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- PDB-8sm2: Crystal Structure of the macaque FcalphaRI bound to macaque IgA Fc. -

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Basic information

Entry
Database: PDB / ID: 8sm2
TitleCrystal Structure of the macaque FcalphaRI bound to macaque IgA Fc.
Components
  • Ig-like domain-containing protein
  • Immunoglobulin subtype domain-containing protein
KeywordsIMMUNE SYSTEM / IGA / FCARI / FcalphaRI / CD89 / ANTIBODY / FC RECEPTOR / IMMUNOGLOBULIN-LIKE DOMAIN
Function / homology
Function and homology information


immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / antibacterial humoral response
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin subtype domain-containing protein / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI162242 United States
CitationJournal: To Be Published
Title: Crystal Structure of the macaque FcalphaRI bound to macaque IgA Fc.
Authors: Tolbert, W.D. / Pazgier, M.
History
DepositionApr 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: Ig-like domain-containing protein
C: Immunoglobulin subtype domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1548
Polymers47,2622
Non-polymers1,8926
Water00
1
A: Ig-like domain-containing protein
C: Immunoglobulin subtype domain-containing protein
hetero molecules

A: Ig-like domain-containing protein
C: Immunoglobulin subtype domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,30816
Polymers94,5254
Non-polymers3,78312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area9680 Å2
ΔGint-25 kcal/mol
Surface area42700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.047, 160.047, 52.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ig-like domain-containing protein


Mass: 23648.801 Da / Num. of mol.: 1 / Fragment: Fc fragment of the macaque IgA
Source method: isolated from a genetically manipulated source
Details: 100% match to GenBank:NP_001035039 / Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: H9H2V9
#2: Protein Immunoglobulin subtype domain-containing protein


Mass: 23613.494 Da / Num. of mol.: 1 / Fragment: macaque FcalphaRI (CD89)
Source method: isolated from a genetically manipulated source
Details: 100% match to GenBank:QJB76120 / Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: EGK_11053 / Cell (production host): HEK 293 GnT1- / Production host: Homo sapiens (human) / References: UniProt: G7NN72
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 4
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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
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: 3.56 Å3/Da / Density % sol: 65.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM ammonium sulfate 12% PEG 3350 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2022
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. obs: 12135 / % possible obs: 98 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.046 / Net I/σ(I): 25.7
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 481 / CC1/2: 0.54 / Rpim(I) all: 0.542 / % possible all: 81.9

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→28.29 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2958 612 5.06 %
Rwork0.2725 --
obs0.2737 12100 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→28.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 122 0 3241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073326
X-RAY DIFFRACTIONf_angle_d1.2614531
X-RAY DIFFRACTIONf_dihedral_angle_d8.658498
X-RAY DIFFRACTIONf_chiral_restr0.088524
X-RAY DIFFRACTIONf_plane_restr0.01570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.460.37641330.35862656X-RAY DIFFRACTION93
3.46-3.960.38861540.34172869X-RAY DIFFRACTION100
3.96-4.990.28751550.27922915X-RAY DIFFRACTION100
4.99-28.290.26221700.24113048X-RAY DIFFRACTION99
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)
14.5816-1.5110.46785.49260.2876.98750.04450.168-0.15440.2592-0.09110.40570.6011-0.43860.03630.8943-0.249-0.09250.60370.04330.4555-44.047226.3113-10.4945
21.8394-0.4289-0.68453.0167-3.94495.955-0.0956-0.1669-0.4492-0.270.2980.12190.7474-0.56990.00612.4156-0.344-0.0460.82230.0030.9922-45.1388-2.167519.8354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 244 through 450)
2X-RAY DIFFRACTION2(chain 'C' and resid 4 through 193)

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