Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B 

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

Macromolecule Content

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

4GQB

Crystal Structure of the human PRMT5:MEP50 Complex

• 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
• Structures With Same Primary Citation


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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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)
Find proteins for O14744 (Homo sapiens) Explore O14744  Go to UniProtKB:  O14744
NIH Common Fund Data Resources
PHAROS  O14744 GTEx  ENSG00000100462

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
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
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805 GTEx  ENSG00000274618GTEx  ENSG00000197238GTEx  ENSG00000197837GTEx  ENSG00000158406GTEx  ENSG00000278705GTEx  ENSG00000197061GTEx  ENSG00000270882GTEx  ENSG00000270276GTEx  ENSG00000273542GTEx  ENSG00000277157GTEx  ENSG00000276966GTEx  ENSG00000276180GTEx  ENSG00000278637GTEx  ENSG00000275126

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0XU	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