5OGI | pdb_00005ogi

Complex of a binding protein and human adenovirus C 5 hexon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.235 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.198 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5OGI

This is version 1.3 of the entry. See complete history

Literature

Adenoviral vector with shield and adapter increases tumor specificity and escapes liver and immune control.

Schmid, M.Ernst, P.Honegger, A.Suomalainen, M.Zimmermann, M.Braun, L.Stauffer, S.Thom, C.Dreier, B.Eibauer, M.Kipar, A.Vogel, V.Greber, U.F.Medalia, O.Pluckthun, A.

(2018) Nat Commun 9: 450-450

  • DOI: https://doi.org/10.1038/s41467-017-02707-6
  • Primary Citation Related Structures: 
    5OGI, 6EQC

  • PubMed Abstract: 

    Most systemic viral gene therapies have been limited by sequestration and degradation of virions, innate and adaptive immunity, and silencing of therapeutic genes within the target cells. Here we engineer a high-affinity protein coat, shielding the most commonly used vector in clinical gene therapy, human adenovirus type 5. Using electron microscopy and crystallography we demonstrate a massive coverage of the virion surface through the hexon-shielding scFv fragment, trimerized to exploit the hexon symmetry and gain avidity. The shield reduces virion clearance in the liver. When the shielded particles are equipped with adaptor proteins, the virions deliver their payload genes into human cancer cells expressing HER2 or EGFR. The combination of shield and adapter also increases viral gene delivery to xenografted tumors in vivo, reduces liver off-targeting and immune neutralization. Our study highlights the power of protein engineering for viral vectors overcoming the challenges of local and systemic viral gene therapies.


  • Organizational Affiliation
    • Department of Biochemistry, University of Zurich, Winterthurerstr, 190, 8057, Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 137.7 kDa 
  • Atom Count: 9,622 
  • Modeled Residue Count: 1,154 
  • Deposited Residue Count: 1,206 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Hexon protein952Human adenovirus 5Mutation(s): 0 
UniProt
Find proteins for P04133 (Human adenovirus C serotype 5)
Explore P04133 
Go to UniProtKB:  P04133
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04133
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv of 9C12 antibody254Mus musculusMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
T [auth A],
U [auth A],
V [auth A],
W [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DIO

Query on DIO



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
X [auth B]
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
S [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.235 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.198 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.185α = 90
b = 158.185β = 90
c = 140.805γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary