4FFY | pdb_00004ffy

Crystal structure of DENV1-E111 single chain variable fragment bound to DENV-1 DIII, strain 16007.

PDB DOI: https://doi.org/10.2210/pdb4FFY/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Mus musculus, dengue virus type 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-06-01 Released: 2012-06-20
Deposition Author(s): Austin, S.K., Nelson, C.A., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.229 (Depositor), 0.224 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural Basis of Differential Neutralization of DENV-1 Genotypes by an Antibody that Recognizes a Cryptic Epitope.

Austin, S.K., Dowd, K.A., Shrestha, B., Nelson, C.A., Edeling, M.A., Johnson, S., Pierson, T.C., Diamond, M.S., Fremont, D.H.

(2012) PLoS Pathog 8: e1002930-e1002930

PubMed: 23055922 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.ppat.1002930
Primary Citation Related Structures:
4FFY, 4FFZ

PubMed Abstract:
We previously developed a panel of neutralizing monoclonal antibodies against Dengue virus (DENV)-1, of which few exhibited inhibitory activity against all DENV-1 genotypes. This finding is consistent with reports observing variable neutralization of different DENV strains and genotypes using serum from individuals that experienced natural infection or immunization. Herein, we describe the crystal structures of DENV1-E111 bound to a novel CC' loop epitope on domain III (DIII) of the E protein from two different DENV-1 genotypes. Docking of our structure onto the available cryo-electron microscopy models of DENV virions revealed that the DENV1-E111 epitope was inaccessible, suggesting that this antibody recognizes an uncharacterized virus conformation. While the affinity of binding between DENV1-E111 and DIII varied by genotype, we observed limited correlation with inhibitory activity. Instead, our results support the conclusion that potent neutralization depends on genotype-dependent exposure of the CC' loop epitope. These findings establish new structural complexity of the DENV virion, which may be relevant for the choice of DENV strain for induction or analysis of neutralizing antibodies in the context of vaccine development.

Organizational Affiliation

Department of Pathology & Immunology, Washington University School of Medicine, Saint Louis, Missouri, United States of America.

Macromolecule Content

Total Structure Weight: 40.23 kDa
Atom Count: 2,715
Modeled Residue Count: 328
Deposited Residue Count: 367
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DENV1-E111 single chain variable fragment (light chain)	A [auth L]	126	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DENV1-E111 single chain variable fragment (heavy chain)	B [auth H]	130	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
envelope glycoprotein	C [auth A]	111	dengue virus type 1	Mutation(s): 0 Gene Names: Envelope domain III
UniProt
Find proteins for Q9J7C6 (Dengue virus type 1) Explore Q9J7C6 Go to UniProtKB: Q9J7C6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9J7C6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H MOL2 format, chain H mmCIF format, chain H	H	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H Interactions & Density Focus chain H
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L] mmCIF format, chain D [auth L]	D [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain G [auth L] SDF format, chain F [auth L] SDF format, chain E [auth L] MOL2 format, chain I [auth H] MOL2 format, chain G [auth L] MOL2 format, chain F [auth L] MOL2 format, chain E [auth L] mmCIF format, chain I [auth H] mmCIF format, chain G [auth L] mmCIF format, chain F [auth L] mmCIF format, chain E [auth L]	E [auth L], F [auth L], G [auth L], I [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain I [auth H] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain I [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.229 (Depositor), 0.224 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.33	α = 90
b = 135.33	β = 90
c = 52.25	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-06-20

Deposition Author(s):

Austin, S.K.

Nelson, C.A.

Fremont, D.H.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2012-06-20
Type: Initial release
Version 1.1: 2012-10-31
Changes: Database references
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary