[English] 日本語
Yorodumi
- PDB-4m66: Crystal structure of the mouse RIP3 kinase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m66
TitleCrystal structure of the mouse RIP3 kinase domain
ComponentsReceptor-interacting serine/threonine-protein kinase 3
KeywordsTRANSFERASE / kinase / protein phosphorylation
Function / homology
Function and homology information


RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / IKK complex recruitment mediated by RIP1 / regulation of activated T cell proliferation / regulation of adaptive immune response / Regulation of necroptotic cell death ...RIPK1-mediated regulated necrosis / regulation of activation-induced cell death of T cells / regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation / TRIF-mediated programmed cell death / execution phase of necroptosis / regulation of T cell mediated cytotoxicity / IKK complex recruitment mediated by RIP1 / regulation of activated T cell proliferation / regulation of adaptive immune response / Regulation of necroptotic cell death / regulation of type II interferon production / programmed necrotic cell death / necroptotic signaling pathway / TRP channels / positive regulation of necroptotic process / regulation of reactive oxygen species metabolic process / T cell homeostasis / activation of protein kinase activity / 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 / thymus development / cellular response to hydrogen peroxide / positive regulation of reactive oxygen species metabolic process / T cell differentiation in thymus / defense response to virus / regulation of apoptotic process / amyloid fibril formation / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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. ...RHIM domain / RIP homotypic interaction motif / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsXie, T. / Peng, W. / Yan, C. / Wu, J. / Shi, Y.
CitationJournal: Cell Rep / Year: 2013
Title: Structural Insights into RIP3-Mediated Necroptotic Signaling
Authors: Xie, T. / Peng, W. / Yan, C. / Wu, J. / Gong, X. / Shi, Y.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 3
B: Receptor-interacting serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)72,4272
Polymers72,4272
Non-polymers00
Water1,910106
1
A: Receptor-interacting serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)36,2131
Polymers36,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Receptor-interacting serine/threonine-protein kinase 3


Theoretical massNumber of molelcules
Total (without water)36,2131
Polymers36,2131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)155.224, 51.634, 107.288
Angle α, β, γ (deg.)90.00, 132.99, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Receptor-interacting serine/threonine-protein kinase 3 / RIP-like protein kinase 3 / Receptor-interacting protein 3 / RIP-3 / mRIP3


Mass: 36213.328 Da / Num. of mol.: 2 / Fragment: UNP residues 1-313 / Mutation: C111A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ripk3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9QZL0, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05M magnesium formate, 13% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 24609 / Num. obs: 24093 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 42.36 Å2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 99.3

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ITH

4ith


Resolution: 2.401→35.888 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.7759 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1222 5.08 %random
Rwork0.2151 ---
all0.2173 24618 --
obs0.2173 24065 97.75 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.828 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 166.26 Å2 / Biso mean: 55.554 Å2 / Biso min: 22.04 Å2
Baniso -1Baniso -2Baniso -3
1-12.972 Å2-0 Å2-10.6462 Å2
2--2.9845 Å2-0 Å2
3----7.511 Å2
Refinement stepCycle: LAST / Resolution: 2.401→35.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4177 0 0 106 4283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084286
X-RAY DIFFRACTIONf_angle_d1.1615821
X-RAY DIFFRACTIONf_chiral_restr0.076659
X-RAY DIFFRACTIONf_plane_restr0.006744
X-RAY DIFFRACTIONf_dihedral_angle_d15.8261584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4011-2.49720.31571280.2542559268799
2.4972-2.61080.26991240.25832549267399
2.6108-2.74840.31141480.259625692717100
2.7484-2.92050.29691290.241125662695100
2.9205-3.14590.29981560.237325762732100
3.1459-3.46220.26751410.232925792720100
3.4622-3.96270.23451240.21272196232085
3.9627-4.99040.22171430.18032591273499
4.9904-35.89190.24731290.19892658278798
Refinement TLS params.Method: refined / Origin x: 17.3987 Å / Origin y: 7.245 Å / Origin z: -19.7831 Å
111213212223313233
T0.2945 Å20.0618 Å20.0059 Å2-0.3266 Å20.0436 Å2--0.2966 Å2
L1.6365 °20.2383 °20.5567 °2-0.7438 °2-0.0497 °2--2.0538 °2
S0.0699 Å °0.0604 Å °-0.1387 Å °-0.0012 Å °-0.1221 Å °-0.2482 Å °0.129 Å °0.5306 Å °0.0258 Å °
Refinement TLS groupSelection details: ALL

+
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