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- PDB-4nfc: Structure of paired immunoglobulin-like type 2 receptor (PILR ) -

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Basic information

Entry
Database: PDB / ID: 4nfc
TitleStructure of paired immunoglobulin-like type 2 receptor (PILR )
ComponentsPaired immunoglobulin-like type 2 receptor beta
KeywordsIMMUNE SYSTEM / IgV-like / immune-related activation receptor / CD99 / cell surface
Function / homology
Function and homology information


activation of transmembrane receptor protein tyrosine kinase activity / MHC class I protein binding / cell surface receptor protein tyrosine kinase signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / plasma membrane
Similarity search - Function
: / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Paired immunoglobulin-like type 2 receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLu, Q. / Lu, G. / Qi, J. / Li, Y. / Zhang, Y. / Wang, H. / Fan, Z. / Yan, J. / Gao, G.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: PILR alpha and PILR beta have a siglec fold and provide the basis of binding to sialic acid
Authors: Lu, Q. / Lu, G. / Qi, J. / Wang, H. / Xuan, Y. / Wang, Q. / Li, Y. / Zhang, Y. / Zheng, C. / Fan, Z. / Yan, J. / Gao, G.F.
History
DepositionOct 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paired immunoglobulin-like type 2 receptor beta
B: Paired immunoglobulin-like type 2 receptor beta


Theoretical massNumber of molelcules
Total (without water)28,0962
Polymers28,0962
Non-polymers00
Water73941
1
A: Paired immunoglobulin-like type 2 receptor beta


Theoretical massNumber of molelcules
Total (without water)14,0481
Polymers14,0481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Paired immunoglobulin-like type 2 receptor beta


Theoretical massNumber of molelcules
Total (without water)14,0481
Polymers14,0481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.803, 42.803, 130.205
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Paired immunoglobulin-like type 2 receptor beta / Activating receptor PILR-beta / Cell surface receptor FDFACT


Mass: 14047.961 Da / Num. of mol.: 2 / Fragment: UNP residues 32-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDFACT, PILR, PILRB, PP1551 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 291 K / pH: 8.5
Details: 3%(w/v) dextran sulfate sodium salt, 0.1M BICINE pH 8.5, 15%(w/v) polyethylene glycol 20,000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13332 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 17.03
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.789 / Rsym value: 0.465 / % possible all: 98.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NFB

4nfb


Resolution: 2.2→35.65 Å / SU ML: 0.28 / σ(F): 1.98 / Phase error: 30.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 659 4.95 %
Rwork0.219 --
obs0.221 13312 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 0 41 2025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0212040
X-RAY DIFFRACTIONf_angle_d1.6282756
X-RAY DIFFRACTIONf_dihedral_angle_d18.416758
X-RAY DIFFRACTIONf_chiral_restr0.093284
X-RAY DIFFRACTIONf_plane_restr0.005352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.202-2.37220.34731520.2876254799
2.3722-2.61090.31421290.2726253899
2.6109-2.98850.29041280.2494256899
2.9885-3.76460.24111290.2074253799
3.7646-35.65650.22631210.1976246395
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)
12.4435-0.64261.61322.6662.00146.28360.0434-0.0467-0.39620.33010.10130.01341.0849-0.4046-0.1860.5175-0.02450.04030.32940.03910.4836-1.60323.53218.9878
22.1724-0.45193.75493.34040.43827.64240.26070.1472-0.041-0.1169-0.19040.11080.2495-0.1611-0.01450.3190.02410.0120.3039-0.01960.361-2.31319.64969.7172
32.1181-0.9968-0.03882.42020.68967.40460.3140.16630.0578-0.2645-0.0553-0.15890.3518-0.1478-0.13390.32270.00280.00060.3427-0.01870.42073.11037.338714.4924
41.7484-1.33941.93674.14730.06916.43290.18320.35750.0151-0.52-0.0931-0.44960.3481.0227-0.15420.32860.04750.03210.54220.02540.467719.234815.56527.6241
53.322-0.26950.97053.68631.89927.338-0.1971-0.0244-0.11710.15350.11220.1471-0.12710.16070.01090.30280.00280.00720.29310.03770.331714.069519.257636.8535
61.4822-0.30090.6562.8593-0.16097.53140.1114-0.0675-0.21030.30640.23540.24660.18190.3207-0.1260.3360.02-0.00550.30940.01190.402413.691713.351732.5357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:37)
2X-RAY DIFFRACTION2chain 'A' and (resseq 38:83)
3X-RAY DIFFRACTION3chain 'A' and (resseq 84:120)
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:37)
5X-RAY DIFFRACTION5chain 'B' and (resseq 38:82)
6X-RAY DIFFRACTION6chain 'B' and (resseq 83:120)

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