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- PDB-4nof: Crystal structure of the second Ig domain from mouse Polymeric Im... -

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Basic information

Entry
Database: PDB / ID: 4nof
TitleCrystal structure of the second Ig domain from mouse Polymeric Immunoglobulin receptor [PSI-NYSGRC-006220]
ComponentsPolymeric immunoglobulin receptor
KeywordsIMMUNE SYSTEM / ortholog / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / IG domain / Polymeric Immunoglobulin Receptor / Immune Function Network / IFN / Atoms-to-Animals: The Immune Function Network
Function / homology
Function and homology information


polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / epidermal growth factor receptor binding / receptor clustering / Neutrophil degranulation / epidermal growth factor receptor signaling pathway ...polymeric immunoglobulin receptor activity / immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor / polymeric immunoglobulin binding / secretory IgA immunoglobulin complex / Fc receptor signaling pathway / detection of chemical stimulus involved in sensory perception of bitter taste / epidermal growth factor receptor binding / receptor clustering / Neutrophil degranulation / epidermal growth factor receptor signaling pathway / recycling endosome membrane / receptor complex / extracellular space / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Polymeric immunoglobulin receptor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSampathkumar, P. / Kumar, P.R. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chowdhury, 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)
CitationJournal: to be published
Title: Crystal structure of the second Ig domain from mouse Polymeric Immunoglobulin receptor
Authors: Sampathkumar, P. / Casadevall, A. / Almo, S.C.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymeric immunoglobulin receptor
B: Polymeric immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3605
Polymers27,8252
Non-polymers5353
Water2,630146
1
A: Polymeric immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1342
Polymers13,9131
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymeric immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2263
Polymers13,9131
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.388, 35.365, 73.238
Angle α, β, γ (deg.)90.000, 105.960, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Polymeric immunoglobulin receptor / / PIgR / Poly-Ig receptor / Secretory component


Mass: 13912.700 Da / Num. of mol.: 2 / Fragment: Ig-like V-type 2 domain residues 133-249
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pigr / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: O70570
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol), Reservoir (0.1 M Citric Acid:NaOH pH 3.5, 25% (w/v) PEG 3350), Cryoprotection (30% Glycerol), Vapor Diffusion, Sitting Drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2013 / Details: MIRRORS
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 30181 / Num. obs: 30181 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.3
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.89 / Num. unique all: 1467 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly-alanine model of PDB code 1XED

1xed


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.838 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1992 1522 5.1 %RANDOM
Rwork0.18 ---
obs0.181 30082 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.83 Å2 / Biso mean: 27.9053 Å2 / Biso min: 13.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å2-0.77 Å2
2--1.15 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 34 146 1855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191790
X-RAY DIFFRACTIONr_bond_other_d0.0030.021733
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9972436
X-RAY DIFFRACTIONr_angle_other_deg0.7683.0044016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.29725.61673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73915324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.406156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
X-RAY DIFFRACTIONr_mcbond_it2.1632.381884
X-RAY DIFFRACTIONr_mcbond_other2.152.377883
X-RAY DIFFRACTIONr_mcangle_it3.4863.5571106
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 124 -
Rwork0.279 2074 -
all-2198 -
obs-2074 96.15 %

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