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Found 1 Document (1.29 seconds)

BMRB: 30458

6D74

Direct Activation of the Executioner Domain of MLKL by a Select Repertoire of Inositol Phosphates

Authors

Royappa, G.C., McNamara, D.E., Moldoveanu, T.

Assembly

Mixed lineage kinase domain-like protein

Entity

1. Mixed lineage kinase domain-like protein (polymer, Thiol state: all free), 156 monomers, 18229.81 Da Detail

MENLKHIITL GQVIHKRCEE MKYCKKQCRR LGHRVLGLIK PLEMLQDQGK RSVPSEKLTT AMNRFKAALE EANGEIEKFS NRSNICRFLT ASQDKILFKD VNRKLSDVWK ELSLLLQVEQ RMPVSPISQG ASWAQEDQQD ADEDRRAFQM LRRDNE

Formula weight

18229.81 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamicssimulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.3 %, Completeness (bb): 99.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.3 % (1850 of 1901)	97.1 % (983 of 1012)	97.1 % (695 of 716)	99.4 % (172 of 173)
Backbone	99.0 % (919 of 928)	99.0 % (311 of 314)	98.9 % (457 of 462)	99.3 % (151 of 152)
Sidechain	96.2 % (1080 of 1123)	96.3 % (672 of 698)	95.8 % (387 of 404)	100.0 % (21 of 21)
Aromatic	87.2 % (82 of 94)	100.0 % (47 of 47)	73.3 % (33 of 45)	100.0 % (2 of 2)
Methyl	98.1 % (151 of 154)	97.4 % (75 of 77)	98.7 % (76 of 77)

1. entity 1

MENLKHIITL GQVIHKRCEE MKYCKKQCRR LGHRVLGLIK PLEMLQDQGK RSVPSEKLTT AMNRFKAALE EANGEIEKFS NRSNICRFLT ASQDKILFKD VNRKLSDVWK ELSLLLQVEQ RMPVSPISQG ASWAQEDQQD ADEDRRAFQM LRRDNE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 500 uM [U-13C; U-15N] protein, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		500 uM

LACS Plot; CA

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

Referencing offset: -0.36 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.36 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.28 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6D74, Strand ID: A Detail

Release date

2018-07-26

Citation 1

MLKL Requires the Inositol Phosphate Code to Execute Necroptosis
Dovey, C.M., Diep, J., Clarke, B.P., Hale, A.T., McNamara, D.E., Guo, H., Brown, N.W., Cao, J.Y., Grace, C.R., Gough, P.J., Bertin, J., Dixon, S.J., Fiedler, D., Mocarski, E.S., Kaiser, W.J., Moldoveanu, T., York, J.D., Carette, J.E.
Mol. Cell (2018), 70, 936-948, PubMed 29883610 , DOI 10.1016/j.molcel.2018.05.010 , Abstract

Show more 1 citaion

Citation 2

Direct Activation of Human MLKL by a Select Repertoire of Inositol Phosphate Metabolites
McNamara, D.E., Dovey, C.M., Hale, A.T., Quarato, G., Grace, C.R., Guibao, C.D., Diep, J., Nourse, A., Cai, C.R., Wu, H., Kalathur, R.C., Green, D.R., York, J.D., Carette, J., Moldoveanu, T.
Cell Chem. Biol. (2019), 26, 863-877, PubMed 31031142 , DOI 10.1016/j.chembiol.2019.03.010 , Abstract

Hide non-primary 1 citaion

Related entities 1. Mixed lineage kinase domain-like protein, : 1 : 3 : 8 : 7 entities Detail

Interaction partners 1. Mixed lineage kinase domain-like protein, : 11 interactors Detail

More details for 11 interactors identified by 5 citations

Experiments performed 4 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30458_6d74.nef
Input source #2: Coordindates	6d74.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

0--------10--------20--------30--------40--------50--------60--------70--------80--------90-------10
GMENLKHIITLGQVIHKRCEEMKYCKKQCRRLGHRVLGLIKPLEMLQDQGKRSVPSEKLTTAMNRFKAALEEANGEIEKFSNRSNICRFLTASQDKILFK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMENLKHIITLGQVIHKRCEEMKYCKKQCRRLGHRVLGLIKPLEMLQDQGKRSVPSEKLTTAMNRFKAALEEANGEIEKFSNRSNICRFLTASQDKILFK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------110-------120-------130-------140-------150------
DVNRKLSDVWKELSLLLQVEQRMPVSPISQGASWAQEDQQDADEDRRAFQMLRRDNE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
DVNRKLSDVWKELSLLLQVEQRMPVSPISQGASWAQEDQQDADEDRRAFQMLRRDNE
-------110-------120-------130-------140-------150-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	157	0	0	100.0

Content subtype: combined_30458_6d74.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1860		99.4 (chain: A, length: 157)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2847 (1)	noe	98.1 (chain: A, length: 157)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	2883 (1)	noe	98.1 (chain: A, length: 157)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	180 (1)	hbond	70.1 (chain: A, length: 157)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 99.4%
- Total number of assignments
  - ¹H chemical shifts: 990
  - ¹³C chemical shifts: 696
  - ¹⁵N chemical shifts: 174
- 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	1015	990	97.5
¹³C chemical shifts	718	696	96.9
¹⁵N chemical shifts	188	174	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	317	313	98.7
¹³C chemical shifts	314	310	98.7
¹⁵N chemical shifts	153	151	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	698	677	97.0
¹³C chemical shifts	404	386	95.5
¹⁵N chemical shifts	35	23	65.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	83	100.0
¹³C chemical shifts	83	82	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	47	100.0
¹³C chemical shifts	45	33	73.3
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 98.1%
- Total number of restraints: 2818
- Weight of restraints: 1.0 (2818)
- Potential type of restraints: upper-bound-parabolic (2818)
- Range of distance target values: 2.66, 6.35 (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_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 98.1%
  - Total number of restraints: 2856
  - Weight of restraints: 1.0 (2856)
  - Potential type of restraints: upper-bound-parabolic (2856)
  - Range of distance target values: 2.39, 6.35 (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: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 70.1%
    - Total number of restraints: 180
    - Weight of restraints: 1.0 (180)
    - Potential type of restraints: upper-bound-parabolic (180)
    - Range of distance target values: 1.8, 2.7 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Keywords LIPID BINDING PROTEIN, Membrane

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Found 1 Document (1.29 seconds)

BMRB: 30458

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Mixed lineage kinase domain-like protein, : 1 : 3 : 8 : 7 entities Detail

Interaction partners 1. Mixed lineage kinase domain-like protein, : 11 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail