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BMRB: 30031

5IM8

Solution Structure of the Microtubule-Targeting COS Domain of MID1

Authors

Wright, K.M., Du, H., Dagnachew, M., Massiah, M.A.

Assembly

E3 ubiquitin-protein ligase Midline-1 (E.C.6.3.2.-)

Entity

1. E3 ubiquitin-protein ligase Midline-1 (E.C.6.3.2.-) (polymer), 60 monomers, 6918.768 Da Detail

LKENDHARFL QTAKNITERV SMATASSQVL IPEINLNDTF DTFALDFSRE KKLLECLDYL

Formula weight

6918.768 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.7 %, Completeness: 83.8 %, Completeness (bb): 89.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.8 % (599 of 715)	83.8 % (310 of 370)	84.3 % (236 of 280)	81.5 % (53 of 65)
Backbone	89.7 % (321 of 358)	88.2 % (105 of 119)	90.6 % (163 of 180)	89.8 % (53 of 59)
Sidechain	79.9 % (333 of 417)	81.7 % (205 of 251)	80.0 % (128 of 160)	0.0 % (0 of 6)
Aromatic	63.5 % (33 of 52)	65.4 % (17 of 26)	61.5 % (16 of 26)
Methyl	82.9 % (63 of 76)	84.2 % (32 of 38)	81.6 % (31 of 38)

1. entity 1

LKENDHARFL QTAKNITERV SMATASSQVL IPEINLNDTF DTFALDFSRE KKLLECLDYL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.8, Details 50 mM TRIS, 10 mM beta-mercaptoethanol, 0.2 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	TRIS	natural abundance		50 mM
3	beta-mercaptoethanol	natural abundance		10 mM
4	sodium azide	natural abundance		0.2 %

LACS Plot; CA

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.01 ppm, Outliers: 4 Detail

LACS Plot; CO

Referencing offset: 0.23 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5IM8, Strand ID: A Detail

Release date

2016-07-05

Citation

Solution structure of the microtubule-targeting COS domain of MID1
Wright, K.M., Du, H., Dagnachew, M., Massiha, M.A.
FEBS J. (2016), 283, 3089-3102, PubMed 27367845 , DOI 10.1111/febs.13795 , Abstract

Related entities 1. E3 ubiquitin-protein ligase Midline-1 (E.C.6.3.2.-), : 1 : 7 : 30 entities Detail

Interaction partners 1. E3 ubiquitin-protein ligase Midline-1 (E.C.6.3.2.-), : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 5 experiments Detail

1 3D HNCACB

Instrument

Agilent Agilent DD2 600 MHz - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.8, Details 50 mM TRIS, 10 mM beta-mercaptoethanol, 0.2 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	TRIS	natural abundance		50 mM
3	beta-mercaptoethanol	natural abundance		10 mM
4	sodium azide	natural abundance		0.2 %

2 3D HNCO

Instrument

Agilent Agilent DD2 600 MHz - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.8, Details 50 mM TRIS, 10 mM beta-mercaptoethanol, 0.2 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	TRIS	natural abundance		50 mM
3	beta-mercaptoethanol	natural abundance		10 mM
4	sodium azide	natural abundance		0.2 %

3 3D 1H-15N NOESY

Instrument

Agilent Agilent DD2 600 MHz - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.8, Details 50 mM TRIS, 10 mM beta-mercaptoethanol, 0.2 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	TRIS	natural abundance		50 mM
3	beta-mercaptoethanol	natural abundance		10 mM
4	sodium azide	natural abundance		0.2 %

4 3D 1H-13C NOESY

Instrument

Agilent Agilent DD2 600 MHz - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.8, Details 50 mM TRIS, 10 mM beta-mercaptoethanol, 0.2 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	TRIS	natural abundance		50 mM
3	beta-mercaptoethanol	natural abundance		10 mM
4	sodium azide	natural abundance		0.2 %

5 3D HCCH-TOCSY

Instrument

Agilent Agilent DD2 600 MHz - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.8, Details 50 mM TRIS, 10 mM beta-mercaptoethanol, 0.2 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1			0.0 ~ 0.0 mM
2	TRIS	natural abundance		50 mM
3	beta-mercaptoethanol	natural abundance		10 mM
4	sodium azide	natural abundance		0.2 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30031_5im8.nef
Input source #2: Coordindates	5im8.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

--------10--------20--------30--------40--------50--------60------
LKENDHARFLQTAKNITERVSMATASSQVLIPEINLNDTFDTFALDFSREKKLLECLDYLHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LKENDHARFLQTAKNITERVSMATASSQVLIPEINLNDTFDTFALDFSREKKLLECLDYLHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	66	0	0	100.0

Content subtype: combined_30031_5im8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	596		81.8 (chain: A, length: 66)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	772 (1)	noe	77.3 (chain: A, length: 66)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	144 (1)	noe	34.8 (chain: A, length: 66)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	51 (1)	noe	24.2 (chain: A, length: 66)
4	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	39 (1)	hbond	36.4 (chain: A, length: 66)
5	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	34 (1)	hbond	31.8 (chain: A, length: 66)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 81.8%
- Total number of assignments
  - ¹H chemical shifts: 313
  - ¹³C chemical shifts: 231
  - ¹⁵N chemical shifts: 52
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 77.3%
- Total number of restraints: 771
- Weight of restraints: 1.0 (771)
- Potential type of restraints: upper-bound-parabolic (771)
- Range of distance target values: 2.8, 7.3 (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: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 34.8%
  - Total number of restraints: 144
  - Weight of restraints: 1.0 (144)
  - Potential type of restraints: upper-bound-parabolic (144)
  - Range of distance target values: 2.8, 6.0 (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: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: noe
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 24.2%
    - Total number of restraints: 50
    - Weight of restraints: 1.0 (50)
    - Potential type of restraints: upper-bound-parabolic (50)
    - Range of distance target values: 3.3, 7.5 (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: DYANA/DIANA_distance_constraints_3
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 36.4%
      - Total number of restraints: 39
        Total hydrogen bond restraints: 39
        O...H-x: 20
        O...h-N: 19
      - Weight of restraints: 1.0 (39)
        Total hydrogen bond restraints: 1.0 (39)
        O...H-x: 1.0 (20)
        O...h-N: 1.0 (19)
      - Potential type of restraints: upper-bound-parabolic (39)
        Total hydrogen bond restraints: upper-bound-parabolic (39)
        O...H-x: upper-bound-parabolic (20)
        O...h-N: upper-bound-parabolic (19)
      - Range of distance target values: 2.5, 3.5 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
      - Saveframe: DYANA/DIANA_distance_constraints_5
        Status: OK
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 66, Sequence coverage: 31.8%
        Total number of restraints: 34
        Total hydrogen bond restraints: 34
        O...H-x: 17
        O...h-N: 17
        Weight of restraints: 1.0 (34)
        Total hydrogen bond restraints: 1.0 (34)
        O...H-x: 1.0 (17)
        O...h-N: 1.0 (17)
        Potential type of restraints: upper-bound-parabolic (34)
        Total hydrogen bond restraints: upper-bound-parabolic (34)
        O...H-x: upper-bound-parabolic (17)
        O...h-N: upper-bound-parabolic (17)
        Range of distance target values: 2.5, 3.5 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map

Keywords helix-loop-helix, microtubules, spectrin