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- PDB-4m69: Crystal structure of the mouse RIP3-MLKL complex -

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Basic information

Entry
Database: PDB / ID: 4m69
TitleCrystal structure of the mouse RIP3-MLKL complex
Components
  • Mixed lineage kinase domain-like protein
  • Receptor-interacting serine/threonine-protein kinase 3
KeywordsTRANSFERASE/SIGNALING PROTEIN / kinase / phosphorylation / TRANSFERASE-SIGNALING PROTEIN complex
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 / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of activated T cell proliferation ...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 / Regulation of necroptotic cell death / IKK complex recruitment mediated by RIP1 / regulation of adaptive immune response / regulation of activated T cell proliferation / regulation of type II interferon production / programmed necrotic cell death / necroptotic signaling pathway / TRP channels / activation of protein kinase activity / positive regulation of necroptotic process / non-canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / protein homotrimerization / T cell homeostasis / 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 / cell junction / T cell differentiation in thymus / regulation of apoptotic process / defense response to virus / amyloid fibril formation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / protein-containing complex binding / protein kinase binding / protein-containing complex / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Mixed lineage kinase domain-like N-terminal domain / RHIM domain / RIP homotypic interaction motif / Adaptor protein Cbl, N-terminal domain superfamily / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...: / Mixed lineage kinase domain-like N-terminal domain / RHIM domain / RIP homotypic interaction motif / Adaptor protein Cbl, N-terminal domain superfamily / : / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Mixed lineage kinase domain-like protein / Receptor-interacting serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 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 ...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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 3
B: Mixed lineage kinase domain-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9138
Polymers67,1202
Non-polymers7946
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-63 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.443, 141.951, 107.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 34861.609 Da / Num. of mol.: 1 / Fragment: UNP residues 1-313
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: Protein Mixed lineage kinase domain-like protein


Mass: 32258.123 Da / Num. of mol.: 1 / Fragment: UNP residues 182-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mlkl / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9D2Y4

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Non-polymers , 5 types, 173 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF CHAIN B IS ISOFORM 2 OF Q9D2Y4 (MLKL_MOUSE).

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 0.35M (NH4)2S04, 17% PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.497→40 Å / Num. all: 28489 / Num. obs: 28489 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 44.15 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 100

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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: 4M66 and 4M68

4m66

4m68


Resolution: 2.497→39.569 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8084 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1439 5.06 %random
Rwork0.2202 ---
obs0.2215 28464 99.78 %-
all-28526 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.677 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso max: 133.7 Å2 / Biso mean: 51.7759 Å2 / Biso min: 21.47 Å2
Baniso -1Baniso -2Baniso -3
1-7.3609 Å20 Å2-0 Å2
2--3.0857 Å2-0 Å2
3----7.2944 Å2
Refinement stepCycle: LAST / Resolution: 2.497→39.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 44 167 4603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014538
X-RAY DIFFRACTIONf_angle_d1.4166156
X-RAY DIFFRACTIONf_chiral_restr0.071685
X-RAY DIFFRACTIONf_plane_restr0.018780
X-RAY DIFFRACTIONf_dihedral_angle_d18.5621722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4966-2.58580.36071400.29892608274898
2.5858-2.68930.32841230.290627162839100
2.6893-2.81170.32441480.282826432791100
2.8117-2.95990.30191540.265726962850100
2.9599-3.14520.26481430.254726682811100
3.1452-3.3880.26211580.237526682826100
3.388-3.72870.2531590.217226882847100
3.7287-4.26770.19521420.190327312873100
4.2677-5.37470.1971360.175327502886100
5.3747-39.57410.23761360.207128572993100
Refinement TLS params.Method: refined / Origin x: -10.1968 Å / Origin y: -40.7329 Å / Origin z: 2.0798 Å
111213212223313233
T0.2611 Å20.0034 Å20.0172 Å2-0.2773 Å20.0274 Å2--0.2541 Å2
L0.9818 °20.7109 °20.4379 °2-1.6509 °20.4021 °2--0.7004 °2
S-0.1017 Å °0.0864 Å °0.1622 Å °-0.0811 Å °-0.0086 Å °0.0291 Å °-0.0869 Å °0.0877 Å °0.109 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA12 - 609
2X-RAY DIFFRACTION1ALLB182 - 658

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