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- PDB-9elw: CRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG1 FC FRAG... -

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Basic information

Entry
Database: PDB / ID: 9elw
TitleCRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG1 FC FRAGMENT- FC-GAMMA RECEPTOR IIA COMPLEX H131 VARIANT
Components
  • IgG receptor IIA H131 variant Fc fragment
  • IgG1 Fc
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / IGG1 / IMMUNOGLOBULIN-LIKE BETA SANDWICH / FC FRAGMENT / FC GAMMA RECEPTOR IIA / CD32A
Function / homology
Function and homology information


regulation of immune system process / IgG binding / extracellular region / plasma membrane
Similarity search - Function
: / 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 ...: / 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
Ig-like domain-containing protein / Low affinity immunoglobulin gamma Fc region receptor III-A
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 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)P01AI162242 United States
CitationJournal: Front Immunol / Year: 2025
Title: Cross-species analysis of FcgRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque.
Authors: Tolbert, W.D. / Nhan, P.B. / Conley, H.E. / Ge, X. / Chandravanshi, M. / Lee, M. / Veilleux, J. / Korzeniowski, M. / Gottumukkala, S. / Ackerman, M.E. / Pollara, J. / Pazgier, M.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 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: IgG1 Fc
B: IgG1 Fc
C: IgG receptor IIA H131 variant Fc fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9047
Polymers69,7153
Non-polymers4,1894
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.164, 127.164, 254.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody IgG1 Fc


Mass: 25143.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: F6RL33
#2: Protein IgG receptor IIA H131 variant Fc fragment


Mass: 19428.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: FCGR2B / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: F6TRF8
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
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: 4.26 Å3/Da / Density % sol: 71.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15% PEG 4000, 0.1 M HEPES pH 7.0

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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 EIGER2 X 16M / Detector: PIXEL / Date: Mar 18, 2024
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.55→50 Å / Num. obs: 15333 / % possible obs: 99.9 % / Redundancy: 17.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.348 / Rpim(I) all: 0.086 / Net I/σ(I): 28.5
Reflection shellResolution: 3.55→3.61 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 744 / CC1/2: 0.52 / Rpim(I) all: 0.918 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.55→46.17 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 42.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.337 746 4.89 %
Rwork0.293 --
obs0.295 15242 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.55→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4769 0 282 0 5051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135188
X-RAY DIFFRACTIONf_angle_d1.7517083
X-RAY DIFFRACTIONf_dihedral_angle_d10.864799
X-RAY DIFFRACTIONf_chiral_restr0.104853
X-RAY DIFFRACTIONf_plane_restr0.013876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-3.810.41791330.36042650X-RAY DIFFRACTION94
3.81-4.20.38631550.32852862X-RAY DIFFRACTION99
4.2-4.810.31241620.27672885X-RAY DIFFRACTION100
4.81-6.050.35241450.31382958X-RAY DIFFRACTION100
6.05-46.170.31831510.27563141X-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)
19.77933.02332.99315.963-0.83197.6418-0.6779-0.52010.56511.3221-0.6545-2.24810.40620.72570.56791.60540.2572-0.58790.74710.10831.688565.8825-20.435351.6957
22.21020.03740.54873.8233-3.20216.1387-0.35510.08280.68051.5111-0.5261-1.8343-1.30621.93971.15941.82020.1383-0.74191.4185-0.05942.937381.69862.297343.0144
33.2328-0.8953-0.62466.4112-4.05622.45780.287-0.04230.0087-0.7411-0.02420.13940.1598-0.3682-0.08571.64310.0251-0.16721.1238-0.17750.735544.28485.278111.5622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 231 THROUGH 444)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 231 THROUGH 444)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID -1 THROUGH 172)

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