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- PDB-2msv: Solution structure of the MLKL N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2msv
TitleSolution structure of the MLKL N-terminal domain
ComponentsMixed lineage kinase domain-like protein
KeywordsMEMBRANE PROTEIN / membrane pore
Function / homology
Function and homology information


execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus ...execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / TRP channels / RIPK1-mediated regulated necrosis / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus / cell surface receptor signaling pathway / protein-containing complex binding / protein kinase binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adaptor protein Cbl, N-terminal domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsSu, L. / Rizo, J. / Quade, B. / Wang, H. / Sun, L. / Wang, X.
CitationJournal: Structure / Year: 2014
Title: A Plug Release Mechanism for Membrane Permeation by MLKL.
Authors: Su, L. / Quade, B. / Wang, H. / Sun, L. / Wang, X. / Rizo, J.
History
DepositionAug 7, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mixed lineage kinase domain-like protein


Theoretical massNumber of molelcules
Total (without water)18,8971
Polymers18,8971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 5000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mixed lineage kinase domain-like protein / hMLKL


Mass: 18896.777 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-154 / Mutation: M1L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLKL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NB16

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D (H)CCH-TOCSY
1613D C(CO)NH
1713D H(CCO)NH
1812D 1H-13C HSQC aliphatic
1912D 1H-13C HSQC aromatic
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11213D 1H-13C NOESY
1131(HB)CB(CGCD)HD
1141(HB)CB(CGCDCE)HE
11522D DQF-COSY
11622D 1H-1H NOESY
11722D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-99% 13C; U-99% 15N] protein, 20 mM HEPES, 100 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
21.5 mM [U-99% 15N] protein, 20 mM HEPES, 100 mM sodium chloride, 2 mM TCEP, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMentity-1[U-99% 13C; U-99% 15N]1
20 mMHEPES-21
100 mMsodium chloride-31
2 mMTCEP-41
1.5 mMentity-5[U-99% 15N]2
20 mMHEPES-62
100 mMsodium chloride-72
2 mMTCEP-82
Sample conditionsIonic strength: 0.12 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
VnmrJVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 5000 / Conformers submitted total number: 20

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