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- EMDB-6663: Structure of RIP2 CARD domain -

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Basic information

Entry
Database: EMDB / ID: 6663
TitleStructure of RIP2 CARD domain
Map data
SampleActive RIP2 signaling complex
  • Receptor-interacting serine/threonine-protein kinase 2
SourceHomo sapiens (human)
Methodhelical reconstruction / cryo EM / 4.85 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
DateDeposition: Oct 31, 2016 / Header (metadata) release: May 23, 2018 / Map release: May 23, 2018 / Last update: May 23, 2018

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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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6663.png

Downloads & links

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Map

Fileemd_6663.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
1.31 Å/pix.
= 262. Å		200 pix
1.31 Å/pix.
= 262. Å		200 pix
1.31 Å/pix.
= 262. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.095 (by author), 0.095 (movie #1):
Minimum - Maximum-0.083640955 - 0.245683
Average (Standard dev.)0.002576287 (0.01656131)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin0.00.00.0
Limit199.0199.0199.0
Spacing200200200
CellA=B=C: 262.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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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: 10.751217 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: 4.9448 Å / Delta phi: -101.188 deg.
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7.4
VitrificationCryogen name: METHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 12.6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionSoftware: RELION / Resolution: 4.85 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The model is only a partial model. Indefinite filament model could be produced by a helical rotation.

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

5h4a

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