BMRBj - BMREntryMaster

Found 1 Document (0.88 seconds)

BMRB: 30704

6VEE

Solution structure of the TTD and linker region of mouse UHRF1 (NP95)

Authors

Lemak, A., Houliston, S., Duan, S., Arrowsmith, C.H.

Assembly

E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27)

Entity

1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27) (polymer), 187 monomers, 21661.31 Da Detail

GHMVWEDTDL GLYKVNEYVD VRDNIFGAWF EAQVVQVQKR ALSEDEPCSS SAVKTSEDDI MYHVKYDDYP EHGVDIVKAK NVRARARTVI PWENLEVGQV VMANYNVDYP RKRGFWYDVE ICRKRQTRTA RELYGNIRLL NDSQLNNCRI MFVDEVLMIE LPKERRPLIA SPSQPPPALR NTGKSGP

Formula weight

21661.31 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.3 %, Completeness: 81.6 %, Completeness (bb): 89.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.6 % (1811 of 2219)	81.9 % (952 of 1163)	80.5 % (691 of 858)	84.8 % (168 of 198)
Backbone	89.4 % (983 of 1100)	90.9 % (338 of 372)	89.1 % (492 of 552)	86.9 % (153 of 176)
Sidechain	76.3 % (989 of 1297)	77.6 % (614 of 791)	74.4 % (360 of 484)	68.2 % (15 of 22)
Aromatic	47.7 % (82 of 172)	59.3 % (51 of 86)	36.6 % (30 of 82)	25.0 % (1 of 4)
Methyl	93.9 % (186 of 198)	93.9 % (93 of 99)	93.9 % (93 of 99)

1. entity 1

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 250 uM [U-99% 13C; U-99% 15N] TTD-linker, 50 mM sodium phosphate, 5 mM DTT, 5 mM TCEP, 2 mM beta-mercaptoethanol, 150 mM sodium chloride, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6VEE, Strand ID: A Detail

Release date

2020-02-27

Citation

Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1
Tauber, M., Kreuz, S., Lemak, A., Mandal, P., Yerkesh, Z., Veluchamy, A., Al-Gashgari, B., Aljahani, A., Cortes-Medina, L.V., Azhibek, D., Fan, L., Ong, M.S., Duan, S., Houliston, S., Arrowsmith, C.H., Fischle, W.
Nucleic Acids Res. (2020), 48, 7728-7747, PubMed 32609811 , DOI 10.1093/nar/gkaa520 , Abstract

Related entities 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 1 : 2 : 32 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 4 interactors Detail

More details for 4 interactors identified by 1 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE II - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details 250 uM [U-99% 13C; U-99% 15N] TTD-linker, 50 mM sodium phosphate, 5 mM DTT, 5 mM TCEP, 2 mM beta-mercaptoethanol, 150 mM sodium chloride, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

3 3D HNCO

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

5 3D HNCA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

7 3D 1H-15N NOESY

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

8 3D HCCH-TOCSY

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

9 3D HBHA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

10 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE II - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium phosphate	natural abundance	50 mM
3	DTT	natural abundance	5 mM
4	TCEP	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	sodium chloride	natural abundance	150 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30704_6vee.nef
Input source #2: Coordindates	6vee.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	None
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)

None

Non-standard residues

None

Sequence alignments

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

-120-----130-------140-------150-------160-------170-------180-------190-------200-------210-------2
GHMVWEDTDLGLYKVNEYVDVRDNIFGAWFEAQVVQVQKRALSEDEPCSSSAVKTSEDDIMYHVKYDDYPEHGVDIVKAKNVRARARTVIPWENLEVGQV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMVWEDTDLGLYKVNEYVDVRDNIFGAWFEAQVVQVQKRALSEDEPCSSSAVKTSEDDIMYHVKYDDYPEHGVDIVKAKNVRARARTVIPWENLEVGQV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

20-------230-------240-------250-------260-------270-------280-------290-------300-----
VMANYNVDYPRKRGFWYDVEICRKRQTRTARELYGNIRLLNDSQLNNCRIMFVDEVLMIELPKERRPLIASPSQPPPALRNTGKSGP
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
VMANYNVDYPRKRGFWYDVEICRKRQTRTARELYGNIRLLNDSQLNNCRIMFVDEVLMIELPKERRPLIASPSQPPPALRNTGKSGP
-------110-------120-------130-------140-------150-------160-------170-------180-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	187	0	0	100.0

Content subtype: combined_30704_6vee.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1767		96.3 (chain: A, length: 187)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3099 (1)	noe	93.6 (chain: A, length: 187)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	105 (1)	hbond	37.4 (chain: A, length: 187)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	258 (258)	.	84.5 (chain: A, length: 187)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 187, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 924
  - ¹³C chemical shifts: 677
  - ¹⁵N chemical shifts: 166
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1163	924	79.4
¹³C chemical shifts	858	677	78.9
¹⁵N chemical shifts	214	166	77.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	372	333	89.5
¹³C chemical shifts	374	324	86.6
¹⁵N chemical shifts	176	150	85.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	791	591	74.7
¹³C chemical shifts	484	353	72.9
¹⁵N chemical shifts	38	16	42.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	104	98	94.2
¹³C chemical shifts	104	98	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	86	51	59.3
¹³C chemical shifts	82	30	36.6
¹⁵N chemical shifts	4	1	25.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 187, Sequence coverage: 93.6%
- Total number of restraints: 3099
- Weight of restraints: 1.0 (3099)
- Potential type of restraints: square-well-parabolic (3099)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 187, Sequence coverage: 37.4%
  - Total number of restraints: 105
  - Weight of restraints: 1.0 (105)
  - Potential type of restraints: square-well-parabolic (105)
  - Range of distance target values: 2.05, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: 187, Sequence coverage: 84.5%
- Total number of restraints: 258
- Total number of restraints per polymer type: 258
- Weight of restraints: 1.0 (258)
- Potential type of restraints: square-well-parabolic (258)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords H3K9me3, Histone, NP95, PEPTIDE BINDING PROTEIN, Tandem Tudor Domain, UHRF1

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.88 seconds)

BMRB: 30704

Sample

Related entities 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 1 : 2 : 32 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 4 interactors Detail

Experiments performed 10 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail