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BMRB: 36404

7DTA

Solution structure of the C-clamp domain from human HDBP1 in complex with DNA

Authors

Duan, B., Xia, B.

Assembly

SLC2A4 regulator/DNA Complex

Entity

1. SLC2A4 regulator (polymer, Thiol state: all other bound), 33 monomers, 4022.729 Da Detail

GDAKKCRKVY GMERRDLWCT ACRWKKACQR FLD

2. DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3') (polymer, Thiol state: not present), 11 monomers, 3437.182 Da Detail

TATGCCGGGA C

3. DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3') (polymer, Thiol state: not present), 11 monomers, 3397.158 Da Detail

GTCCCGGCAT A

4. ZINC ION (non-polymer), 65.409 Da

Total weight

10922.479 Da

Max. entity weight

4022.729 Da

Entity Connection

metal coordination 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS6:SG	4:ZN1:ZN
2	metal coordination	sing	1:CYS19:SG	4:ZN1:ZN
3	metal coordination	sing	1:CYS22:SG	4:ZN1:ZN
4	metal coordination	sing	1:CYS28:SG	4:ZN1:ZN

Source organism

Exptl. method

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.5 %, Completeness (bb): 89.5 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

	Total	¹H	¹³C	¹⁵N
All	92.5 % (583 of 630)	96.3 % (419 of 435)	80.5 % (124 of 154)	97.6 % (40 of 41)
Backbone	89.5 % (315 of 352)	96.8 % (215 of 222)	69.1 % (67 of 97)	100.0 % (33 of 33)
Sidechain	96.8 % (299 of 309)	95.8 % (204 of 213)	100.0 % (88 of 88)	87.5 % (7 of 8)
Aromatic	90.7 % (78 of 86)	87.7 % (57 of 65)	100.0 % (19 of 19)	100.0 % (2 of 2)
Methyl	100.0 % (24 of 24)	100.0 % (14 of 14)	100.0 % (10 of 10)

1. SLC2A4 regulator

GDAKKCRKVY GMERRDLWCT ACRWKKACQR FLD

2. DNA (5'-D(*TP*AP*TP*GP*CP*CP*GP*GP*GP*AP*C)-3')

TATGCCGGGA C

3. DNA (5'-D(*GP*TP*CP*CP*CP*GP*GP*CP*AP*TP*A)-3')

GTCCCGGCAT A

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

Release date

2021-12-19

Citation

Selective Nonmethylated CpG DNA Recognition Mechanism of Cysteine Clamp Domains
Duan, B., Fu, D., Zhang, C., Ding, P., Dong, X., Xia, B.
J. Am. Chem. Soc. (2021), 143, 7688-7697, PubMed 33983734 , DOI 10.1021/jacs.1c00599 , Abstract

Related entities 1. SLC2A4 regulator, : 1 : 2 : 25 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

3 3D HNCACB

Instrument

Bruker AVANCE III HD - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE III HD - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

5 3D 1H-13C NOESY

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

6 3D 1H-15N NOESY

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

7 3D CCH-COSY

Instrument

Bruker AVANCE III HD - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

8 2D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

9 2D F1, F2-15N/13C-filtered 1H-1H NOESY

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

10 3D F1-15N/13C filtered, F2-15N edited NOESY

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

11 3D F1-15N/13C filtered, F2-13C edited NOESY

Instrument

Bruker AVANCE III HD - 950 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.5 mM [U-13C; U-15N] C-clamp, 0.5 mM HD5-DNA, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C-clamp	[U-13C; U-15N]	protein	0.5 (±0.01) mM
2	HD5-DNA_1	natural abundance	DNA	0.5 (±0.01) mM
3	HD5-DNA_2	natural abundance	DNA	0.5 (±0.01) mM
4	sodium phosphate	natural abundance	buffer	10 mM
5	NaCl	natural abundance	salt	10 mM
6	H2O	natural abundance	solvent	95 %
7	D2O	[U-2H]	solvent	5 %

Chemical shift validation 6 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr36404_3.str
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)
1:6:CYS:SG	4:1:ZN:ZN	reduced, CA 67.313, CB 30.883 ppm	unknown	n/a
1:19:CYS:SG	4:1:ZN:ZN	reduced, CA 58.669, CB 30.45 ppm	unknown	n/a
1:22:CYS:SG	4:1:ZN:ZN	reduced, CA 65.543, CB 28.9 ppm	unknown	n/a
1:28:CYS:SG	4:1:ZN:ZN	oxidized 3.9%, reduced 96.1%, CA 62.36, CB 33.12 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr36404_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	611		100.0 (chain: 2, length: 11), 100.0 (chain: 1, length: 33), 100.0 (chain: 3, length: 11)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 2, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: 1, Chain length: 33, Sequence coverage: 100.0%
  - Entity_assembly_ID: 3, Chain length: 11, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 450
  - ¹³C chemical shifts: 121
  - ¹⁵N chemical shifts: 40
- Completeness of assignments
  - Entity_assemble_ID: 2
  - Entity_assemble_ID: 1
  - Entity_assemble_ID: 3
- Redox state of CYS
- 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: 1

Keywords C-clamp, DNA BINDING PROTEIN, unmethylated CpG binding, zinc finger