[English] 日本語
Yorodumi
- PDB-6lk6: MLKL mutant - T357AS358A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lk6
TitleMLKL mutant - T357AS358A
ComponentsMixed lineage kinase domain-like protein
KeywordsTRANSFERASE / Protein Phosphorylation
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsWang, H. / Li, S. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31571427 China
CitationJournal: Cell Death Dis / Year: 2021
Title: The MLKL kinase-like domain dimerization is an indispensable step of mammalian MLKL activation in necroptosis signaling.
Authors: Zhang, Y. / Liu, J. / Yu, D. / Zhu, X. / Liu, X. / Liao, J. / Li, S. / Wang, H.
History
DepositionDec 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mixed lineage kinase domain-like protein


Theoretical massNumber of molelcules
Total (without water)33,5891
Polymers33,5891
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13330 Å2
Unit cell
Length a, b, c (Å)70.821, 75.709, 128.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 33588.871 Da / Num. of mol.: 1 / Mutation: T357A, S358A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLKL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NB16
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14%(w/v) PEG 6000, 5% EG, 0.1M HEPES(pH7.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 13419 / % possible obs: 75.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.074 / Rrim(I) all: 0.18 / Χ2: 3.015 / Net I/σ(I): 5.9 / Num. measured all: 73178
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) allΧ2% possible allCC1/2
2.32-2.371.10.128230.0910.1570.5852.6
2.37-2.424.20.3615720.1730.4020.59965.70.939
2.42-2.484.40.3116600.1410.3430.57874.60.933
2.48-2.544.60.3087010.140.340.55480.50.947
2.54-2.614.50.2947870.1360.3250.65588.40.946
2.61-2.694.60.2948160.1410.3280.64993.90.901
2.69-2.774.60.2738460.1340.3060.72796.90.935
2.77-2.8750.268900.1270.2910.87298.50.915
2.87-2.995.80.2658620.1210.2930.82699.70.942
2.99-3.125.90.2268870.1010.2480.9751000.958
3.12-3.2960.2128990.0950.2331.28699.90.964
3.29-3.495.80.1948890.090.2141.83399.80.959
3.49-3.766.40.1798860.0770.1952.55599.90.978
3.76-4.146.40.1668910.0720.1814.3371000.969
4.14-4.745.90.1589230.0740.1755.07199.60.943
4.74-5.976.40.1369070.0590.1494.4851000.967
5.97-505.70.1369800.0620.1514.68399.90.971

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M67

4m67


Resolution: 2.41→40.32 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 9.264 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 629 4.8 %RANDOM
Rwork0.2093 ---
obs0.2111 12364 94.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.85 Å2 / Biso mean: 58.553 Å2 / Biso min: 36.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-0 Å2-0 Å2
2--1.82 Å2-0 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 2.41→40.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 0 20 2158
Biso mean---53.79 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0132177
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172116
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.6472930
X-RAY DIFFRACTIONr_angle_other_deg1.1271.5784918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86121.739115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42715422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9691517
X-RAY DIFFRACTIONr_chiral_restr0.0470.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
LS refinement shellResolution: 2.41→2.47 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.309 32 -
Rwork0.281 664 -
obs--68.71 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more