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- PDB-5eiq: Human OSCAR ligand-binding domain -

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Basic information

Entry
Database: PDB / ID: 5eiq
TitleHuman OSCAR ligand-binding domain
ComponentsOsteoclast-associated immunoglobulin-like receptor
KeywordsIMMUNE SYSTEM / Immunoglobulin-like / collagen binding / immune receptor / osteoclast / BALBES NMR
Function / homology
Function and homology information


collagen receptor activity / osteoclast differentiation / specific granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / tertiary granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Osteoclast-associated immunoglobulin-like receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHinerman, J.M. / Conrady, D.G. / Herr, A.B.
CitationJournal: Blood / Year: 2016
Title: Structural basis for collagen recognition by the immune receptor OSCAR.
Authors: Zhou, L. / Hinerman, J.M. / Blaszczyk, M. / Miller, J.L. / Conrady, D.G. / Barrow, A.D. / Chirgadze, D.Y. / Bihan, D. / Farndale, R.W. / Herr, A.B.
History
DepositionOct 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Osteoclast-associated immunoglobulin-like receptor


Theoretical massNumber of molelcules
Total (without water)20,7321
Polymers20,7321
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.938, 48.486, 74.945
Angle α, β, γ (deg.)90.000, 91.820, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer confirmed by analytical ultracentrifugation

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Components

#1: Protein Osteoclast-associated immunoglobulin-like receptor / hOSCAR / Polymeric immunoglobulin receptor 3 / Poly-Ig receptor 3


Mass: 20731.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSCAR / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IYS5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5 / Details: 0.1 M NaCitrate pH 5.0, 30% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.006→48.486 Å / Num. all: 12996 / Num. obs: 12996 / % possible obs: 99.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 27.35 Å2 / Rpim(I) all: 0.1 / Rrim(I) all: 0.19 / Rsym value: 0.128 / Net I/av σ(I): 4.885 / Net I/σ(I): 7.7 / Num. measured all: 47065
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
2.01-2.113.60.651.9680518820.4890.651.998.4
2.11-2.243.60.4491.6647417860.3470.4492.898.1
2.24-2.43.70.3631.9598416360.2730.3633.798.4
2.4-2.593.70.2832.4578315670.2150.2834.899.6
2.59-2.843.70.1863.4532714440.1390.1866.999.9
2.84-3.173.60.1185.5477313080.0910.1189.499.8
3.17-3.663.60.0738.7419411740.0590.07313.699.6
3.66-4.483.60.05810.6357110050.050.05816.699.6
4.48-6.343.50.05510.426547520.0450.05518.599.4
6.34-48.4863.40.04711.815004420.0420.04718.999.4

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Processing

Software
NameVersionClassification
BUSTER-TNTrefinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
BUSTER2.10.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P2T

3p2t


Resolution: 2.01→40.7 Å / Cor.coef. Fo:Fc: 0.9403 / Cor.coef. Fo:Fc free: 0.9113 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.191 / SU Rfree Blow DPI: 0.159 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 625 4.85 %RANDOM
Rwork0.1788 ---
obs0.1808 12884 99.02 %-
Displacement parametersBiso max: 115.35 Å2 / Biso mean: 32.54 Å2 / Biso min: 7.84 Å2
Baniso -1Baniso -2Baniso -3
1--5.0363 Å20 Å21.932 Å2
2--5.8832 Å20 Å2
3----0.8469 Å2
Refine analyzeLuzzati coordinate error obs: 0.247 Å
Refinement stepCycle: final / Resolution: 2.01→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 0 155 1619
Biso mean---35.98 -
Num. residues----188
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d477SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes226HARMONIC5
X-RAY DIFFRACTIONt_it1516HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion183SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1736SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1516HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2081HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion4.01
X-RAY DIFFRACTIONt_other_torsion13.89
LS refinement shellResolution: 2.01→2.2 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2264 138 4.54 %
Rwork0.211 2901 -
all0.2117 3039 -
obs--99.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8282-0.23250.85011.6638-0.69591.7212-0.0520.06030.0770.0850.0519-0.1449-0.09190.08890.0001-0.13270.00840.0299-0.053-0.0044-0.10112.3717-0.92171.2556
20.9812-0.008-0.11912.8226-0.55360.7748-0.001-0.1608-0.09480.0155-0.0817-0.0291-0.0037-0.09240.0827-0.04640.00010.01360.07290.0013-0.096412.2385-6.23028.1076
33.99970.51311.82193.17640.00461.6916-0.0192-0.15220.11510.24640.0071-0.0255-0.0416-0.17340.0122-0.0319-0.0130.05680.0054-0.0067-0.05968.32951.35052.9171
42.4424-1.44061.31562.1986-1.31913.644-0.04190.32040.1258-0.5997-0.10830.1388-0.24390.19360.15020.1727-0.0013-0.0983-0.07260.0164-0.19384.22411.3168-29.2713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 42}A3 - 42
2X-RAY DIFFRACTION2{A|48 - 58}A48 - 58
3X-RAY DIFFRACTION3{A|59 - 101}A59 - 101
4X-RAY DIFFRACTION4{A|102 - 190}A102 - 190

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