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- EMDB-6663: Structure of RIP2 CARD domain -

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Basic information

Entry
Database: EMDB / ID: EMD-6663
TitleStructure of RIP2 CARD domain
Map data
Sample
  • Organelle or cellular component: Active RIP2 signaling complex
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 2
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 4.85 Å
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 /
Abstract: Signals arising from bacterial infections are detected by pathogen recognition receptors (PRRs) and are transduced by specialized adapter proteins in mammalian cells. The Receptor-interacting- ...Signals arising from bacterial infections are detected by pathogen recognition receptors (PRRs) and are transduced by specialized adapter proteins in mammalian cells. The Receptor-interacting-serine/threonine-protein kinase 2 (RIPK2 or RIP2) is such an adapter protein that is critical for signal propagation of the Nucleotide-binding-oligomerization-domain-containing proteins 1/2 (NOD1 and NOD2). Dysregulation of this signaling pathway leads to defects in bacterial detection and in some cases autoimmune diseases. Here, we show that the Caspase-activation-and-recruitment-domain (CARD) of RIP2 (RIP2-CARD) forms oligomeric structures upon stimulation by either NOD1-CARD or NOD2-2CARD. We reconstitute this complex, termed the RIPosome in vitro and solve the cryo-EM filament structure of the active RIP2-CARD complex at 4.1 Å resolution. The structure suggests potential mechanisms by which CARD domains from NOD1 and NOD2 initiate the oligomerization process of RIP2-CARD. Together with structure guided mutagenesis experiments at the CARD-CARD interfaces, we demonstrate molecular mechanisms how RIP2 is activated and self-propagating such signal.
History
DepositionOct 31, 2016-
Header (metadata) releaseMay 23, 2018-
Map releaseMay 23, 2018-
UpdateMay 23, 2018-
Current statusMay 23, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.095
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.095
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6663.png

Downloads & links

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Map

FileDownload / File: emd_6663.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.31 Å
Density
Contour LevelBy AUTHOR: 0.095 / Movie #1: 0.095
Minimum - Maximum-0.083640955 - 0.245683
Average (Standard dev.)0.002576287 (±0.01656131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 262.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z262.000262.000262.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0840.2460.003

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Supplemental data

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Half map: #1

Fileemd_6663_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_6663_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Active RIP2 signaling complex

EntireName: Active RIP2 signaling complex
Components
  • Organelle or cellular component: Active RIP2 signaling complex
    • Protein or peptide: Receptor-interacting serine/threonine-protein kinase 2

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Supramolecule #1: Active RIP2 signaling complex

SupramoleculeName: Active RIP2 signaling complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pSNAP

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Macromolecule #1: Receptor-interacting serine/threonine-protein kinase 2

MacromoleculeName: Receptor-interacting serine/threonine-protein kinase 2
type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.751217 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TNSAGIAQQW IQSKREDIVN QMTEACLNQS LDALLSRDLI MKEDYELVST KPTRTSKVRQ LLDTTDIQGE EFAKVIVQKL KDNKQMGLQ PYPEI

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: METHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 12.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 2.0beta)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0beta)
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.9448 Å
Applied symmetry - Helical parameters - Δ&Phi: -101.188 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0beta)
Details: The model is only a partial model. Indefinite filament model could be produced by a helical rotation.
Number images used: 118954

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model


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