3B6E | pdb_00003b6e

Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain

• PDB DOI: https://doi.org/10.2210/pdb3B6E/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-29 Released: 2007-11-13 
• Deposition Author(s): Karlberg, T., Welin, M., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.204 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain.

Karlberg, T., Welin, M., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.13 kDa 
• Atom Count: 1,664 
• Modeled Residue Count: 182 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-induced helicase C domain-containing protein 1	A	216	Homo sapiens	Mutation(s): 0  Gene Names: IFIH1, MDA5, RH116 EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYX4 (Homo sapiens) Explore Q9BYX4  Go to UniProtKB:  Q9BYX4
PHAROS:  Q9BYX4 GTEx:  ENSG00000115267

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.204 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.83	α = 90
b = 72.83	β = 90
c = 182.78	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XSCALE	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Karlberg, T., Welin, M., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Kallas, A., Kotenyova, T., Lehtio, L., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations