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- EMDB-6842: Structure of RIP2 CARD domain -

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Basic information

Entry
Database: EMDB / ID: 6842
TitleStructure of RIP2 CARD domain
Map data200 A long segment of RIP-CARD filament
SampleActive RIP2 signaling complex
  • Receptor-interacting serine/threonine-protein kinase 2
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 / positive regulation of alpha-beta T cell proliferation / activation of cysteine-type endopeptidase activity / toll-like receptor 4 signaling pathway / positive regulation of interferon-alpha production / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta secretion / response to exogenous dsRNA / positive regulation of interferon-beta production / T cell proliferation / 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 cell death / positive regulation of peptidyl-threonine phosphorylation / 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 / positive regulation of peptidyl-serine phosphorylation / T cell receptor signaling pathway / 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 ERK1 and ERK2 cascade / positive regulation of NF-kappaB transcription factor activity / non-specific serine/threonine protein kinase / defense response to Gram-positive bacterium / inflammatory response / positive regulation of apoptotic process / apoptotic process / innate immune response / signaling receptor binding / protein serine/threonine kinase activity / negative regulation of apoptotic process / signal transduction / 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
SourceHomo sapiens (human)
Methodhelical 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 ReportPDB-ID: 5yrn

SummaryFull reportAbout validation report
DateDeposition: Nov 9, 2017 / Header (metadata) release: Nov 14, 2018 / Map release: Nov 14, 2018 / Last update: Nov 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.029
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.029
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5yrn
  • Surface level: 0.029
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5yrn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6842.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.23 Å/pix.
= 246. Å
200 pix
1.23 Å/pix.
= 246. Å
200 pix
1.23 Å/pix.
= 246. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density
Contour Level:0.029 (by author), 0.029 (movie #1):
Minimum - Maximum-0.031169191 - 0.08184105
Average (Standard dev.)0.0011434028 (0.005348552)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin-69.0-69.0-69.0
Limit130.0130.0130.0
Spacing200200200
CellA=B=C: 246.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z246.000246.000246.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-69-69-69
NC/NR/NS200200200
D min/max/mean-0.0310.0820.001

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Supplemental data

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Sample components

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Entire Active RIP2 signaling complex

EntireName: Active RIP2 signaling complex / Number of components: 2

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Component #1: cellular-component, Active RIP2 signaling complex

Cellular-componentName: Active RIP2 signaling complex / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pSNAP

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Component #2: protein, Receptor-interacting serine/threonine-protein kinase 2

ProteinName: Receptor-interacting serine/threonine-protein kinase 2
Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 12.621438 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 4.936 Å / Delta phi: -101.373 deg.
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7.4
VitrificationCryogen name: METHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3100

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF
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.
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Rfree value / Refinement space: RECIPROCAL / Overall bvalue: 202.699999999999989
Output model

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