5YYL

Structure of Major Royal Jelly Protein 1 Oligomer

  • Classification: SIGNALING PROTEIN
  • Organism(s): Apis mellifera
  • Mutation(s): No 

  • Deposited: 2017-12-10 Released: 2018-08-08 
  • Deposition Author(s): Tian, W., Chen, Z.
  • Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Architecture of the native major royal jelly protein 1 oligomer.

Tian, W.Li, M.Guo, H.Peng, W.Xue, X.Hu, Y.Liu, Y.Zhao, Y.Fang, X.Wang, K.Li, X.Tong, Y.Conlon, M.A.Wu, W.Ren, F.Chen, Z.

(2018) Nat Commun 9: 3373-3373

  • DOI: https://doi.org/10.1038/s41467-018-05619-1
  • Primary Citation of Related Structures:  
    5YYL

  • PubMed Abstract: 

    Honeybee caste development is nutritionally regulated by royal jelly (RJ). Major royal jelly protein 1 (MRJP1), the most abundant glycoprotein among soluble royal jelly proteins, plays pivotal roles in honeybee nutrition and larvae development, and exhibits broad pharmacological activities in humans. However, its structure has long remained unknown. Herein, we identify and report a 16-molecule architecture of native MRJP1 oligomer containing four MRJP1, four apisimin, and eight unanticipated 24-methylenecholesterol molecules at 2.65 Å resolution. MRJP1 has a unique six-bladed β-propeller fold with three disulfide bonds, and it interacts with apisimin mainly by hydrophobic interaction. Every four 24-methylenecholesterol molecules are packaged by two MRJP1 and two apisimin molecules. This assembly dimerizes to form an H-shaped MRJP1 4 -apisimin 4 -24-methylenecholesterol 8 complex via apisimin in a conserved and pH-dependent fashion. Our findings offer a structural basis for understanding the pharmacological effects of MRJPs and 24-methylenecholesterol, and provide insights into their unique physiological roles in bees.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Major royal jelly protein 1
A, B
432Apis melliferaMutation(s): 0 
UniProt
Find proteins for O18330 (Apis mellifera)
Explore O18330 
Go to UniProtKB:  O18330
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18330
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Apisimin
C, D
78Apis melliferaMutation(s): 0 
UniProt
Find proteins for Q8ISL8 (Apis mellifera)
Explore Q8ISL8 
Go to UniProtKB:  Q8ISL8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ISL8
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.582α = 90
b = 211.582β = 90
c = 149.968γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
BUCCANEERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2016YFC1200400

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Structure summary