6URH | pdb_00006urh

Crystal structure of broadly neutralizing antibody AR3X in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain

• PDB DOI: https://doi.org/10.2210/pdb6URH/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Orthohepacivirus hominis, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2019-10-23 Released: 2020-03-18 
• Deposition Author(s): Flyak, A.I., Bjorkman, P.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.233 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Models: experimental

Literature

An ultralong CDRH2 in HCV neutralizing antibody demonstrates structural plasticity of antibodies against E2 glycoprotein.

Flyak, A.I., Ruiz, S.E., Salas, J., Rho, S., Bailey, J.R., Bjorkman, P.J.

(2020) Elife 9

• PubMed: 32125272 
• DOI: https://doi.org/10.7554/eLife.53169
• Primary Citation Related Structures: 
  6URH


• PubMed Abstract: 
  

  A vaccine protective against diverse HCV variants is needed to control the HCV epidemic. Structures of E2 complexes with front layer-specific broadly neutralizing antibodies (bNAbs) isolated from HCV-infected individuals, revealed a disulfide bond-containing CDRH3 that adopts straight (individuals who clear infection) or bent (individuals with chronic infection) conformation. To investigate whether a straight versus bent disulfide bond-containing CDRH3 is specific to particular HCV-infected individuals, we solved a crystal structure of the HCV E2 ectodomain in complex with AR3X, a bNAb with an unusually long CDRH2 that was isolated from the chronically-infected individual from whom the bent CDRH3 bNAbs were derived. The structure revealed that AR3X utilizes both its ultralong CDRH2 and a disulfide motif-containing straight CDRH3 to recognize the E2 front layer. These results demonstrate that both the straight and bent CDRH3 classes of HCV bNAb can be elicited in a single individual, revealing a structural plasticity of VH1-69 -derived bNAbs.

---

Organizational Affiliation: 
• Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.
Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 83.12 kDa 
• Atom Count: 5,124 
• Modeled Residue Count: 616 
• Deposited Residue Count: 732 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HCV envelope glycoprotein E2	A [auth C]	264	Orthohepacivirus hominis	Mutation(s): 0
UniProt
Find proteins for A0A2P0NE26 (Hepacivirus hominis) Explore A0A2P0NE26  Go to UniProtKB:  A0A2P0NE26
Glycosylation
Glycosylation Sites: 5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AR3X Heavy Chain	B [auth H]	254	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AR3X Light Chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth B]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G12615HA GlyCosmos: G12615HA GlyGen: G12615HA

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth E]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.233 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.73	α = 90
b = 69.231	β = 90
c = 176.699	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Flyak, A.I., Bjorkman, P.J.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI127469

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary