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- PDB-9c9c: Protein receptor -

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Basic information

Entry
Database: PDB / ID: 9c9c
TitleProtein receptor
ComponentsLeukocyte immunoglobulin-like receptor subfamily B member 2
KeywordsIMMUNE SYSTEM / protein
Function / homology
Function and homology information


negative regulation of antigen processing and presentation / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / negative regulation of postsynaptic density organization / positive regulation of long-term synaptic depression / MHC class Ib protein binding ...negative regulation of antigen processing and presentation / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / negative regulation of postsynaptic density organization / positive regulation of long-term synaptic depression / MHC class Ib protein binding / immune response-regulating signaling pathway / positive regulation of T cell tolerance induction / interleukin-10-mediated signaling pathway / protein phosphatase 1 binding / regulation of dendritic cell differentiation / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / positive regulation of regulatory T cell differentiation / negative regulation of protein metabolic process / negative regulation of calcium ion transport / MHC class I protein binding / tertiary granule membrane / ficolin-1-rich granule membrane / cellular defense response / cell adhesion molecule binding / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of interleukin-6 production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell signaling / amyloid-beta binding / cellular response to lipopolysaccharide / adaptive immune response / learning or memory / cell surface receptor signaling pathway / immune response / Neutrophil degranulation / protein-containing complex binding / cell surface / signal transduction / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytoplasm
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
IMIDAZOLE / Leukocyte immunoglobulin-like receptor subfamily B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsMacLachlan, B. / Awad, W. / Vivian, J. / Rossjohn, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: Protein complex
Authors: MacLachlan, B.
History
DepositionJun 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukocyte immunoglobulin-like receptor subfamily B member 2
B: Leukocyte immunoglobulin-like receptor subfamily B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,32810
Polymers46,9392
Non-polymers3898
Water8,773487
1
A: Leukocyte immunoglobulin-like receptor subfamily B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7125
Polymers23,4691
Non-polymers2434
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leukocyte immunoglobulin-like receptor subfamily B member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6165
Polymers23,4691
Non-polymers1464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.165, 63.056, 144.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

21A-576-

HOH

31A-634-

HOH

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily B member 2 / LIR-2 / Leukocyte immunoglobulin-like receptor 2 / CD85 antigen-like family member D / ...LIR-2 / Leukocyte immunoglobulin-like receptor 2 / CD85 antigen-like family member D / Immunoglobulin-like transcript 4 / ILT-4 / Monocyte/macrophage immunoglobulin-like receptor 10 / MIR-10


Mass: 23469.316 Da / Num. of mol.: 2 / Fragment: residues 22-220 (Uniprot numbering)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB2, ILT4, LIR2, MIR10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N423
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: imidazole, peg

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.66→48.25 Å / Num. obs: 54877 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.93 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 15.9
Reflection shellResolution: 1.66→1.69 Å / Num. unique obs: 2657 / CC1/2: 0.622

