Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 119.57 kDa 
• Atom Count: 8103 
• Modelled Residue Count: 974 
• Deposited Residue Count: 1032 
• Unique protein chains: 2

6EPK

CRYSTAL STRUCTURE OF THE PRECURSOR MEMBRANE PROTEIN-ENVELOPE PROTEIN HETERODIMER FROM THE YELLOW FEVER VIRUS

• PDB DOI: 10.2210/pdb6EPK/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Yellow fever virus
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2017-10-11 Released: 2018-10-31 
• Deposition Author(s): Rey, F.A., Duquerroy, S., Crampon, E., Barba-Spaeth, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.186 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 

Literature

CRYSTAL STRUCTURE OF THE PRECURSOR MEMBRANE PROTEIN-ENVELOPE PROTEIN HETERODIMER FROM THE YELLOW FEVER VIRUS

Rey, F.A., Duquerroy, S., Crampon, E., Barba-Spaeth, G.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A, C [auth D]	427	Yellow fever virus	Mutation(s): 0  EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for Q6DV88 (Yellow fever virus (strain Ghana/Asibi/1927)) Explore Q6DV88  Go to UniProtKB:  Q6DV88

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Precursor Membrane Protein	B, D [auth E]	89	Yellow fever virus	Mutation(s): 0  Gene Names: prM EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for P03314 (Yellow fever virus (strain 17D vaccine)) Explore P03314  Go to UniProtKB:  P03314

Oligosaccharides

Help

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

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F, H	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G82348BZ GlyCosmos:  G82348BZ GlyGen:  G82348BZ

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth D], BA [auth D], CA [auth D], DA [auth D], EA [auth D], FA [auth D], GA [auth D], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], RA [auth E], W [auth B], X [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	LA [auth D], MA [auth D], NA [auth D], OA [auth D], PA [auth D], QA [auth D], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], Y [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.186 
• R-Value Work: 0.162 
• R-Value Observed: 0.163 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.88	α = 90
b = 99.88	β = 90
c = 238.824	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-10-11 
• Released Date: 2018-10-31 
Deposition Author(s): Rey, F.A., Duquerroy, S., Crampon, E., Barba-Spaeth, G.

Revision History  

• Version 1.0: 2018-10-31
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary