5YYL

Structure of Major Royal Jelly Protein 1 Oligomer

• PDB DOI: https://doi.org/10.2210/pdb5YYL/pdb

• 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)

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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 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 116.01 kDa 
• Atom Count: 6,562 
• Modelled Residue Count: 864 
• Deposited Residue Count: 1,020 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major royal jelly protein 1	A, B	432	Apis mellifera	Mutation(s): 0
UniProt
Find proteins for O18330 (Apis mellifera) Explore O18330  Go to UniProtKB:  O18330

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Apisimin	C, D	78	Apis mellifera	Mutation(s): 0
UniProt
Find proteins for Q8ISL8 (Apis mellifera) Explore Q8ISL8  Go to UniProtKB:  Q8ISL8

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
94R	F [auth A], H [auth B], I [auth C], J [auth C]	(3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol C28 H46 O INDVLXYUCBVVKW-PXBBAZSNSA-N
NAG	G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 211.582	α = 90
b = 211.582	β = 90
c = 149.968	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BUCCANEER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Tian, W., Chen, Z.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2016YFC1200400

Revision History  

• 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