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→39.26 Å / SU ML: 0.2112 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1956 2777 5.06 %
Rwork0.1736 52059 -
obs0.1747 54836 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.78 Å2
Refinement stepCycle: LAST / Resolution: 1.66→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2932 0 20 487 3439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583279
X-RAY DIFFRACTIONf_angle_d0.85654532
X-RAY DIFFRACTIONf_chiral_restr0.0583496
X-RAY DIFFRACTIONf_plane_restr0.0076587
X-RAY DIFFRACTIONf_dihedral_angle_d14.32551234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.690.31451400.30032539X-RAY DIFFRACTION98.75
1.69-1.720.28771310.27272567X-RAY DIFFRACTION98.79
1.72-1.750.28171420.24242538X-RAY DIFFRACTION99
1.75-1.790.23521300.22392576X-RAY DIFFRACTION98.83
1.79-1.830.24271470.2092510X-RAY DIFFRACTION99.18
1.83-1.870.21071470.19192583X-RAY DIFFRACTION99.2
1.87-1.920.25611450.19112569X-RAY DIFFRACTION99.2
1.92-1.970.20851290.18152577X-RAY DIFFRACTION99.3
1.97-2.030.21851220.18082587X-RAY DIFFRACTION99.38
2.03-2.090.22541600.18452558X-RAY DIFFRACTION99.49
2.09-2.170.18881350.15452578X-RAY DIFFRACTION99.45
2.17-2.250.20031380.1612601X-RAY DIFFRACTION99.67
2.25-2.360.17811400.16542588X-RAY DIFFRACTION99.71
2.36-2.480.22181530.1752597X-RAY DIFFRACTION99.71
2.48-2.630.19791080.18532670X-RAY DIFFRACTION99.75
2.63-2.840.24931160.19572627X-RAY DIFFRACTION99.64
2.84-3.120.20531420.18022648X-RAY DIFFRACTION99.89
3.12-3.580.18291350.16162656X-RAY DIFFRACTION99.86
3.58-4.50.13741510.13672698X-RAY DIFFRACTION100
4.5-39.260.18391660.17092792X-RAY DIFFRACTION99.26
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)
10.204828874414-0.237875168217-0.07550830549070.4591630170640.1775473695950.5420373353760.01740814482820.0609130274483-0.038518204450.06584229496170.0262903283807-0.05567694873830.0534499918317-0.175258985154-1.07086015597E-90.0867379240243-0.0159918784785-0.0111109808040.1240456661230.01235482964320.0855765920467-11.5857732653-21.1370267268-3.65291279999
20.169457058040.249781759714-0.2922916673410.03295958683710.551988794145-0.0745435301979-0.01835923413460.1408118750150.008227924528870.1036898269030.0775104559801-0.0804178119455-0.15097550669-0.0943276396283-1.01493038089E-70.1233878991970.00871016610502-0.04650798581860.1387914830960.01425774565140.120175763309-7.35691629912-14.72275425090.0390603904262
3-0.2359327914150.1495935587230.5001490192271.117760930920.8427583062120.5988417611460.0292300583695-4.68256506149E-5-0.01504618096190.09406317029940.07307629886170.01647087687640.105297013648-0.0151866353015.17930573464E-90.133522239048-0.0080444495749-0.0036069072150.0869613170266-0.003124802971780.125599508391-0.961179301167-1.3163911290216.4779098829
40.257698908626-0.03876631277670.09609768466330.170216523768-0.247025167060.1025376609090.07700742951310.0342259486234-0.1252638850170.0421961355959-0.0486979449953-0.09578329506480.06312624469850.2307330719773.90209207977E-80.10110780878-0.004050666585270.0001764754771640.155814820967-0.002529618661740.14110314954113.741292258416.15510898121.5603044941
50.417187310759-0.4011773979250.4803917426-0.1682182464510.1792122891910.5013894830360.03180062838780.07877422243320.123393594350.0287703997202-0.009005962783910.0300834838744-0.09589750800610.00881834214688-7.87229914886E-80.111278630676-0.01116236913360.001499262210480.1078638508590.005248427577230.117364095056.5327991592423.369240253919.0309794592
60.3715802256960.06566679170720.1373317856010.2385641257190.09990178953760.08303935568320.0007079657204490.117709646482-0.0276405892919-0.0107129967959-0.006861377785280.0233568037910.004284182439250.13528362846.28568802349E-70.08932572470930.002555674881290.007852536609420.1672355797480.01395049732250.09059708271478.5915215818817.65484051539.03469032374
70.1177256307940.1753361601040.02871363289860.0802506421663-0.3416055908980.1100061556020.0009825024989660.0710713729448-0.0957762778986-0.00629922964911-0.132824638445-0.159806045816-0.1019708213040.1171035194329.49301980334E-80.1332562773380.003896921822110.006177308177150.1215456326890.01291230764260.16932795528111.1828303969-0.29383161098439.335070646
80.07925598261250.1696332726420.3240388987141.07851713409-0.8144080531730.686683608601-0.009937982893280.0697513273998-0.077587206055-0.00916028234913-0.0831514516276-0.104671942136-0.03221334111460.114562807184-2.95537975127E-80.1264833034210.003486410659270.005029459318570.1309243589290.01865965887020.1372383004647.32056564754-0.29816058453637.8978584025
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 69 )AA4 - 691 - 66
22chain 'A' and (resid 70 through 109 )AA70 - 10967 - 106
33chain 'A' and (resid 110 through 200 )AA110 - 200107 - 190
44chain 'B' and (resid 5 through 30 )BB5 - 301 - 26
55chain 'B' and (resid 31 through 73 )BB31 - 7327 - 69
66chain 'B' and (resid 74 through 92 )BB74 - 9270 - 88
77chain 'B' and (resid 93 through 119 )BB93 - 11989 - 115
88chain 'B' and (resid 120 through 199 )BB120 - 199116 - 189

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