7D6Y

eIF4E in Complex with a Disulphide-Free Autonomous VH Domain

• PDB DOI: https://doi.org/10.2210/pdb7D6Y/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-10-02 Released: 2021-10-06 
• Deposition Author(s): Brown, C.J., Frosi, Y., Jiang, S., Lin, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways

Frosi, Y., Lin, Y.C., Jiang, S., Ramlan, S.R., Hew, K., Asial, I., Engman, A.H., Goh, M., Thean, D., Nordlund, P., Lane, D.P., Brown, C.J.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 43.02 kDa 
• Atom Count: 2,977 
• Modelled Residue Count: 314 
• Deposited Residue Count: 378 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E	A	217	Homo sapiens	Mutation(s): 0  Gene Names: EIF4E, EIF4EL1, EIF4F
UniProt & NIH Common Fund Data Resources
Find proteins for P06730 (Homo sapiens) Explore P06730  Go to UniProtKB:  P06730
PHAROS:  P06730 GTEx:  ENSG00000151247

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VH Domain (1C5)	B	161	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGO	C [auth A]	[[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE C12 H20 N4 O14 P3 LPHBJZOLBGBNJF-XYHAGOFUSA-O
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.848	α = 90
b = 45.324	β = 93.192
c = 39.763	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Brown, C.J., Frosi, Y., Jiang, S., Lin, Y.C.

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description