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BMRB: 18874

2M1R

PHD domain of ING4 N214D mutant

Authors

Assembly

ING4 PHD mutant N214D

Entity

1. ING4 PHD mutant N214D (polymer, Thiol state: all free), 63 monomers, 7316.377 Da Detail

MDMPVDPNEP TYCLCHQVSY GEMIGCDDPD CSIEWFHFAC VGLTTKPRGK WFCPRCSQER KKK

2. ING4 PHD mutant N214D, entity ZN (non-polymer), 65.409 × 2 Da

Total weight

7447.195 Da

Max. entity weight

7316.377 Da

Entity Connection

metal coordination 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS26:SG	2:ZN1:ZN
2	metal coordination	sing	1:CYS31:SG	2:ZN1:ZN
3	metal coordination	sing	1:CYS53:SG	2:ZN1:ZN
4	metal coordination	sing	1:CYS56:SG	2:ZN1:ZN
5	metal coordination	sing	1:CYS13:SG	2:ZN1:ZN
6	metal coordination	sing	1:CYS15:SG	2:ZN1:ZN
7	metal coordination	sing	1:CYS40:SG	2:ZN1:ZN
8	metal coordination	sing	1:HIS37:ND1	2:ZN1:ZN

Source organism

Exptl. method

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.2 %, Completeness (bb): 98.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	85.2 % (386 of 453)	83.1 % (325 of 391)	98.4 % (61 of 62)
Backbone	98.9 % (179 of 181)	99.2 % (123 of 124)	98.2 % (56 of 57)
Sidechain	76.1 % (207 of 272)	75.7 % (202 of 267)	100.0 % (5 of 5)
Aromatic	63.4 % (26 of 41)	61.5 % (24 of 39)	100.0 % (2 of 2)
Methyl	100.0 % (18 of 18)	100.0 % (18 of 18)

1. ING4 PHD mutant N214D

MDMPVDPNEP TYCLCHQVSY GEMIGCDDPD CSIEWFHFAC VGLTTKPRGK WFCPRCSQER KKK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5 (±0.1), Details 0.5 mL of protein sample in 5mm NMR tube at 25 C

#	Name	Isotope labeling	Type	Concentration
1	ING4 PHD mutant N214D	[U-100% 15N]		0.5 (±0.05) mM
2	DSS	natural abundance		30 uM
3	DTT	natural abundance		1 (±0.1) mM
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±5.0) mM

Protein Blocks Logo

Calculated from 25 models in PDB: 2M1R, Strand ID: A Detail

Release date

2012-12-12

Citation

Functional impact of cancer-associated mutations in the tumor suppressor protein ING4
Blanco, F.J., Palmero, I.
Carcinogenesis (2010), 31, 1932-1938, PubMed 20705953 , DOI 10.1093/carcin/bgq171 , Abstract

Related entities 1. ING4 PHD mutant N214D, : 1 : 7 : 114 entities Detail

Interaction partners 1. ING4 PHD mutant N214D, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 5 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz Cryoprobe triple resonance Z-gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5 (±0.1), Details 0.5 mL of protein sample in 5mm NMR tube at 25 C

#	Name	Isotope labeling	Type	Concentration
1	ING4 PHD mutant N214D	[U-100% 15N]		0.5 (±0.05) mM
2	DSS	natural abundance		30 uM
3	DTT	natural abundance		1 (±0.1) mM
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±5.0) mM

2 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz Cryoprobe triple resonance Z-gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5 (±0.1), Details 0.5 mL of protein sample in 5mm NMR tube at 25 C

#	Name	Isotope labeling	Type	Concentration
1	ING4 PHD mutant N214D	[U-100% 15N]		0.5 (±0.05) mM
2	DSS	natural abundance		30 uM
3	DTT	natural abundance		1 (±0.1) mM
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±5.0) mM

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz Cryoprobe triple resonance Z-gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5 (±0.1), Details 0.5 mL of protein sample in 5mm NMR tube at 25 C

#	Name	Isotope labeling	Type	Concentration
1	ING4 PHD mutant N214D	[U-100% 15N]		0.5 (±0.05) mM
2	DSS	natural abundance		30 uM
3	DTT	natural abundance		1 (±0.1) mM
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±5.0) mM

4 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz Cryoprobe triple resonance Z-gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5 (±0.1), Details 0.5 mL of protein sample in 5mm NMR tube at 25 C

#	Name	Isotope labeling	Type	Concentration
1	ING4 PHD mutant N214D	[U-100% 15N]		0.5 (±0.05) mM
2	DSS	natural abundance		30 uM
3	DTT	natural abundance		1 (±0.1) mM
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±5.0) mM

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 700 MHz Triple resonance XYZ gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 6.5 (±0.1), Details 0.5 mL of protein sample in 5mm NMR tube at 25 C

#	Name	Isotope labeling	Type	Concentration
1	ING4 PHD mutant N214D	[U-100% 15N]		0.5 (±0.05) mM
2	DSS	natural abundance		30 uM
3	DTT	natural abundance		1 (±0.1) mM
4	sodium phosphate	natural abundance		20 (±2.0) mM
5	sodium chloride	natural abundance		50 (±5.0) mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18874_2m1r.nef
Input source #2: Coordindates	2m1r.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)
1:20:TYR:OH	2:1:ZN:ZN	unknown	unknown	n/a
1:31:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:53:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:15:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:40: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
B	2	ZN	ZINC ION	None

Sequence alignments

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

---190-----200-------210-------220-------230-------240---------
MDMPVDPNEPTYCLCHQVSYGEMIGCDDPDCSIEWFHFACVGLTTKPRGKWFCPRCSQERKKK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDMPVDPNEPTYCLCHQVSYGEMIGCDDPDCSIEWFHFACVGLTTKPRGKWFCPRCSQERKKK
--------10--------20--------30--------40--------50--------60---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	63	0	0	100.0

Content subtype: combined_18874_2m1r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	393		100.0 (chain: A, length: 63)
1	Distance restraints	AMBER_distance_constraints_2	Warning	1994 (1)	noe	95.2 (chain: A, length: 63)
1	Dihedral angle restraints	AMBER_dihedral_4	OK	1	.	No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 332
  - ¹⁵N chemical shifts: 61
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: AMBER_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 95.2%
- Total number of restraints: 1987
- Weight of restraints: 1.0 (1987)
- Potential type of restraints: square-well-parabolic (1987)
- Range of distance target values: 2.35, 8.02 (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: AMBER_dihedral_4
- Status: OK
- Experiment type: .

Keywords cancer, ING4, PHD, tumor supressor