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- PDB-3q2c: Binding properties to HLA class I molecules and the structure of ... -

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Basic information

Entry
Database: PDB / ID: 3q2c
TitleBinding properties to HLA class I molecules and the structure of the leukocyte Ig-like receptor A3 (LILRA3/ILT6/LIR4/CD85e)
ComponentsLeukocyte immunoglobulin-like receptor subfamily A member 3
KeywordsIMMUNE SYSTEM / LILRA3 / ILT6 / Activating receptor / HLA binding
Function / homology
Function and homology information


inhibitory MHC class I receptor activity / immune response-regulating signaling pathway / interleukin-10-mediated signaling pathway / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Neutrophil degranulation / extracellular region / plasma membrane
Similarity search - Function
Alpha-1B-glycoprotein/leukocyte immunoglobulin-like receptor / : / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Alpha-1B-glycoprotein/leukocyte immunoglobulin-like receptor / : / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Leukocyte immunoglobulin-like receptor subfamily A member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRyu, M. / Chen, Y. / Qi, J.X. / Liu, J. / Shi, Y. / Cheng, H. / Gao, G.F.
CitationJournal: Plos One / Year: 2011
Title: LILRA3 binds both classical and non-classical HLA class I molecules but with reduced affinities compared to LILRB1/LILRB2: structural evidence
Authors: Ryu, M. / Chen, Y. / Qi, J. / Liu, J. / Fan, Z. / Nam, G. / Shi, Y. / Cheng, H. / Gao, G.F.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukocyte immunoglobulin-like receptor subfamily A member 3


Theoretical massNumber of molelcules
Total (without water)10,7921
Polymers10,7921
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.308, 27.817, 48.257
Angle α, β, γ (deg.)90.00, 111.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily A member 3 / CD85 antigen-like family member E / Immunoglobulin-like transcript 6 / ILT-6 / Leukocyte ...CD85 antigen-like family member E / Immunoglobulin-like transcript 6 / ILT-6 / Leukocyte immunoglobulin-like receptor 4 / LIR-4 / Monocyte inhibitory receptor HM43/HM31


Mass: 10792.341 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP residues 24-120 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N6C8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 3 OF DATABASE Q8N6C8 (LIRA3_HUMAN). RESIDUE VAL 82 (UNP RESIDUE ...THE SEQUENCE IS BASED ON REFERENCE 3 OF DATABASE Q8N6C8 (LIRA3_HUMAN). RESIDUE VAL 82 (UNP RESIDUE NUMBER 105) IS A SEQUENCE CONFLICT.

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0M ammonium sulfate, 0.1M HEPES buffer (pH 7.5), 0.75% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 20, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 3558 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 92.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VDG

1vdg


Resolution: 2.5→23.947 Å / SU ML: 0.18 / σ(F): 0.16 / Phase error: 29.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2574 153 4.37 %
Rwork0.2247 --
obs0.2261 3503 94.45 %
all-3503 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.554 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.4937 Å20 Å20.5254 Å2
2--16.1412 Å20 Å2
3----3.6475 Å2
Refinement stepCycle: LAST / Resolution: 2.5→23.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 0 32 787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005777
X-RAY DIFFRACTIONf_angle_d1.0251058
X-RAY DIFFRACTIONf_dihedral_angle_d16.681282
X-RAY DIFFRACTIONf_chiral_restr0.075120
X-RAY DIFFRACTIONf_plane_restr0.004131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5004-2.86170.30611080.2798974X-RAY DIFFRACTION90
2.8617-3.60340.24211190.24381060X-RAY DIFFRACTION96
3.6034-23.94850.24191240.2171117X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 22.2116 Å / Origin y: 1.8417 Å / Origin z: 14.1459 Å
111213212223313233
T0.2216 Å2-0.0119 Å20.0103 Å2-0.2248 Å20.0088 Å2--0.2323 Å2
L0.9517 °20.2607 °20.2347 °2-0.8385 °2-0.3426 °2--0.7364 °2
S-0.0667 Å °-0.0035 Å °-0.0911 Å °-0.1321 Å °0.0703 Å °-0.0731 Å °0.0744 Å °-0.0462 Å °-0 Å °
Refinement TLS groupSelection details: all

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