2ZPK | pdb_00002zpk

Crystal structure of P20.1 Fab fragment in complex with its antigen peptide

• PDB DOI: https://doi.org/10.2210/pdb2ZPK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Mutation(s): No 


• Deposited: 2008-07-16 Released: 2008-12-23 
• Deposition Author(s): Nogi, T., Sanagawa, T., Takagi, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Novel affinity tag system using structurally defined antibody-tag interaction: application to single-step protein purification

Nogi, T., Sangawa, T., Tabata, S., Nagae, M., Tamura-Kawakami, K., Beppu, A., Hattori, M., Yasui, N., Takagi, J.

(2008) Protein Sci 17: 2120-2126

• PubMed: 18787202 
• DOI: https://doi.org/10.1110/ps.038299.108
• Primary Citation Related Structures: 
  2ZPK


• PubMed Abstract: 
  

  Biologically important human proteins often require mammalian cell expression for structural studies, presenting technical and economical problems in the production/purification processes. We introduce a novel affinity peptide tagging system that uses a low affinity anti-peptide monoclonal antibody. Concatenation of the short recognition sequence enabled the successful engineering of an 18-residue affinity tag with ideal solution binding kinetics, providing a low-cost purification means when combined with nondenaturing elution by water-miscible organic solvents. Three-dimensional information provides a firm structural basis for the antibody-peptide interaction, opening opportunities for further improvements/modifications.

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Organizational Affiliation: 
• Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.

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 and generated by PISA (software)

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.37 kDa 
• Atom Count: 7,143 
• Modeled Residue Count: 853 
• Deposited Residue Count: 872 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG1-lambda P20.1 Fab (light chain)	A [auth L], D [auth M]	212	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IgG1-lambda P20.1 Fab (heavy chain)	B [auth H], E [auth I]	216	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteinase-activated receptor 4	C [auth P], F [auth Q]	8	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RI0 (Homo sapiens) Explore Q96RI0  Go to UniProtKB:  Q96RI0
PHAROS:  Q96RI0 GTEx:  ENSG00000127533

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth H], H [auth M], I	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth L], D [auth M]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.204 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.045	α = 99.93
b = 65.271	β = 93.5
c = 85.03	γ = 96.46

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Nogi, T., Sanagawa, T., Takagi, J.

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2019-12-25
  Changes: Derived calculations, Polymer sequence
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary