3DPR

Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3

• PDB DOI: https://doi.org/10.2210/pdb3DPR/pdb

• Classification: VIRUS
• Organism(s): rhinovirus A2, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-09 Released: 2009-04-07 
• Deposition Author(s): Querol-Audi, J., Pous, J., Fita, I., Verdaguer, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.441 (Depositor), 0.486 (DCC) 
• R-Value Work: 
  0.425 (Depositor), 0.483 (DCC) 
• R-Value Observed: 
  0.426 (Depositor) 

Literature

Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition

Querol-Audi, J., Konecsni, T., Pous, J., Carugo, O., Fita, I., Verdaguer, N., Blaas, D.

(2009) FEBS Lett 583: 235-240

• PubMed: 19073182 
• DOI: https://doi.org/10.1016/j.febslet.2008.12.014
• Primary Citation of Related Structures:  
  3DPR


• PubMed Abstract: 
  

  X-ray structures of human rhinovirus 2 (HRV2) in complex with soluble very-low-density lipoprotein receptors encompassing modules 1, 2, and 3 (V123) and five V3 modules arranged in tandem (V33333) demonstrates multi-modular binding around the virion's five-fold axes. Occupancy was 60% for V123 and 100% for V33333 explaining the high-avidity of the interaction. Surface potentials of 3D-models of all minor group HRVs and K-type major group HRVs were compared; hydrophobic interactions between a conserved lysine in the viruses and a tryptophan in the receptor modules together with coulombic attraction via diffuse opposite surface potentials determine minor group HRV receptor specificity.

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Organizational Affiliation: 

Institut de Biologia Molecular de Barcelona (CSIC), Parc Científic de Barcelona, Barcelona, Spain.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 300-mer - A60B60C60D60E60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 300-mer - A120B60C60D60 

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

Macromolecule Content

• Total Structure Weight: 99.91 kDa 
• Atom Count: 6,450 
• Modelled Residue Count: 820 
• Deposited Residue Count: 894 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP1	A	289	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP2	B	261	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP3	C	237	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein VP4	D	68	rhinovirus A2	Mutation(s): 0
UniProt
Find proteins for P04936 (Human rhinovirus 2) Explore P04936  Go to UniProtKB:  P04936

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
LDL-receptor class A 3	E	39	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P98155 (Homo sapiens) Explore P98155  Go to UniProtKB:  P98155
PHAROS:  P98155 GTEx:  ENSG00000147852

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DAO	F [auth A]	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N
CA	G [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.441 (Depositor), 0.486 (DCC) 
• R-Value Work:  0.425 (Depositor), 0.483 (DCC) 
• R-Value Observed: 0.426 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 498.117	α = 90
b = 498.117	β = 90
c = 658.425	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Querol-Audi, J., Pous, J., Fita, I., Verdaguer, N.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-01-30
  Changes: Refinement description
• Version 1.3: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.4: 2024-10-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary