	sing	1:CYS50:SG	2:ZN1:ZN

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.2 %, Completeness: 71.3 %, Completeness (bb): 73.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.3 % (547 of 767)	74.4 % (296 of 398)	63.1 % (186 of 295)	87.8 % (65 of 74)
Backbone	73.6 % (296 of 402)	85.5 % (118 of 138)	61.3 % (122 of 199)	86.2 % (56 of 65)
Sidechain	71.7 % (307 of 428)	68.5 % (178 of 260)	75.5 % (120 of 159)	100.0 % (9 of 9)
Aromatic	63.6 % (42 of 66)	63.6 % (21 of 33)	62.5 % (20 of 32)	100.0 % (1 of 1)
Methyl	88.3 % (53 of 60)	96.7 % (29 of 30)	80.0 % (24 of 30)

1. entity 1

MAHHHHHHSS GLEVLFQGPR RAGTCCANCQ TTTTTLWRRN ANGDPVCNAC GLYYKLHNVN RPLTMKKE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

LACS Plot; CA

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5O9B, Strand ID: A Detail

Release date

2018-05-13

Citation

Solution NMR structure of human GATA2 C-terminal zinc finger domain
Nurmohamed, S.S., Broadhurst, R.W., May, G., Enver, T.

Related entities 1. Endothelial transcription factor GATA-2, entity 1, : 1 : 14 entities Detail

Experiments performed 10 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker DRX800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

2 3D 1H-13C NOESY

Instrument

Bruker DRX800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

3 3D HNCA

Instrument

Bruker DRX500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

4 3D HNCACB

Instrument

Bruker DRX500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

5 3D CBCA(CO)NH

Instrument

Bruker DRX500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

6 3D 1H-15N TOCSY

Instrument

Bruker DRX500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

7 3D HBHA(CO)NH

Instrument

Bruker DRX500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

8 3D HNCO

Instrument

Bruker DRX500 - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

9 2D 1H-15N HSQC

Instrument

Bruker DRX800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

10 2D 1H-13C HSQC

Instrument

Bruker DRX800 - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 Pa, Temperature 273 K, pH 7, Details 10 mg/L [U-99% 13C; U-99% 15N] GATA2 Zinc Finger 2, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	GATA2 Zinc Finger 2	[U-99% 13C; U-99% 15N]		10 mg/L

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34149_5o9b.nef
Input source #2: Coordindates	5o9b.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:26:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:29:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:47:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:50:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---------------------------10--------20--------30--------40---------
MAHHHHHHSSGLEVLFQGPRRAGTCCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNVNRPLTMKKE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAHHHHHHSSGLEVLFQGPRRAGTCCANCQTTTTTLWRRNANGDPVCNACGLYYKLHNVNRPLTMKKE
--------10--------20--------30--------40--------50--------60--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	68	0	0	100.0

Content subtype: combined_34149_5o9b.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	536		89.7 (chain: A, length: 68)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1161 (1)	noe	72.1 (chain: A, length: 68)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 89.7%
- Total number of assignments
  - ¹H chemical shifts: 294
  - ¹³C chemical shifts: 178
  - ¹⁵N chemical shifts: 64
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 68, Sequence coverage: 72.1%
- Total number of restraints: 1161
- Weight of restraints: 1.0 (1161)
- Potential type of restraints: square-well-parabolic (1161)
- Range of distance target values: 2.0, 4.8 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Keywords GATA, Haematopoeisis, Transcription factor, transcription