5VCN | pdb_00005vcn

THE CRYSTAL STRUCTURE OF DER P 1 ALLERGEN COMPLEXED WITH FAB FRAGMENT OF MAB 5H8

• PDB DOI: https://doi.org/10.2210/pdb5VCN/pdb
• Entry: 5VCN supersedes: 4PP1

• Classification: IMMUNE SYSTEM
• Organism(s): Dermatophagoides pteronyssinus, Mus musculus
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2017-03-31 Released: 2017-04-26 
• Deposition Author(s): Osinski, T., Majorek, K.A., Pomes, A., Offermann, L.R., Osinski, S., Glesner, J., Vailes, L.D., Chapman, M.D., Minor, W., Chruszcz, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.265 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.219 (Depositor) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Models: experimental

Literature

Structural Analysis of Der p 1-Antibody Complexes and Comparison with Complexes of Proteins or Peptides with Monoclonal Antibodies.

Osinski, T., Pomes, A., Majorek, K.A., Glesner, J., Offermann, L.R., Vailes, L.D., Chapman, M.D., Minor, W., Chruszcz, M.

(2015) J Immunol 195: 307-316

• PubMed: 26026055 
• DOI: https://doi.org/10.4049/jimmunol.1402199
• Primary Citation Related Structures: 
  4POZ, 5VCN, 5VCO


• PubMed Abstract: 
  

  Der p 1 is a major allergen from the house dust mite, Dermatophagoides pteronyssinus, that belongs to the papain-like cysteine protease family. To investigate the antigenic determinants of Der p 1, we determined two crystal structures of Der p 1 in complex with the Fab fragments of mAbs 5H8 or 10B9. Epitopes for these two Der p 1-specific Abs are located in different, nonoverlapping parts of the Der p 1 molecule. Nevertheless, surface area and identity of the amino acid residues involved in hydrogen bonds between allergen and Ab are similar. The epitope for mAb 10B9 only showed a partial overlap with the previously reported epitope for mAb 4C1, a cross-reactive mAb that binds Der p 1 and its homolog Der f 1 from Dermatophagoides farinae. Upon binding to Der p 1, the Fab fragment of mAb 10B9 was found to form a very rare α helix in its third CDR of the H chain. To provide an overview of the surface properties of the interfaces formed by the complexes of Der p 1-10B9 and Der p 1-5H8, along with the complexes of 4C1 with Der p 1 and Der f 1, a broad analysis of the surfaces and hydrogen bonds of all complexes of Fab-protein or Fab-peptide was performed. This work provides detailed insight into the cross-reactive and specific allergen-Ab interactions in group 1 mite allergens. The surface data of Fab-protein and Fab-peptide interfaces can be used in the design of conformational epitopes with reduced Ab binding for immunotherapy.

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Organizational Affiliation: 
• University of Virginia, Charlottesville, VA 22908; Adam Mickiewicz University, 61-712 Poznan, Poland;
Indoor Biotechnologies, Inc., Charlottesville, VA 22903; and.
University of South Carolina, Columbia, SC 29208.
University of Virginia, Charlottesville, VA 22908;
University of South Carolina, Columbia, SC 29208 [e-mail].

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 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 153.33 kDa 
• Atom Count: 9,870 
• Modeled Residue Count: 1,291 
• Deposited Residue Count: 1,384 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDASE 1	A, B	222	Dermatophagoides pteronyssinus	Mutation(s): 0  EC: 3.4.22.65
UniProt
Find proteins for P08176 (Dermatophagoides pteronyssinus) Explore P08176  Go to UniProtKB:  P08176
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT CHAIN OF FAB FRAGMENT OF MAB 5H8	C, E	210	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAVY CHAIN OF FAB FRAGMENT OF MAB 5H8	D, F	260	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	H [auth A], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	I [auth A], M [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	G [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.265 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.219 (Depositor) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.743	α = 90
b = 73.263	β = 91.09
c = 200.34	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Osinski, T., Majorek, K.A., Pomes, A., Offermann, L.R., Osinski, S., Glesner, J., Vailes, L.D., Chapman, M.D., Minor, W., Chruszcz, M.
• This entry supersedes: 4PP1

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI077653
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM53163

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2017-05-03
  Changes: Derived calculations
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.6: 2022-04-27
  Changes: Data collection
• Version 1.7: 2023-10-04
  Changes: Data collection, Refinement description
• Version 1.8: 2024-11-20
  Changes: Structure summary