BMRBj - BMREntryMaster

Found 1 Document (2.626 seconds)

BMRB: 30703

6VED

Solution structure of the TTD and linker region of UHRF1

Authors

Lemak, A., Houliston, S., Duan, S., Ong, M.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), 168 monomers, 19448.57 Da Detail

GLYKVNEYVD ARDTNMGAWF EAQVVRVTRK APSRDEPCSS TSRPALEEDV IYHVKYDDYP ENGVVQMNSR DVRARARTII KWQDLEVGQV VMLNYNPDNP KERGFWYDAE ISRKRETRTA RELYANVVLG DDSLNDCRII FVDEVFKIER PGEGSPMVDN PMRRKSGP

Formula weight

19448.57 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 92.9 %, Completeness: 84.4 %, Completeness (bb): 88.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.4 % (1657 of 1963)	84.4 % (871 of 1032)	83.9 % (634 of 756)	86.9 % (152 of 175)
Backbone	88.2 % (871 of 988)	89.3 % (299 of 335)	87.7 % (434 of 495)	87.3 % (138 of 158)
Sidechain	81.8 % (928 of 1134)	82.1 % (572 of 697)	81.4 % (342 of 420)	82.4 % (14 of 17)
Aromatic	61.1 % (88 of 144)	75.0 % (54 of 72)	47.8 % (33 of 69)	33.3 % (1 of 3)
Methyl	97.5 % (156 of 160)	97.5 % (78 of 80)	97.5 % (78 of 80)

1. entity 1

GLYKVNEYVD ARDTNMGAWF EAQVVRVTRK APSRDEPCSS TSRPALEEDV IYHVKYDDYP ENGVVQMNSR DVRARARTII KWQDLEVGQV VMLNYNPDNP KERGFWYDAE ISRKRETRTA RELYANVVLG DDSLNDCRII FVDEVFKIER PGEGSPMVDN PMRRKSGP

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, 150 mM sodium chloride, 25 mM sodium phosphate, 5 mM DTT, 2 mM beta-mercaptoethanol, 2 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 6VED, 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 : 10 : 21 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 25 interactors Detail

More details for 25 interactors identified by 8 citations

Experiments performed 9 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, 150 mM sodium chloride, 25 mM sodium phosphate, 5 mM DTT, 2 mM beta-mercaptoethanol, 2 mM TCEP, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	TTD-linker	[U-99% 13C; U-99% 15N]	250 uM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 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 chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 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 chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 mM

4 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 chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 mM

5 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 chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 mM

6 3D 1H-13C NOESY 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 chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 mM

7 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 chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 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 chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 mM

9 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 chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	25 mM
4	DTT	natural abundance	5 mM
5	beta-mercaptoethanol	natural abundance	2 mM
6	TCEP	natural abundance	2 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30703_6ved.nef
Input source #2: Coordindates	6ved.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

-----140-------150-------160-------170-------180-------190-------200-------210-------220-------230--
GLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GLYKVNEYVDARDTNMGAWFEAQVVRVTRKAPSRDEPCSSTSRPALEEDVIYHVKYDDYPENGVVQMNSRDVRARARTIIKWQDLEVGQVVMLNYNPDNP
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----240-------250-------260-------270-------280-------290-------300
KERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KERGFWYDAEISRKRETRTARELYANVVLGDDSLNDCRIIFVDEVFKIERPGEGSPMVDNPMRRKSGP
-------110-------120-------130-------140-------150-------160--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	168	0	0	100.0

Content subtype: combined_30703_6ved.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1622		91.1 (chain: A, length: 168)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3171 (1)	noe	89.9 (chain: A, length: 168)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	106 (1)	hbond	44.6 (chain: A, length: 168)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	234 (234)	.	85.7 (chain: A, length: 168)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 91.1%
- Total number of assignments
  - ¹H chemical shifts: 857
  - ¹³C chemical shifts: 616
  - ¹⁵N chemical shifts: 149
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1032	857	83.0
¹³C chemical shifts	756	616	81.5
¹⁵N chemical shifts	193	149	77.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	335	296	88.4
¹³C chemical shifts	336	283	84.2
¹⁵N chemical shifts	158	135	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	697	561	80.5
¹³C chemical shifts	420	333	79.3
¹⁵N chemical shifts	35	14	40.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	85	100.0
¹³C chemical shifts	85	85	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	50	69.4
¹³C chemical shifts	69	29	42.0
¹⁵N chemical shifts	3	1	33.3

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 168, Sequence coverage: 89.9%
- Total number of restraints: 3171
- Weight of restraints: 1.0 (3171)
- Potential type of restraints: square-well-parabolic (3171)
- 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: 168, Sequence coverage: 44.6%
  - Total number of restraints: 106
  - Weight of restraints: 1.0 (106)
  - Potential type of restraints: square-well-parabolic (106)
  - 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: 168, Sequence coverage: 85.7%
- Total number of restraints: 234
- Total number of restraints per polymer type: 234
- Weight of restraints: 1.0 (234)
- Potential type of restraints: square-well-parabolic (234)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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

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Found 1 Document (2.626 seconds)

BMRB: 30703

Sample

Related entities 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 1 : 2 : 10 : 21 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase UHRF1 (E.C.2.3.2.27), : 25 interactors Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail