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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.441
R-Value Work: 0.425
R-Value Observed: 0.426

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04936
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P98155
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAO Query on DAO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth E] MOL2 format, chain G [auth E] mmCIF format, chain G [auth E]	G [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.441
R-Value Work: 0.425
R-Value Observed: 0.426
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Revision History (Full details and data files)

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