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BMRB: 18944

2M34

NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens

Authors

Proudfoot, A., Serrano, P., Geralt, M., Wuthrich, K.

Assembly

Gbx1

Entity

1. Gbx1 (polymer, Thiol state: all free), 71 monomers, 8327.546 Da Detail

SAPGGKSRRR RTAFTSEQLL ELEKEFHCKK YLSLTERSQI AHALKLSEVQ VKIWFQNRRA KWKRIKAGNV S

Formula weight

8327.546 Da

Source organism

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 86.9 %, Completeness (bb): 83.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.9 % (771 of 887)	92.6 % (437 of 472)	76.9 % (259 of 337)	96.2 % (75 of 78)
Backbone	83.3 % (353 of 424)	97.2 % (140 of 144)	69.5 % (146 of 210)	95.7 % (67 of 70)
Sidechain	91.3 % (485 of 531)	90.5 % (297 of 328)	92.3 % (180 of 195)	100.0 % (8 of 8)
Aromatic	85.7 % (60 of 70)	88.6 % (31 of 35)	81.8 % (27 of 33)	100.0 % (2 of 2)
Methyl	98.6 % (69 of 70)	97.1 % (34 of 35)	100.0 % (35 of 35)

1. Gbx1

SAPGGKSRRR RTAFTSEQLL ELEKEFHCKK YLSLTERSQI AHALKLSEVQ VKIWFQNRRA KWKRIKAGNV S

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]		0.8 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M34, Strand ID: A Detail

Release date

2016-10-19

Citation

Dynamic Local Polymorphisms in the Gbx1 Homeodomain Induced by DNA Binding
Proudfoot, A.K., Geralt, M., Elsliger, M., Wilson, I.A., Wuthrich, K., Serrano, P.
Structure (2016), 24, 1372-1379, PubMed 27396829 , DOI 10.1016/j.str.2016.05.013 , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 19511 released on 2016-10-19
    Title NMR Structure of the homeodomain transcription factor Gbx1 from Homo sapiens solved in the presence of the DNA sequence CGACTAATTAGTCG
  BMRB: 25849 released on 2015-10-25
    Title NMR Structure of the homeodomain transcription factor Gbx1[E17R,R52E} from Homo sapiens

Related entities 1. Gbx1, : 1 : 2 : 2 : 2 : 270 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]		0.8 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]		0.8 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]		0.8 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]		0.8 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 APSY 4D-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]		0.8 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 APSY 5D-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]		0.8 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 APSY 5D-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	Gbx1	[U-98% 13C; U-98% 15N]		0.8 mM
2	sodium chloride	natural abundance		50 mM
3	sodium phosphate	natural abundance		20 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18944_2m34.nef
Input source #2: Coordindates	2m34.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70-
SAPGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKAGNVS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SAPGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKAGNVS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	71	0	0	100.0

Content subtype: combined_18944_2m34.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	749		97.2 (chain: A, length: 71)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1408 (1)	noe	94.4 (chain: A, length: 71)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 97.2%
- Total number of assignments
  - ¹H chemical shifts: 430
  - ¹³C chemical shifts: 245
  - ¹⁵N chemical shifts: 74
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 71, Sequence coverage: 94.4%
- Total number of restraints: 1396
- Weight of restraints: 1.0 (1396)
- Potential type of restraints: upper-bound-parabolic (1396)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords DNA binding, Homeodomain