1H8T | pdb_00001h8t

Echovirus 11

PDB DOI: https://doi.org/10.2210/pdb1H8T/pdb

Classification: VIRUS
Organism(s): Echovirus E11
Mutation(s): No

Deposited: 2001-02-15 Released: 2002-07-11
Deposition Author(s): Stuart, A., McKee, T., Williams, P.A., Harley, C., Stuart, D.I., Brown, T.D.K., Lea, S.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.255 (Depositor), 0.244 (DCC)
R-Value Work:
0.246 (Depositor), 0.247 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Determination of the Structure of a Decay Accelerating Factor-Binding Clinical Isolate of Echovirus 11 Allows Mapping of Mutants with Altered Receptor Requirements for Infection

Stuart, A., Mckee, T., Williams, P.A., Harley, C., Shen, S., Stuart, D.I., Brown, T.D.K., Lea, S.M.

(2002) J Virol 76: 7694

PubMed: 12097583 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/jvi.76.15.7694-7704.2002
Primary Citation Related Structures:
1H8T

PubMed Abstract:
We have used X-ray crystallography to determine the structure of a decay accelerating factor (DAF)-binding, clinic-derived isolate of echovirus 11 (EV11-207). The structures of the capsid proteins closely resemble those of capsid proteins of other picornaviruses. The structure allows us to interpret a series of amino acid changes produced by passaging EV11-207 in different cell lines as highlighting the locations of multiple receptor-binding sites on the virion surface. We suggest that a DAF-binding site is located at the fivefold axes of the virion, while the binding site for a distinct but as yet unidentified receptor is located within the canyon surrounding the virion fivefold axes.

Organizational Affiliation

Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom.

Macromolecule Content

Total Structure Weight: 95.55 kDa
Atom Count: 6,575
Modeled Residue Count: 842
Deposited Residue Count: 860
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ECHOVIRUS 11 COAT PROTEIN VP1	A	292	Echovirus E11	Mutation(s): 0
UniProt
Find proteins for Q8JKE8 (Echovirus E11) Explore Q8JKE8 Go to UniProtKB: Q8JKE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JKE8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ECHOVIRUS 11 COAT PROTEIN VP2	B	262	Echovirus E11	Mutation(s): 0
UniProt
Find proteins for Q8JKE8 (Echovirus E11) Explore Q8JKE8 Go to UniProtKB: Q8JKE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JKE8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ECHOVIRUS 11 COAT PROTEIN VP3	C	238	Echovirus E11	Mutation(s): 0
UniProt
Find proteins for Q8JKE8 (Echovirus E11) Explore Q8JKE8 Go to UniProtKB: Q8JKE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JKE8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ECHOVIRUS 11 COAT PROTEIN VP4	D	68	Echovirus E11	Mutation(s): 0
UniProt
Find proteins for Q8JKE8 (Echovirus E11) Explore Q8JKE8 Go to UniProtKB: Q8JKE8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8JKE8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MYR Query on MYR Download:Ideal Coordinates CCD File SDF format, chain F [auth D] MOL2 format, chain F [auth D] mmCIF format, chain F [auth D]	F [auth D]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Interactions & Density Focus chain F [auth D]
DOA Query on DOA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	12-AMINO-DODECANOIC ACID C₁₂ H₂₅ N O₂ PBLZLIFKVPJDCO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.255 (Depositor), 0.244 (DCC)
R-Value Work: 0.246 (Depositor), 0.247 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 300.85	α = 90
b = 300.85	β = 90
c = 1476.62	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2002-07-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-07-11
Type: Initial release
Version 1.1: 2012-01-11
Changes: Derived calculations, Other, Refinement description, Version format compliance
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Other
Version 2.1: 2023-12-13
Changes: Refinement description