Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Macromolecule Content

• Total Structure Weight: 31.52 kDa 
• Atom Count: 2038 
• Modelled Residue Count: 259 
• Deposited Residue Count: 276 
• Unique protein chains: 2

3P8M

Human dynein light chain (DYNLL2) in complex with an in vitro evolved peptide dimerized by leucine zipper

• PDB DOI: 10.2210/pdb3P8M/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-10-14 Released: 2011-08-31 
• Deposition Author(s): Rapali, P., Radnai, L., Suveges, D., Hetenyi, C., Harmat, V., Tolgyesi, F., Wahlgren, W.Y., Katona, G., Nyitray, L., Pal, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.295 
• R-Value Work: 0.248 
• R-Value Observed: 0.250 

Literature

Directed evolution reveals the binding motif preference of the LC8/DYNLL hub protein and predicts large numbers of novel binders in the human proteome.

Rapali, P., Radnai, L., Suveges, D., Harmat, V., Tolgyesi, F., Wahlgren, W.Y., Katona, G., Nyitray, L., Pal, G.

(2011) PLoS One 6: e18818-e18818

• PubMed: 21533121 
• DOI: 10.1371/journal.pone.0018818
• Primary Citation of Related Structures:  
  2XQQ, 3P8M


• PubMed Abstract: 
  

LC8 dynein light chain (DYNLL) is a eukaryotic hub protein that is thought to function as a dimerization engine. Its interacting partners are involved in a wide range of cellular functions. In its dozens of hitherto identified binding partners DYNLL binds to a linear peptide segment. The known segments define a loosely characterized binding motif: [D/S](-4)K(-3)X(-2)[T/V/I](-1)Q(0)[T/V](1)[D/E](2). The motifs are localized in disordered segments of the DYNLL-binding proteins and are often flanked by coiled coil or other potential dimerization domains. Based on a directed evolution approach, here we provide the first quantitative characterization of the binding preference of the DYNLL binding site. We displayed on M13 phage a naïve peptide library with seven fully randomized positions around a fixed, naturally conserved glutamine. The peptides were presented in a bivalent manner fused to a leucine zipper mimicking the natural dimer to dimer binding stoichiometry of DYNLL-partner complexes. The phage-selected consensus sequence V(-5)S(-4)R(-3)G(-2)T(-1)Q(0)T(1)E(2) resembles the natural one, but is extended by an additional N-terminal valine, which increases the affinity of the monomeric peptide twentyfold. Leu-zipper dimerization increases the affinity into the subnanomolar range. By comparing crystal structures of an SRGTQTE-DYNLL and a dimeric VSRGTQTE-DYNLL complex we find that the affinity enhancing valine is accommodated in a binding pocket on DYNLL. Based on the in vitro evolved sequence pattern we predict a large number of novel DYNLL binding partners in the human proteome. Among these EML3, a microtubule-binding protein involved in mitosis contains an exact match of the phage-evolved consensus and binds to DYNLL with nanomolar affinity. These results significantly widen the scope of the human interactome around DYNLL and will certainly shed more light on the biological functions and organizing role of DYNLL in the human and other eukaryotic interactomes.

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Organizational Affiliation: 

Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynein light chain 2	A, B	92	Homo sapiens	Mutation(s): 0  Gene Names: DYNLL2, DLC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FJ2 (Homo sapiens) Explore Q96FJ2  Go to UniProtKB:  Q96FJ2
PHAROS:  Q96FJ2 GTEx:  ENSG00000264364

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
General control protein GCN4	D [auth C], C [auth D]	46	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: GCN4, AAS3, ARG9, YEL009C
UniProt
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P03069  Go to UniProtKB:  P03069

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.295 
• R-Value Work: 0.248 
• R-Value Observed: 0.250 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.839	α = 90
b = 68.415	β = 90
c = 101.677	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-14 
• Released Date: 2011-08-31 
Deposition Author(s): Rapali, P., Radnai, L., Suveges, D., Hetenyi, C., Harmat, V., Tolgyesi, F., Wahlgren, W.Y., Katona, G., Nyitray, L., Pal, G.

Revision History  

• Version 1.0: 2011-08-31
  Type: Initial release