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Found 1 Document (1.346 seconds)

BMRB: 25933

2NAA

NSD1-PHD_5-C5HCH tandem domain structure

Authors

Berardi, A., Quilici, G., Spiliotopoulos, D., Musco, G.

Assembly

NSD1-PHD 5-C5HCH tandem domain

Entity

1. NSD1-PHD 5-C5HCH tandem domain, entity 1 (polymer), 94 monomers, 10463.90 Da Detail

GAMEREDECF SCGDAGQLVS CKKPGCPKVY HADCLNLTKR PAGKWECPWH QCDVCGKEAA SFCEMCPSSF CKQHREGMLF ISKLDGRLSC TEHD

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

Total weight

10725.536 Da

Max. entity weight

10463.9 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.1 %, Completeness (bb): 95.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.1 % (989 of 1051)	94.9 % (524 of 552)	92.3 % (373 of 404)	96.8 % (92 of 95)
Backbone	95.8 % (531 of 554)	96.3 % (184 of 191)	94.5 % (259 of 274)	98.9 % (88 of 89)
Sidechain	92.8 % (541 of 583)	94.2 % (340 of 361)	91.2 % (197 of 216)	66.7 % (4 of 6)
Aromatic	89.8 % (79 of 88)	100.0 % (44 of 44)	78.6 % (33 of 42)	100.0 % (2 of 2)
Methyl	94.6 % (53 of 56)	92.9 % (26 of 28)	96.4 % (27 of 28)

1. entity 1

GAMEREDECF SCGDAGQLVS CKKPGCPKVY HADCLNLTKR PAGKWECPWH QCDVCGKEAA SFCEMCPSSF CKQHREGMLF ISKLDGRLSC TEHD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	0.3 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
7	entity_1	[U-99% 15N]	0.3 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
10	entity_1	natural abundance		0.3 mM
11	D2O	natural abundance		100 %

Sample #5

Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
12	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
13	D2O	natural abundance		100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.12 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2NAA, Strand ID: A Detail

Release date

2016-07-20

Citation

Structural basis for PHDVC5HCHNSD1-C2HRNizp1 interaction: implications for Sotos syndrome
Berardi, A., Quilici, G., Spiliotopoulos, D., Corral-Rodriguez, M., Martin, F., Degano, M., Tonon, G., Musco, G.
Nucleic Acids Res. (2016), 44, 3448-3463, PubMed 26896805 , DOI 10.1093/nar/gkw103 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 25934 released on 2016-02-22
Title Nizp1-C2HR zinc finger structure

Related entities 1. NSD1-PHD 5-C5HCH tandem domain, entity 1, : 1 : 3 : 55 entities Detail

Interaction partners 1. NSD1-PHD 5-C5HCH tandem domain, entity 1, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
7	entity_1	[U-99% 15N]	0.3 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
12	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
13	D2O	natural abundance		100 %

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	0.3 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
10	entity_1	natural abundance		0.3 mM
11	D2O	natural abundance		100 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
1	entity_1	natural abundance	0.3 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
10	entity_1	natural abundance		0.3 mM
11	D2O	natural abundance		100 %

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

9 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
12	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
13	D2O	natural abundance		100 %

13 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
7	entity_1	[U-99% 15N]	0.3 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

14 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
4	entity_1	[U-99% 13C; U-99% 15N]	0.3 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

15 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Concentration
7	entity_1	[U-99% 15N]	0.3 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

16 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 295 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
12	entity_1	[U-99% 13C; U-99% 15N]		0.3 mM
13	D2O	natural abundance		100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25933_2naa.nef
Input source #2: Coordindates	2naa.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)
1:93:HIS:NE2	2:4:ZN:ZN	unknown	unknown	n/a
1:50:HIS:NE2	2:2:ZN:ZN	unknown	unknown	n/a
1:74:HIS:ND1	2:3:ZN:ZN	unknown	unknown	n/a
1:31:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:21:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:66:CYS:SG	2:4:ZN:ZN	unknown	unknown	n/a
1:26:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:63:CYS:SG	2:4:ZN:ZN	unknown	unknown	n/a
1:52:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:71:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:47:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:9:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:12:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:55:CYS:SG	2:3:ZN:ZN	unknown	unknown	n/a
1:90:CYS:SG	2:4:ZN:ZN	unknown	unknown	n/a
1:34: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
B	3	ZN	ZINC ION	None
B	4	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90----
GAMEREDECFSCGDAGQLVSCKKPGCPKVYHADCLNLTKRPAGKWECPWHQCDVCGKEAASFCEMCPSSFCKQHREGMLFISKLDGRLSCTEHD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GAMEREDECFSCGDAGQLVSCKKPGCPKVYHADCLNLTKRPAGKWECPWHQCDVCGKEAASFCEMCPSSFCKQHREGMLFISKLDGRLSCTEHD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	94	0	0	100.0

Content subtype: combined_25933_2naa.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	16		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	984		100.0 (chain: A, length: 94)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1636 (1)	noe	98.9 (chain: A, length: 94)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	7 (1)	hbond	11.7 (chain: A, length: 94)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	114 (114)	.	84.0 (chain: A, length: 94)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_3	Warning	23 (23)	.	24.5 (chain: A, length: 94)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 366
  - ¹H chemical shifts: 525
  - ¹⁵N chemical shifts: 93
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
31	HIS	HE2	11.309
31	HIS	NE2	168.006
61	SER	HG	1.421
68	SER	HG	4.301

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	404	366	90.6
¹H chemical shifts	552	522	94.6
¹⁵N chemical shifts	99	92	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	188	176	93.6
¹H chemical shifts	191	188	98.4
¹⁵N chemical shifts	89	88	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	216	190	88.0
¹H chemical shifts	361	334	92.5
¹⁵N chemical shifts	10	4	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	31	28	90.3
¹H chemical shifts	31	27	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	42	29	69.0
¹H chemical shifts	44	44	100.0
¹⁵N chemical shifts	2	2	100.0

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: 94, Sequence coverage: 98.9%
- Total number of restraints: 1625
- Weight of restraints: 1.0 (1625)
- Potential type of restraints: square-well-parabolic (1625)
- Range of distance target values: 1.6, 5.97 (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
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 11.7%
  - Total number of restraints: 7
  - Weight of restraints: 1.0 (7)
  - Potential type of restraints: square-well-parabolic (7)
  - Range of distance target values: 2.21, 2.21 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 84.0%
- Total number of restraints: 114
- Total number of restraints per polymer type: 114
- Weight of restraints: 1.0 (114)
- Potential type of restraints: square-well-parabolic (114)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 24.5%
- Total number of restraints: 23
- Potential type of restraints: undefined (23)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords NSD1, PHD finger, PHD5C5HCH, tandem

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Found 1 Document (1.346 seconds)

BMRB: 25933

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. NSD1-PHD 5-C5HCH tandem domain, entity 1, : 1 : 3 : 55 entities Detail

Interaction partners 1. NSD1-PHD 5-C5HCH tandem domain, entity 1, : 2 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 6 contents Detail