6VKF

CCHFV GP38 (IbAr10200)

PDB DOI: https://doi.org/10.2210/pdb6VKF/pdb

Classification: VIRAL PROTEIN
Organism(s): Crimean-Congo hemorrhagic fever orthonairovirus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-01-20 Released: 2020-02-05
Deposition Author(s): Mishra, A.K., McLellan, J.S.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.256
R-Value Work: 0.223
R-Value Observed: 0.224

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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Structure and Characterization of Crimean-Congo Hemorrhagic Fever Virus GP38.

Mishra, A.K., Moyer, C.L., Abelson, D.M., Deer, D.J., El Omari, K., Duman, R., Lobel, L., Lutwama, J.J., Dye, J.M., Wagner, A., Chandran, K., Cross, R.W., Geisbert, T.W., Zeitlin, L., Bornholdt, Z.A., McLellan, J.S.

(2020) J Virol 94

PubMed: 31996434 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1128/JVI.02005-19
Primary Citation of Related Structures:
6VKF

PubMed Abstract:

Crimean-Congo hemorrhagic fever virus (CCHFV) is the causative agent of the most widespread tick-borne viral infection in humans. CCHFV encodes a secreted glycoprotein (GP38) of unknown function that is the target of a protective antibody. Here, we present the crystal structure of GP38 at a resolution of 2.5 Å, which revealed a novel fold primarily consisting of a 3-helix bundle and a β-sandwich. Sequence alignment and homology modeling showed distant homology between GP38 and the ectodomain of Gn (a structural glycoprotein in CCHFV), suggestive of a gene duplication event. Analysis of convalescent-phase sera showed high titers of GP38 antibodies indicating immunogenicity in humans during natural CCHFV infection. The only protective antibody for CCHFV in an adult mouse model reported to date, 13G8, bound GP38 with subnanomolar affinity and protected against heterologous CCHFV challenge in a STAT1-knockout mouse model. Our data strongly suggest that GP38 should be evaluated as a vaccine antigen and that its structure provides a foundation to investigate functions of this protein in the viral life cycle. IMPORTANCE Crimean-Congo hemorrhagic fever virus (CCHFV) is a priority pathogen that poses a high risk to public health. Due to the high morbidity and mortality rates associated with CCHFV infection, there is an urgent need to develop medical countermeasures for disease prevention and treatment. CCHFV GP38, a secreted glycoprotein of unknown function unique to the Nairoviridae family, was recently shown to be the target of a protective antibody against CCHFV. Here, we present the crystal structure of GP38, which revealed a novel fold with distant homology to another CCHFV glycoprotein that is suggestive of a gene duplication event. We also demonstrate that antibody 13G8 protects STAT1-knockout mice against heterologous CCHFV challenge using a clinical isolate from regions where CCHFV is endemic. Collectively, these data advance our understanding of GP38 structure and antigenicity and should facilitate future studies investigating its function.

Organizational Affiliation:

Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA jmclellan@austin.utexas.edu.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GP38	A, B	268	Crimean-Congo hemorrhagic fever orthonairovirus	Mutation(s): 0
UniProt
Find proteins for Q8JSZ3 (Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)) Explore Q8JSZ3 Go to UniProtKB: Q8JSZ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8JSZ3
Protein Feature View Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	2		N-Glycosylation	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.52 Å
R-Value Free: 0.256
R-Value Work: 0.223
R-Value Observed: 0.224
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.35	α = 90
b = 97.87	β = 103.87
c = 66.01	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
XDS	data reduction
Aimless	data scaling
XSCALE	data scaling
PHASER	phasing
SHELXD	phasing
PHENIX	model building
BUCCANEER	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-05

Deposition Author(s):

Mishra, A.K.

McLellan, J.S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-02-05
Type: Initial release
Version 1.1: 2020-03-11
Changes: Database references
Version 1.2: 2020-04-15
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary