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BMRB: 19914

2MNZ

NMR Structure of KDM5B PHD1 finger in complex with H3K4me0(1-10aa)

Authors

Zhang, Y., Yang, H., Guo, X., Rong, N., Song, Y., Xu, Y., Lan, W., Xu, Y., Cao, C.

Assembly

KDM5B PHD1 finger in complex with H3K4me0(1-10aa)

Entity

1. KDM5B PHD1 finger in complex with H3K4me0(1-10aa), entity 1 (polymer), 55 monomers, 6126.948 Da Detail

AVDLYVCLLC GSGNDEDRLL LCDGCDDSYH TFCLIPPLHD VPKGDWRCPK CLAQE

2. ZINC ION (non-polymer), 65.409 × 2 Da
3. KDM5B PHD1 finger in complex with H3K4me0(1-10aa), entity 3 (polymer, Thiol state: not present), 10 monomers, 1146.300 Da Detail

ARTKQTARKS

Total weight

7404.0664 Da

Max. entity weight

6126.948 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 78.4 %, Completeness (bb): 72.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.4 % (570 of 727)	88.6 % (335 of 378)	64.1 % (182 of 284)	81.5 % (53 of 65)
Backbone	72.5 % (277 of 382)	94.6 % (123 of 130)	54.5 % (104 of 191)	82.0 % (50 of 61)
Sidechain	84.2 % (342 of 406)	85.5 % (212 of 248)	82.5 % (127 of 154)	75.0 % (3 of 4)
Aromatic	87.0 % (40 of 46)	73.9 % (17 of 23)	100.0 % (22 of 22)	100.0 % (1 of 1)
Methyl	86.4 % (57 of 66)	93.9 % (31 of 33)	78.8 % (26 of 33)

1. entity 1

AVDLYVCLLC GSGNDEDRLL LCDGCDDSYH TFCLIPPLHD VPKGDWRCPK CLAQE

3. entity 3

ARTKQTARKS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2014-08-03

Citation

The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B
Zhang, Y., Yang, H., Guo, X., Rong, N., Rong, Y., Xu, Y., Lan, W., Xu, Y., Cao, C.
Protein. Cell (2014), 5, 837-850, PubMed 24952722 , DOI 10.1007/s13238-014-0078-4 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 19913 released on 2014-08-03
Title NMR Structure of KDM5B PHD1 finger

Related entities 1. KDM5B PHD1 finger in complex with H3K4me0(1-10aa), entity 1, : 2 : 4 : 241 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

4 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

6 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

7 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

10 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]		0.8 ~ 2.0 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19914_2mnz.nef
Input source #2: Coordindates	2mnz.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)
1:30:HIS:ND1	3:1:ZN:ZN	unknown	unknown	n/a
1:51:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:10:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:7:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:33:CYS:SG	3:1:ZN:ZN	unknown	unknown	n/a
1:48:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:25:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a
1:22:CYS:SG	3:2:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	ZN	ZINC ION	None
C	2	ZN	ZINC ION	None

Sequence alignments

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

--310-------320-------330-------340-------350-------360
AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
AVDLYVCLLCGSGNDEDRLLLCDGCDDSYHTFCLIPPLHDVPKGDWRCPKCLAQE
--------10--------20--------30--------40--------50-----

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

-----370--
ARTKQTARKS
||||||||||
ARTKQTARKS
--------10

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	55	0	0	100.0
B	B	10	0	0	100.0

Content subtype: combined_19914_2mnz.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	554		100.0 (chain: A, length: 55), 100.0 (chain: B, length: 10)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	1907 (1)	noe	100.0 (chain: A, length: 55)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	100 (1)	noe	29.1 (chain: A, length: 55), 60.0 (chain: B, length: 10)
3	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	41 (1)	hbond	40.0 (chain: A, length: 55), 50.0 (chain: B, length: 10)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	103 (103)	.	100.0 (chain: A, length: 55)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 338
  - ¹⁵N chemical shifts: 51
  - ¹³C chemical shifts: 165
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 100.0%
- Total number of restraints: 1905
- Weight of restraints: 1.0 (1905)
- Potential type of restraints: square-well-parabolic (1905)
- Range of distance target values: 2.35, 4.55 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
  - Chain_ID: C
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 29.1%
    - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 60.0%
  - Total number of restraints: 100
  - Weight of restraints: 1.0 (100)
  - Potential type of restraints: square-well-parabolic (100)
  - Range of distance target values: 2.65, 5.4 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_2
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 55, Sequence coverage: 40.0%
      - Entity_assembly_ID: B, Chain length: 10, Sequence coverage: 50.0%
    - Total number of restraints: 41
    - Weight of restraints: 1.0 (41)
    - Potential type of restraints: square-well-parabolic (41)
    - Range of distance target values: 2.05, 3.55 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
      - Chain_ID: C
        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: 55, Sequence coverage: 100.0%
- Total number of restraints: 103
- Total number of restraints per polymer type: 103
- Weight of restraints: 1.0 (103)
- Potential type of restraints: square-well-parabolic (103)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords demethylase, H3K4, KDM5B, PHD1, repression