4NOF | pdb_00004nof

Crystal structure of the second Ig domain from mouse Polymeric Immunoglobulin receptor [PSI-NYSGRC-006220]

• PDB DOI: https://doi.org/10.2210/pdb4NOF/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2013-11-19 Released: 2013-12-04 
• Deposition Author(s): Sampathkumar, P., Kumar, P.R., Ahmed, M., Banu, R., Bhosle, R., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S.J., Glenn, A.S., Hillerich, B., Khafizov, K., Attonito, J., Love, J.D., Patel, H., Patel, R., Seidel, R.D., Smith, B., Stead, M., Casadevall, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the second Ig domain from mouse Polymeric Immunoglobulin receptor

Sampathkumar, P., Casadevall, A., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.36 kDa 
• Atom Count: 1,896 
• Modeled Residue Count: 217 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymeric immunoglobulin receptor	A, B	125	Mus musculus	Mutation(s): 0  Gene Names: Pigr
UniProt
Find proteins for O70570 (Mus musculus) Explore O70570  Go to UniProtKB:  O70570
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: O70570-1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.388	α = 90
b = 35.365	β = 105.96
c = 73.238	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-04 
Deposition Author(s): Sampathkumar, P., Kumar, P.R., Ahmed, M., Banu, R., Bhosle, R., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chowdhury, S., Fiser, A., Garforth, S.J., Glenn, A.S., Hillerich, B., Khafizov, K., Attonito, J., Love, J.D., Patel, H., Patel, R., Seidel, R.D., Smith, B., Stead, M., Casadevall, A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC), Atoms-to-Animals: The Immune Function Network (IFN)

Revision History  

• Version 1.0: 2013-12-04
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-06
  Changes: Structure summary