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BMRB: 17494

2L9Z

Zinc knuckle in PRDM4

Authors

Briknarova, K., Atwater, D.Z., Glicken, J.M., Maynard, S.J., Ness, T.E.

Assembly

Zinc knuckle in PRDM4

Entity

1. PRDM4(366-402) (polymer, Thiol state: all other bound), 39 monomers, 4313.859 Da Detail

GSKENMATLF TIWCTLCDRA YPSDCPEHGP VTFVPDTPI

2. ZN (non-polymer, Thiol state: not present), 65.409 Da

Total weight

4379.268 Da

Max. entity weight

4313.859 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS28:ND1	2:ZN1:ZN
2	na	sing	1:CYS14:SG	2:ZN1:ZN
3	na	sing	1:CYS17:SG	2:ZN1:ZN
4	na	sing	1:CYS25:SG	2:ZN1:ZN

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 96.9 %, Completeness (bb): 92.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	96.9 % (251 of 259)	97.8 % (218 of 223)	91.7 % (33 of 36)
Backbone	92.7 % (101 of 109)	93.3 % (70 of 75)	91.2 % (31 of 34)
Sidechain	100.0 % (150 of 150)	100.0 % (148 of 148)	100.0 % (2 of 2)
Aromatic	100.0 % (23 of 23)	100.0 % (22 of 22)	100.0 % (1 of 1)
Methyl	100.0 % (19 of 19)	100.0 % (19 of 19)

1. PRDM4(366-402)

GSKENMATLF TIWCTLCDRA YPSDCPEHGP VTFVPDTPI

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	PRDM4(366-402)	natural abundance		0.5 mM
2	ZINC ION	natural abundance		2.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %
5	d11-Tris	natural abundance		50 mM
6	d16-TCEP	natural abundance		2.5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	PRDM4(366-402)	natural abundance		0.5 mM
8	ZINC ION	natural abundance		2.5 mM
9	D2O	natural abundance		100 %
10	d11-Tris	natural abundance		50 mM
11	d16-TCEP	natural abundance		2.5 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
12	PRDM4(366-402)	[U-100% 15N]		0.25 mM
13	ZINC ION	natural abundance		1.6 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %
16	d11-Tris	natural abundance		50 mM
17	d16-TCEP	natural abundance		2.5 mM

Protein Blocks Logo

Calculated from 10 models in PDB: 2L9Z, Strand ID: A Detail

Release date

2011-05-31

Citation

The PR/SET domain in PRDM4 is preceded by a zinc knuckle
Briknarova, K., Atwater, D.Z., Glicken, J.M., Maynard, S.J., Ness, T.E.
Proteins (2011), 79, 2341-2345, PubMed 21604305 , DOI 10.1002/prot.23057 , Abstract

Related entities 1. PRDM4(366-402), : 1 : 15 entities Detail

Interaction partners 1. PRDM4(366-402), : 5 interactors Detail

More details for 5 interactors identified by 4 citations

Experiments performed 10 experiments Detail

1 2D DQF-COSY

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	PRDM4(366-402)	natural abundance		0.5 mM
2	ZINC ION	natural abundance		2.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %
5	d11-Tris	natural abundance		50 mM
6	d16-TCEP	natural abundance		2.5 mM

2 2D 1H-1H TOCSY

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	PRDM4(366-402)	natural abundance		0.5 mM
2	ZINC ION	natural abundance		2.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %
5	d11-Tris	natural abundance		50 mM
6	d16-TCEP	natural abundance		2.5 mM

3 2D 1H-1H NOESY

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	PRDM4(366-402)	natural abundance		0.5 mM
2	ZINC ION	natural abundance		2.5 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %
5	d11-Tris	natural abundance		50 mM
6	d16-TCEP	natural abundance		2.5 mM

4 ECOSY

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
7	PRDM4(366-402)	natural abundance		0.5 mM
8	ZINC ION	natural abundance		2.5 mM
9	D2O	natural abundance		100 %
10	d11-Tris	natural abundance		50 mM
11	d16-TCEP	natural abundance		2.5 mM

5 2D 1H-15N HSQC

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
12	PRDM4(366-402)	[U-100% 15N]		0.25 mM
13	ZINC ION	natural abundance		1.6 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %
16	d11-Tris	natural abundance		50 mM
17	d16-TCEP	natural abundance		2.5 mM

6 3D HNHA

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
12	PRDM4(366-402)	[U-100% 15N]		0.25 mM
13	ZINC ION	natural abundance		1.6 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %
16	d11-Tris	natural abundance		50 mM
17	d16-TCEP	natural abundance		2.5 mM

7 3D HNHB

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
12	PRDM4(366-402)	[U-100% 15N]		0.25 mM
13	ZINC ION	natural abundance		1.6 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %
16	d11-Tris	natural abundance		50 mM
17	d16-TCEP	natural abundance		2.5 mM

8 3D 1H-15N TOCSY

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
12	PRDM4(366-402)	[U-100% 15N]		0.25 mM
13	ZINC ION	natural abundance		1.6 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %
16	d11-Tris	natural abundance		50 mM
17	d16-TCEP	natural abundance		2.5 mM

9 3D 1H-15N NOESY

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
12	PRDM4(366-402)	[U-100% 15N]		0.25 mM
13	ZINC ION	natural abundance		1.6 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %
16	d11-Tris	natural abundance		50 mM
17	d16-TCEP	natural abundance		2.5 mM

10 2D 1H-15N HMQC

Instrument

Varian Uniform NMR System - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.15 (±0.1)

#	Name	Isotope labeling	Type	Concentration
12	PRDM4(366-402)	[U-100% 15N]		0.25 mM
13	ZINC ION	natural abundance		1.6 mM
14	H2O	natural abundance		90 %
15	D2O	natural abundance		10 %
16	d11-Tris	natural abundance		50 mM
17	d16-TCEP	natural abundance		2.5 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17494_2l9z.nef
Input source #2: Coordindates	2l9z.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)
1:28:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:14:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:17:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:25: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

----370-------380-------390-------400--
GSKENMATLFTIWCTLCDRAYPSDCPEHGPVTFVPDTPI
|||||||||||||||||||||||||||||||||||||||
GSKENMATLFTIWCTLCDRAYPSDCPEHGPVTFVPDTPI
--------10--------20--------30---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	39	0	0	100.0

Content subtype: combined_17494_2l9z.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_chem_shift_list_1	Warning	254		97.4 (chain: A, length: 39)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	949 (1)	noe	92.3 (chain: A, length: 39)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	26 (26)	.	71.8 (chain: A, length: 39)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 39, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 218
  - ¹⁵N chemical shifts: 36
- Completeness of assignments
  - Entity_assemble_ID: A
- Tautomeric state of HIS
- 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_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 39, Sequence coverage: 92.3%
- Total number of restraints: 949
- Weight of restraints: 1.0 (949)
- Potential type of restraints: square-well-parabolic (949)
- Range of distance target values: 1.48, 6.58 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 39, Sequence coverage: 71.8%
- Total number of restraints: 26
- Total number of restraints per polymer type: 26
- Weight of restraints: 1.0 (26)
- Potential type of restraints: square-well-parabolic (26)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords meisetz, PRDM10, PRDM4, PRDM6, PRDM9, PR domain, SET domain, zinc-binding domain, zinc knuckle