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- PDB-6grq: Paired immunoglobulin-like receptor B (PirB) or Leukocyte immunog... -

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Basic information

Entry
Database: PDB / ID: 6grq
TitlePaired immunoglobulin-like receptor B (PirB) or Leukocyte immunoglobulin-like receptor subfamily B member 3 (LILRB3) full extracellular domain
ComponentsPaired immunoglobulin-like receptor B
KeywordsIMMUNE SYSTEM / neuronal growth inhibition / B cell down regulation
Function / homology
Function and homology information


inhibitory MHC class I receptor activity / cytokine-mediated signaling pathway / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Paired immunoglobulin-like receptor B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsVlieg, H.C. / Huizinga, E.G. / Janssen, B.J.C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research723.012.002 Netherlands
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structure and flexibility of the extracellular region of the PirB receptor.
Authors: Vlieg, H.C. / Huizinga, E.G. / Janssen, B.J.C.
History
DepositionJun 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 2.1Jan 17, 2024Group: 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: Paired immunoglobulin-like receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1023
Polymers67,4561
Non-polymers6462
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint10 kcal/mol
Surface area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.375, 106.375, 217.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Paired immunoglobulin-like receptor B


Mass: 67456.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pirb, Lilrb3 / Production host: Homo sapiens (human) / References: UniProt: Q8K4V6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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


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

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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: 4.57 Å3/Da / Density % sol: 73.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.1 M LiCL, 14% PEG 6000, 0.1M citic acid buffer pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→53.19 Å / Num. obs: 19634 / % possible obs: 100 % / Redundancy: 22.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.277 / Net I/σ(I): 8.2
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 22.5 % / Rmerge(I) obs: 2.767 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3949 / CC1/2: 0.542 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D3V, 4LLA

2d3v

4lla


Resolution: 3.3→53.188 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2953 1736 4.91 %
Rwork0.2479 --
obs0.2502 35367 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.3→53.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 42 0 4264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034386
X-RAY DIFFRACTIONf_angle_d0.7935959
X-RAY DIFFRACTIONf_dihedral_angle_d12.0411580
X-RAY DIFFRACTIONf_chiral_restr0.032654
X-RAY DIFFRACTIONf_plane_restr0.003757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3002-3.39730.40581390.39092891X-RAY DIFFRACTION100
3.3973-3.50690.5151360.45062748X-RAY DIFFRACTION97
3.5069-3.63220.41251330.36432801X-RAY DIFFRACTION98
3.6322-3.77760.41881390.41592623X-RAY DIFFRACTION92
3.7776-3.94950.48221510.38112648X-RAY DIFFRACTION93
3.9495-4.15760.34551470.22642813X-RAY DIFFRACTION100
4.1576-4.4180.23011680.18982872X-RAY DIFFRACTION100
4.418-4.75890.22571190.15542861X-RAY DIFFRACTION100
4.7589-5.23750.19181690.16542805X-RAY DIFFRACTION100
5.2375-5.99440.26041510.19332861X-RAY DIFFRACTION100
5.9944-7.54890.28511500.24812855X-RAY DIFFRACTION100
7.5489-53.19440.28121340.25332853X-RAY DIFFRACTION100
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)
12.6561-1.60894.37183.0446-2.20966.5704-0.16810.24310.43530.03270.22120.3922-0.0793-0.7801-0.07790.84370.11890.10521.40130.11920.5888-73.7261-24.3437-12.301
24.99362.6272-3.71928.2686-3.13128.911-0.34330.0491-0.6462-0.32180.2521-0.28190.7991-0.05260.08760.47950.1885-0.01620.7101-0.18330.438-45.5165-35.3728-16.5929
39.42612.45635.23676.80192.56218.0935-0.3468-0.29040.983-0.84760.1619-0.1317-0.52820.00950.04220.99270.16410.10790.7657-0.05960.848-28.1183-14.7238-18.8687
48.25425.1334-2.20836.36610.48512.77480.35-0.1989-0.48890.4844-0.5333-0.2109-0.0050.38530.07660.66110.1146-0.28990.94720.10140.63660.2168-20.0713-13.9709
54.3998-3.1904-0.48479.1652-5.0224.7817-0.4386-0.26271.39410.0918-0.5713-0.4407-1.24820.67090.84811.2308-0.1812-0.33591.13890.22491.105612.54665.3968-9.4607
65.9724.912-1.30035.1376-0.26066.7461.6022-0.5343-0.4380.8047-1.9895-2.14920.31511.70190.87411.3859-0.3824-0.44041.54530.75871.439933.2680.52140.2859
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 119)
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 221)
3X-RAY DIFFRACTION3chain 'A' and (resid 222 through 316 )
4X-RAY DIFFRACTION4chain 'A' and (resid 317 through 419)
5X-RAY DIFFRACTION5chain 'A' and (resid 420 through 518 )
6X-RAY DIFFRACTION6chain 'A' and (resid 519 through 610)

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