4I9X

Crystal structure of human cytomegalovirus glycoprotein UL141 targeting the death receptor TRAIL-R2

• PDB DOI: https://doi.org/10.2210/pdb4I9X/pdb

• Classification: APOPTOSIS
• Organism(s): Human herpesvirus 5 strain Merlin, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-12-05 Released: 2013-04-03 
• Deposition Author(s): Nemcovicova, I., Zajonc, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.274 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.13 kDa 
• Atom Count: 4,933 
• Modelled Residue Count: 588 
• Deposited Residue Count: 684 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein UL141	A, B	215	Human herpesvirus 5 strain Merlin	Mutation(s): 0
UniProt
Find proteins for Q6RJQ3 (Human cytomegalovirus (strain Merlin)) Explore Q6RJQ3  Go to UniProtKB:  Q6RJQ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 10B	C, D	127	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O14763 (Homo sapiens) Explore O14763  Go to UniProtKB:  O14763
PHAROS:  O14763 GTEx:  ENSG00000120889

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, F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	H [auth A], I [auth B], K [auth D], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.274 
• R-Value Work: 0.223 
• R-Value Observed: 0.224 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.916	α = 90
b = 97.043	β = 90
c = 141.422	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SHELXS	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-03 
Deposition Author(s): Nemcovicova, I., Zajonc, D.M.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary