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- PDB-5yrn: Structure of RIP2 CARD domain -

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Basic information

Entry
Database: PDB / ID: 5yrn
TitleStructure of RIP2 CARD domain
ComponentsReceptor-interacting serine/threonine-protein kinase 2
KeywordsTRANSFERASE / Innate Immune signaling complex / IMMUNE SYSTEM
Function / homologySerine-threonine/tyrosine-protein kinase, catalytic domain / NOD1/2 Signaling Pathway / Protein kinase domain / Receptor-interacting serine/threonine-protein kinase 2 / Serine/threonine-protein kinase, active site / Caspase recruitment domain / Protein tyrosine kinase / CARD domain / Death-like domain superfamily / Serine/Threonine protein kinases active-site signature. ...Serine-threonine/tyrosine-protein kinase, catalytic domain / NOD1/2 Signaling Pathway / Protein kinase domain / Receptor-interacting serine/threonine-protein kinase 2 / Serine/threonine-protein kinase, active site / Caspase recruitment domain / Protein tyrosine kinase / CARD domain / Death-like domain superfamily / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile. / CARD caspase recruitment domain profile. / Protein kinase-like domain superfamily / Downstream TCR signaling / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / activated TAK1 mediates p38 MAPK activation / Interleukin-1 signaling / Ovarian tumor domain proteases / p75NTR recruits signalling complexes / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of immature T cell proliferation / nucleotide-binding oligomerization domain containing 1 signaling pathway / response to interleukin-18 / positive regulation of T-helper 1 cell differentiation / toll-like receptor 2 signaling pathway / positive regulation of cytokine-mediated signaling pathway / caspase binding / JUN kinase kinase kinase activity / cellular response to peptidoglycan / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of xenophagy / cellular response to muramyl dipeptide / LIM domain binding / CARD domain binding / response to interleukin-12 / activation of cysteine-type endopeptidase activity / positive regulation of alpha-beta T cell proliferation / toll-like receptor 4 signaling pathway / positive regulation of chemokine production / positive regulation of interferon-alpha production / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta secretion / response to exogenous dsRNA / T cell proliferation / positive regulation of interferon-beta production / positive regulation of interleukin-2 production / cellular response to lipoteichoic acid / positive regulation of interleukin-6 production / activation of JUN kinase activity / nucleotide-binding oligomerization domain containing signaling pathway / positive regulation of tumor necrosis factor production / positive regulation of protein ubiquitination / positive regulation of peptidyl-threonine phosphorylation / positive regulation of cell death / lipopolysaccharide-mediated signaling pathway / interleukin-1-mediated signaling pathway / JNK cascade / positive regulation of interferon-gamma production / I-kappaB kinase/NF-kappaB signaling / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of peptidyl-tyrosine phosphorylation / adaptive immune response / T cell receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / positive regulation of I-kappaB kinase/NF-kappaB signaling / vesicle / positive regulation of protein binding / activation of MAPK activity / cytoskeleton / MAPK cascade / positive regulation of NF-kappaB transcription factor activity / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / positive regulation of ERK1 and ERK2 cascade / inflammatory response / positive regulation of apoptotic process / apoptotic process / innate immune response / signaling receptor binding / protein serine/threonine kinase activity / signal transduction / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / cytosol / cytoplasm / Receptor-interacting serine/threonine-protein kinase 2
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 4.1 Å resolution
AuthorsWu, B. / Gong, Q.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of RIP2 activation and signaling.
Authors: Qin Gong / Ziqi Long / Franklin L Zhong / Daniel Eng Thiam Teo / Yibo Jin / Zhan Yin / Zhao Zhi Boo / Yaming Zhang / Jiawen Zhang / Renliang Yang / Shashi Bhushan / Bruno Reversade / Zongli Li / Bin Wu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 9, 2017 / Release: Nov 14, 2018

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Assembly

Deposited unit
A: Receptor-interacting serine/threonine-protein kinase 2
B: Receptor-interacting serine/threonine-protein kinase 2
C: Receptor-interacting serine/threonine-protein kinase 2
D: Receptor-interacting serine/threonine-protein kinase 2
E: Receptor-interacting serine/threonine-protein kinase 2
F: Receptor-interacting serine/threonine-protein kinase 2
G: Receptor-interacting serine/threonine-protein kinase 2
H: Receptor-interacting serine/threonine-protein kinase 2
I: Receptor-interacting serine/threonine-protein kinase 2
J: Receptor-interacting serine/threonine-protein kinase 2
K: Receptor-interacting serine/threonine-protein kinase 2
L: Receptor-interacting serine/threonine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)151,45712
Polyers151,45712
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Bis-Tris Native gel Fluorescent Polarization Imaging Negative-stain EM
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TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)17480
ΔGint (kcal/M)-9
Surface area (Å2)48810

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Components

#1: Protein/peptide
Receptor-interacting serine/threonine-protein kinase 2 / CARD-containing interleukin-1 beta-converting enzyme-associated kinase / CARD-containing IL-1 beta ICE-kinase / RIP-like-interacting CLARP kinase / Receptor-interacting protein 2 / RIP-2 / Tyrosine-protein kinase RIPK2


Mass: 12621.438 Da / Num. of mol.: 12 / Fragment: CARD domain / Source: (gene. exp.) Homo sapiens (human) / Gene: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092 / Production host: Escherichia coli (E. coli)
References: UniProt: O43353, non-specific serine/threonine protein kinase, non-specific protein-tyrosine kinase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Active RIP2 signaling complex / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pSNAP
Buffer solutionpH: 7.4
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationCryogen name: METHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 3 / Number of real images: 3100

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Processing

SoftwareName: PHENIX / Version: dev_2405: / Classification: refinement
EM software
IDNameVersionCategory
2RELION2.0betaimage acquisition
4RELION2.0betaCTF correction
7PHENIX1.13model fitting
9RELION2.0betainitial Euler assignment
10RELION2.0betafinal Euler assignment
11RELION2.0betaclassification
12RELION2.0beta3D reconstruction
13Coot0.8.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -101.373 deg. / Axial rise/subunit: 4.936 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 658160
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 142330
Details: Model building was based on a cropped-out density segment. Pseudo-crystallographic refinement showed that the central segment of the map is good until 3.5-3.7 A.
Symmetry type: HELICAL
Atomic model buildingOverall b value: 202.7 / Ref protocol: RIGID BODY FIT / Ref space: RECIPROCAL / Target criteria: Rfree value
Number of atoms included #1Total: 9000
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0078328
ELECTRON MICROSCOPYf_angle_d0.88111184
ELECTRON MICROSCOPYf_dihedral_angle_d7.6737476
ELECTRON MICROSCOPYf_chiral_restr0.0511332
ELECTRON MICROSCOPYf_plane_restr0.0051440

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