Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.66 kDa 
• Atom Count: 2,641 
• Modelled Residue Count: 327 
• Deposited Residue Count: 350 
• Unique protein chains: 1

 2RB4

Crystal structure of the Helicase domain of human DDX25 RNA helicase

• PDB DOI: 10.2210/pdb2RB4/pdb
• Entry: 2RB4 supersedes: 2G2J

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-09-18 Released: 2007-10-02 
• Deposition Author(s): Lehtio, L., Hogbom, M., Uppenberg, J., Arrowsmith, C.H., Berglund, H., Edwards, A.M., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., 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: 2.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 

Literature

Comparative Structural Analysis of Human DEAD-Box RNA Helicases.

Schutz, P., Karlberg, T., van den Berg, S., Collins, R., Lehtio, L., Hogbom, M., Holmberg-Schiavone, L., Tempel, W., Park, H.W., Hammarstrom, M., Moche, M., Thorsell, A.G., Schuler, H.

(2010) PLoS One 5: 12791-12791

• PubMed: 20941364 
• DOI: 10.1371/journal.pone.0012791
• Primary Citation of Related Structures:  
  2G9N, 2P6N, 2PL3, 2RB4, 3B7G, 3BER, 3BOR, 3DKP, 3FE2, 3IUY, 3LY5


• PubMed Abstract: 
  

DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

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Organizational Affiliation: 

Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DDX25	A, B	175	Homo sapiens	Mutation(s): 0  Gene Names: DDX25, GRTH EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHL0 (Homo sapiens) Explore Q9UHL0  Go to UniProtKB:  Q9UHL0
PHAROS:  Q9UHL0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.31	α = 90
b = 70.31	β = 90
c = 187.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Lehtio, L., Hogbom, M., Uppenberg, J., Arrowsmith, C.H., Berglund, H., Edwards, A.M., Ehn, M., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Ogg, D., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)
• This entry supersedes: 2G2J

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Data collection