6EPK

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


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 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Envelope protein EA,
C [auth D]
427Yellow fever virusMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DV88
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Precursor Membrane ProteinB,
D [auth E]
89Yellow fever virusMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03314
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseF, H 6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G82348BZ
GlyCosmos:  G82348BZ
GlyGen:  G82348BZ
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
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
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
LA [auth D],
MA [auth D],
NA [auth D],
OA [auth D],
PA [auth D],
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
 Ligand Interaction
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 = 99.88α = 90
b = 99.88β = 90
c = 238.824γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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