Biological Assembly 1  

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

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 

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

Macromolecule Content

• Total Structure Weight: 112.16 kDa 
• Atom Count: 7656 
• Modelled Residue Count: 937 
• Deposited Residue Count: 1003 
• Unique protein chains: 3

4GQB

Crystal Structure of the human PRMT5:MEP50 Complex

• PDB DOI: 10.2210/pdb4GQB/pdb

• Classification: TRANSFERASE/PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-08-22 Released: 2012-10-17 
• Deposition Author(s): Antonysamy, S., Bonday, Z., Campbell, R., Doyle, B., Druzina, Z., Gheyi, T., Han, B., Jungheim, L.N., Qian, Y., Rauch, C., Russell, M., Sauder, J.M., Wasserman, S.R., Weichert, K., Willard, F.S., Zhang, A., Emtage, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Crystal structure of the human PRMT5:MEP50 complex.

Antonysamy, S., Bonday, Z., Campbell, R.M., Doyle, B., Druzina, Z., Gheyi, T., Han, B., Jungheim, L.N., Qian, Y., Rauch, C., Russell, M., Sauder, J.M., Wasserman, S.R., Weichert, K., Willard, F.S., Zhang, A., Emtage, S.

(2012) Proc Natl Acad Sci U S A 109: 17960-17965

• PubMed: 23071334 
• DOI: 10.1073/pnas.1209814109
• Primary Citation of Related Structures:  
  4GQB


• PubMed Abstract: 
  

Protein arginine methyltransferases (PRMTs) play important roles in several cellular processes, including signaling, gene regulation, and transport of proteins and nucleic acids, to impact growth, differentiation, proliferation, and development. PRMT5 symmetrically di-methylates the two-terminal ω-guanidino nitrogens of arginine residues on substrate proteins. PRMT5 acts as part of a multimeric complex in concert with a variety of partner proteins that regulate its function and specificity. A core component of these complexes is the WD40 protein MEP50/WDR77/p44, which mediates interactions with binding partners and substrates. We have determined the crystal structure of human PRMT5 in complex with MEP50 (methylosome protein 50), bound to an S-adenosylmethionine analog and a peptide substrate derived from histone H4. The structure of the surprising hetero-octameric complex reveals the close interaction between the seven-bladed β-propeller MEP50 and the N-terminal domain of PRMT5, and delineates the structural elements of substrate recognition.

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Organizational Affiliation: 

Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA 92121, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 5	A	637	Homo sapiens	Mutation(s): 0  Gene Names: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 EC: 2.1.1 (PDB Primary Data), 2.1.1.125 (PDB Primary Data), 2.1.1.320 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O14744 (Homo sapiens) Explore O14744  Go to UniProtKB:  O14744
PHAROS:  O14744 GTEx:  ENSG00000100462

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylosome protein 50	B	344	Homo sapiens	Mutation(s): 0  Gene Names: WDR77, MEP50, HKMT1069, Nbla10071, WD45
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQA1 (Homo sapiens) Explore Q9BQA1  Go to UniProtKB:  Q9BQA1
PHAROS:  Q9BQA1 GTEx:  ENSG00000116455

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4 peptide	C	22	Homo sapiens	Mutation(s): 1  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0XU	D [auth A]	(2S,5S,6E)-2,5-diamino-6-[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxydihydrofuran-2(3H)-ylidene]hexanoic acid C15 H21 N7 O5 YNKCTZQHSHSLNN-XVIGKWCNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.222 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.981	α = 90
b = 138.762	β = 90
c = 178.472	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-08-22 
• Released Date: 2012-10-17 
Deposition Author(s): Antonysamy, S., Bonday, Z., Campbell, R., Doyle, B., Druzina, Z., Gheyi, T., Han, B., Jungheim, L.N., Qian, Y., Rauch, C., Russell, M., Sauder, J.M., Wasserman, S.R., Weichert, K., Willard, F.S., Zhang, A., Emtage, S.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2012-11-14
  Changes: Database references
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary