Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 54.72 kDa 
• Atom Count: 3773 
• Residue Count: 470 
• Unique protein chains: 1

3LLM

Crystal Structure Analysis of a RNA Helicase

• DOI: 10.2210/pdb3LLM/pdb

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


• Deposited: 2010-01-29 Released: 2010-05-12 
• Deposition Author(s): Schutz, P., Karlberg, T., Collins, R., Arrowsmith, C.H., Berglund, H., Bountra, C., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kallas, A., Kraulis, P., Kotenyova, T., Kotzsch, A., Markova, N., Moche, M., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Siponen, M.I., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H.M., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Literature

Crystal structure of human RNA helicase A (DHX9): structural basis for unselective nucleotide base binding in a DEAD-box variant protein.

Schutz, P., Wahlberg, E., Karlberg, T., Hammarstrom, M., Collins, R., Flores, A., Schuler, H.

(2010) J Mol Biol 400: 768-782

• PubMed: 20510246 
• DOI: 10.1016/j.jmb.2010.05.046
• Structures With Same Primary Citation


• PubMed Abstract: 
  

RNA helicases of the DExD/H-box superfamily are critically involved in all RNA-related processes. No crystal structures of human DExH-box domains had been determined previously, and their structures were difficult to predict owing to the low level of homology among DExH-motif-containing proteins from diverse species. Here we present the crystal structures of the conserved domain 1 of the DEIH-motif-containing helicase DHX9 and of the DEAD-box helicase DDX20. Both contain a RecA-like core, but DHX9 differs from DEAD-box proteins in the arrangement of secondary structural elements and is more similar to viral helicases such as NS3. The N-terminus of the DHX9 core contains two long alpha-helices that reside on the surface of the core without contributing to nucleotide binding. The RNA-polymerase-II-interacting minimal transactivation domain sequence forms an extended loop structure that resides in a hydrophobic groove on the surface of the DEIH domain. DHX9 lacks base-selective contacts and forms an unspecific but important stacking interaction with the base of the bound nucleotide, and our biochemical analysis confirms that the protein can hydrolyze ATP, guanosine 5'-triphosphate, cytidine 5'-triphosphate, and uridine 5'-triphosphate. Together, these findings allow the localization of functional motifs within the three-dimensional structure of a human DEIH helicase and show how these enzymes can bind nucleotide with high affinity in the absence of a Q-motif.

---

Organizational Affiliation: 

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ATP-dependent RNA helicase A	A, B	235	Homo sapiens	Mutation(s): 0  Gene Names: DDX9, DHX9, LKP, NDH2 EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt)
Find proteins for Q08211 (Homo sapiens) Go to UniProtKB:  Q08211
NIH Common Fund Data Resources
PHAROS  Q08211 GTEx  ENSG00000135829

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
CAC	A	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL	B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ADP	Kd:  18000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.7	α = 90
b = 113.7	β = 90
c = 141.65	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	data collection
MOSFLM	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-29 
• Released Date: 2010-05-12 
Deposition Author(s): Schutz, P., Karlberg, T., Collins, R., Arrowsmith, C.H., Berglund, H., Bountra, C., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kallas, A., Kraulis, P., Kotenyova, T., Kotzsch, A., Markova, N., Moche, M., Nielsen, T.K., Nordlund, P., Nyman, T., Persson, C., Roos, A.K., Siponen, M.I., Svensson, L., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Wisniewska, M., Schuler, H.M., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance