[English] 日本語
Yorodumi
- PDB-6zz1: Crystal structure of MLKL executioner domain in complex with a co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zz1
TitleCrystal structure of MLKL executioner domain in complex with a covalent inhibitor
ComponentsMixed lineage kinase domain-like protein
KeywordsLIPID BINDING PROTEIN / Necroptosis
Function / homology
Function and homology information


execution phase of necroptosis / Microbial modulation of RIPK1-mediated regulated necrosis / necroptotic signaling pathway / RIPK1-mediated regulated necrosis / TRP channels / 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 / RIPK1-mediated regulated necrosis / TRP channels / protein homotrimerization / necroptotic process / Regulation of necroptotic cell death / cell junction / defense response to virus / cell surface receptor signaling pathway / protein kinase binding / protein-containing complex binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Mixed lineage kinase domain-like N-terminal domain / Adaptor protein Cbl, N-terminal domain superfamily / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-QOK / Mixed lineage kinase domain-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsFiegen, D. / Bauer, M. / Nar, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Locking mixed-lineage kinase domain-like protein in its auto-inhibited state prevents necroptosis.
Authors: Rubbelke, M. / Fiegen, D. / Bauer, M. / Binder, F. / Hamilton, J. / King, J. / Thamm, S. / Nar, H. / Zeeb, M.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mixed lineage kinase domain-like protein
B: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8214
Polymers35,2852
Non-polymers5372
Water2,774154
1
A: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9112
Polymers17,6421
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9112
Polymers17,6421
Non-polymers2681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.709, 56.709, 90.501
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

-
Components

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


Mass: 17642.326 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-QOK / 7-(2-methoxyethoxymethyl)-1,3-dimethyl-purine-2,6-dione


Mass: 268.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 32 % Polyethylene glycol monomethyl ether 2,000, 0.15 M Potassium bromide, 0.1 M TRIS, pH 9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 1.64→19.705 Å / Num. obs: 28984 / % possible obs: 82.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.029 / Rsym value: 0.029 / Net I/σ(I): 24.6
Reflection shellResolution: 1.64→1.746 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1449 / Rsym value: 0.797 / % possible all: 24.3

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
autoPROCdata reduction
XDSJan 31, 202data reduction
autoPROC1.1.7data scaling
Aimlessdata scaling
DIMPLEphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4btf

4btf


Resolution: 1.64→20.05 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1501 -RANDOM
Rwork0.1966 ---
obs0.1983 28985 82.8 %-
Displacement parametersBiso mean: 52.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.1109 Å20 Å20 Å2
2---0.1109 Å20 Å2
3---0.2219 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.64→20.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 38 154 2496
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012415HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.93235HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d931SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes449HARMONIC5
X-RAY DIFFRACTIONt_it2373HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion298SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2141SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.61
X-RAY DIFFRACTIONt_other_torsion16.8
LS refinement shellResolution: 1.64→1.7 Å
RfactorNum. reflection% reflection
Rfree0.1848 36 -
Rwork0.2184 --
obs0.2162 580 15.54 %

+
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