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- PDB-4nob: Crystal structure of the 1st Ig domain from mouse Polymeric Immun... -

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Basic information

Entry
Database: PDB / ID: 4nob
TitleCrystal structure of the 1st Ig domain from mouse Polymeric Immunoglobulin receptor [PSI-NYSGRC-006220]
ComponentsPolymeric immunoglobulin receptor
KeywordsIMMUNE SYSTEM / ortholog / Ig domain / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / 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: 1.51 Å
AuthorsKumar, P.R. / Banu, R. / Bhosle, R. / Calarese, D.A. / Celikgil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S.J. ...Kumar, P.R. / 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 1st Ig domain from mouse Polymeric Immunoglobulin receptor
Authors: Kumar, P.R. / 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: Polymeric immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3716
Polymers13,9391
Non-polymers4325
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.275, 46.803, 62.062
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 13939.219 Da / Num. of mol.: 1 / Fragment: Ig-like V-type 1 domain residues 20-133
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.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 5% glycerol), Reservoir (0.2M MgCl2, 0.1M Bis-Tris-HCl, 25% (v/v) PEG 3350), Cryoprotection (33% Ethylene glycol), Vapor Diffusion, Sitting Drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 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: 1.51→50 Å / Num. obs: 18980 / % possible obs: 99.4 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.077 / Χ2: 0.974 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.51-1.5480.3538531.043193.3
1.54-1.569.40.339231.058197.8
1.56-1.5910.80.3079301.0831100
1.59-1.6312.20.2919321.043198.6
1.63-1.6612.30.2519161.0871100
1.66-1.7120.239421.046199.3
1.7-1.7412.50.2119441.0971100
1.74-1.7912.50.1879281.118199.5
1.79-1.8412.20.1619501.119199.8
1.84-1.912.70.1419431.0781100
1.9-1.9712.10.1189341.052199.8
1.97-2.0512.20.1029521.0261100
2.05-2.1412.30.0949580.9891100
2.14-2.2612.50.0829500.911100
2.26-2.412.60.0779640.8671100
2.4-2.5812.40.079550.769199.9
2.58-2.8412.40.0639680.7261100
2.84-3.25130.0599760.6951100
3.25-4.112.30.0599950.7341100
4.1-5011.50.06810671.069199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XED

1xed


Resolution: 1.51→37.37 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2109 / WRfactor Rwork: 0.1745 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8837 / SU B: 1.059 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0684 / SU Rfree: 0.0704 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1891 945 5.1 %RANDOM
Rwork0.161 ---
obs0.1625 18374 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.96 Å2 / Biso mean: 17.001 Å2 / Biso min: 8.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å20 Å2
2---0.32 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.51→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms858 0 27 110 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02907
X-RAY DIFFRACTIONr_bond_other_d0.0010.02817
X-RAY DIFFRACTIONr_angle_refined_deg2.2141.9771227
X-RAY DIFFRACTIONr_angle_other_deg0.9473.0041880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6522540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.29515141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.227154
X-RAY DIFFRACTIONr_chiral_restr0.1380.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_mcbond_it1.9331.326451
X-RAY DIFFRACTIONr_mcbond_other1.931.321450
X-RAY DIFFRACTIONr_mcangle_it3.1841.968562
LS refinement shellResolution: 1.509→1.548 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 39 -
Rwork0.171 968 -
all-1007 -
obs--73.66 %

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