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- PDB-5d4k: Crystal structure of the human polymeric Ig receptor (pIgR) ectodomain -

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Basic information

Entry
Database: PDB / ID: 5d4k
TitleCrystal structure of the human polymeric Ig receptor (pIgR) ectodomain
ComponentsPolymeric immunoglobulin receptor
KeywordsIMMUNE SYSTEM / Ig Super Family (IgSF) / polymeric Ig-binding protein / mucosal immunity / Secretory Component
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 / azurophil granule membrane / receptor clustering / epidermal growth factor receptor signaling pathway / receptor complex ...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 / azurophil granule membrane / receptor clustering / epidermal growth factor receptor signaling pathway / receptor complex / Neutrophil degranulation / extracellular space / extracellular exosome / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.599 Å
AuthorsStadtmueller, B.M. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI04123 United States
Cancer Research InstituteIrving Postdoctoral Fellowship United States
CitationJournal: Elife / Year: 2016
Title: The structure and dynamics of secretory component and its interactions with polymeric immunoglobulins.
Authors: Stadtmueller, B.M. / Huey-Tubman, K.E. / Lopez, C.J. / Yang, Z. / Hubbell, W.L. / Bjorkman, P.J.
History
DepositionAug 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,41214
Polymers122,9662
Non-polymers2,44612
Water1,04558
1
A: Polymeric immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7067
Polymers61,4831
Non-polymers1,2236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymeric immunoglobulin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7067
Polymers61,4831
Non-polymers1,2236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.258, 242.434, 63.046
Angle α, β, γ (deg.)90.000, 114.890, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 2 - 549 / Label seq-ID: 2 - 549

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Polymeric immunoglobulin receptor / / Poly-Ig receptor / Hepatocellular carcinoma-associated protein TB6


Mass: 61483.004 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 19-565)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIGR / Plasmid: pTT5 / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human) / References: UniProt: P01833
#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 6
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
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium sulfate, 0.1M BisTris pH 5.5, 31% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2012
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.599→39.623 Å / Num. all: 49242 / Num. obs: 49242 / % possible obs: 96.5 % / Redundancy: 3 % / Biso Wilson estimate: 51.53 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.07 / Rsym value: 0.058 / Net I/av σ(I): 11.696 / Net I/σ(I): 13.7 / Num. measured all: 145998
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.6-2.7430.5591.42110871350.3730.5592.295.6
2.74-2.9130.3472.22066269340.2330.3473.598.4
2.91-3.112.90.2043.81813063460.1410.2045.496.1
3.11-3.363.10.1176.61852960320.0780.1179.498
3.36-3.6830.06910.91669555320.0460.06914.897.5
3.68-4.112.80.04615.61394548950.0320.04620.195.4
4.11-4.753.10.03319.61347844110.0230.03327.997.2
4.75-5.812.90.03220.61062036280.0220.03229.194.9
5.81-8.2230.0318.2837027930.0210.0328.494.2
8.22-39.6232.90.02124.9446115360.0150.02137.492.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PHASER2.4.0phasing
PDB_EXTRACT3.15data extraction
Coot0.7.2model building
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XED

1xed


Resolution: 2.599→36.984 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 28.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 1997 4.3 %Random
Rwork0.2009 44453 --
obs0.2032 46450 91.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 271.63 Å2 / Biso mean: 69.2157 Å2 / Biso min: 22.82 Å2
Refinement stepCycle: final / Resolution: 2.599→36.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8320 0 276 58 8654
Biso mean--101.9 48.94 -
Num. residues----1075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018671
X-RAY DIFFRACTIONf_angle_d1.24111728
X-RAY DIFFRACTIONf_chiral_restr0.0481305
X-RAY DIFFRACTIONf_plane_restr0.0061515
X-RAY DIFFRACTIONf_dihedral_angle_d13.9233153
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6224X-RAY DIFFRACTION7.626TORSIONAL
12B6224X-RAY DIFFRACTION7.626TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5995-2.66440.39671260.30532701282777
2.6644-2.73650.35851250.28052901302684
2.7365-2.8170.31521320.26312991312387
2.817-2.90780.30231460.26573098324489
2.9078-3.01170.35771370.26353094323189
3.0117-3.13230.38111450.24763079322489
3.1323-3.27470.25811470.22953340348795
3.2747-3.44730.23261490.21273290343995
3.4473-3.66310.26431480.20443351349996
3.6631-3.94560.24421500.1853346349695
3.9456-4.34210.2111540.17033306346095
4.3421-4.96910.19671490.15023356350596
4.9691-6.25570.23921420.18373282342493
6.2557-36.98730.23661470.19563318346594

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