[English] 日本語
- EMDB-6663: Structure of RIP2 CARD domain -

Open data

ID or keywords:


no data

Basic information

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

Structure visualization

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

Downloads & links


Fileemd_6663.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Contour Level:0.095 (by author), 0.095 (movie #1):
Minimum - Maximum-0.083640955 - 0.245683
Average (Standard dev.)0.002576287 (0.01656131)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0840.2460.003

Supplemental data

Sample components

Entire Active RIP2 signaling complex

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

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

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)

Experimental details

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

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
CameraDetector: FEI FALCON II (4k x 4k)

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.

Atomic model buiding

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

About Yorodumi


Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more