[English] 日本語
Yorodumi
- PDB-5zck: Structure of the RIP3 core region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zck
TitleStructure of the RIP3 core region
Componentspeptide from Receptor-interacting serine/threonine-protein kinase 3
KeywordsPROTEIN FIBRIL / RIP3 / Core region
Function / homology
Function and homology information


regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of adaptive immune response / regulation of activated T cell proliferation / positive regulation of phosphatase activity / regulation of type II interferon production / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death ...regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / regulation of adaptive immune response / regulation of activated T cell proliferation / positive regulation of phosphatase activity / regulation of type II interferon production / TRIF-mediated programmed cell death / TLR3-mediated TICAM1-dependent programmed cell death / Microbial modulation of RIPK1-mediated regulated necrosis / programmed necrotic cell death / SARS-CoV-1-mediated effects on programmed cell death / necroptotic signaling pathway / positive regulation of necroptotic process / RIP-mediated NFkB activation via ZBP1 / TRP channels / RIPK1-mediated regulated necrosis / activation of protein kinase activity / T cell homeostasis / non-canonical NF-kappaB signal transduction / necroptotic process / lymph node development / positive regulation of intrinsic apoptotic signaling pathway / spleen development / reactive oxygen species metabolic process / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / thymus development / apoptotic signaling pathway / protein modification process / Regulation of necroptotic cell death / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of NF-kappaB transcription factor activity / T cell differentiation in thymus / regulation of apoptotic process / defense response to virus / amyloid fibril formation / protein autophosphorylation / transcription coactivator activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / protein-containing complex binding / signal transduction / protein-containing complex / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RHIM domain / RIP homotypic interaction motif / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.271 Å
AuthorsLi, J. / Wu, H.
Funding support China, 1items
OrganizationGrant numberCountry
Natural Science Foundation of China31470724 China
CitationJournal: Cell / Year: 2018
Title: The Structure of the Necrosome RIPK1-RIPK3 Core, a Human Hetero-Amyloid Signaling Complex.
Authors: Mompean, M. / Li, W. / Li, J. / Laage, S. / Siemer, A.B. / Bozkurt, G. / Wu, H. / McDermott, A.E.
History
DepositionFeb 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_detector / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_detector.detector / _diffrn_detector.pdbx_collection_date / _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: peptide from Receptor-interacting serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4242
Polymers4011
Non-polymers231
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-3 kcal/mol
Surface area720 Å2
Unit cell
Length a, b, c (Å)4.813, 17.151, 29.564
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide peptide from Receptor-interacting serine/threonine-protein kinase 3 / / RIP-3 core region


Mass: 401.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y572
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 1.52 Å3/Da / Density % sol: 19.07 % / Description: long needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M magnesium chloride, 0.1 M sodium cacodylate, 20% (v/v) PEG 200

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.27→14.83 Å / Num. obs: 776 / % possible obs: 98.2 % / Redundancy: 20 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 54.5
Reflection shellResolution: 1.27→1.32 Å / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ON9

2on9


Resolution: 1.271→14.83 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.42
RfactorNum. reflection% reflectionSelection details
Rfree0.1525 79 10.18 %Random selection
Rwork0.1371 ---
obs0.1386 776 98.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.271→14.83 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms28 0 1 2 31
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727
X-RAY DIFFRACTIONf_angle_d1.02436
X-RAY DIFFRACTIONf_dihedral_angle_d14.0929
X-RAY DIFFRACTIONf_chiral_restr0.0495
X-RAY DIFFRACTIONf_plane_restr0.0015
LS refinement shellResolution: 1.271→1.32 Å
RfactorNum. reflection% reflection
Rfree0.1525 79 -
Rwork0.1371 697 -
obs--98 %

+
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