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- PDB-11ex: Crystal structure of hIgG1-Fc in complex with FcRL5 -

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Basic information

Entry
Database: PDB / ID: 11ex
TitleCrystal structure of hIgG1-Fc in complex with FcRL5
Components
  • Fc receptor-like protein 5
  • Immunoglobulin heavy constant gamma 1
KeywordsIMMUNE SYSTEM / Antibody / IgG1 / Fc / Immunology / FcRL5
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / single fertilization / Classical antibody-mediated complement activation / immunoglobulin receptor binding / FCGR activation / B cell activation ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / single fertilization / Classical antibody-mediated complement activation / immunoglobulin receptor binding / FCGR activation / B cell activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / coreceptor activity / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / transmembrane signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / blood microparticle / antibacterial humoral response / Initial triggering of complement / adaptive immune response / signaling receptor complex / cell surface receptor signaling pathway / immune response / external side of plasma membrane / cell surface / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 heavy constant gamma 1 / Fc receptor-like protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsGuo, M. / Yan, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA281106 United States
CitationJournal: To Be Published
Title: Crystal structure of hIgG1-Fc in complex with FcRL5
Authors: Guo, M. / Yan, Z.
History
DepositionFeb 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Fc receptor-like protein 5
A: Immunoglobulin heavy constant gamma 1
B: Immunoglobulin heavy constant gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0576
Polymers77,3153
Non-polymers2,7423
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.716, 138.716, 130.511
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"

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Components

#1: Protein Fc receptor-like protein 5 / FcR-like protein 5 / FcRL5 / BXMAS1 / Fc receptor homolog 5 / FcRH5 / Immune receptor translocation- ...FcR-like protein 5 / FcRL5 / BXMAS1 / Fc receptor homolog 5 / FcRH5 / Immune receptor translocation-associated protein 2


Mass: 29625.678 Da / Num. of mol.: 1 / Mutation: F26S, K45E, L111P, E128G, H155R, W251R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCRL5, FCRH5, IRTA2, UNQ503/PRO820 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q96RD9
#2: Protein Immunoglobulin heavy constant gamma 1 / Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma- ...Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma-1 chain C region NIE


Mass: 23844.883 Da / Num. of mol.: 2 / Mutation: K320E, Q342A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01857
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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: 1463.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 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]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
Has ligand of interestY
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: 4.76 Å3/Da / Density % sol: 74.14 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1MES, pH6.5, 25%(w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97905 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 3.42→88.39 Å / Num. obs: 20062 / % possible obs: 99.9 % / Redundancy: 20.7 % / CC1/2: 0.956 / Rmerge(I) obs: 0.672 / Rpim(I) all: 0.151 / Rrim(I) all: 0.689 / Net I/σ(I): 3.6 / Num. measured all: 414740
Reflection shellResolution: 3.42→3.48 Å / % possible obs: 96.7 % / Redundancy: 21.7 % / Rmerge(I) obs: 3.57 / Num. measured all: 20961 / Num. unique obs: 964 / CC1/2: 0.154 / Rpim(I) all: 0.785 / Rrim(I) all: 3.656 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data scaling
xia2data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→88.39 Å / SU ML: 0.6801 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.4466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2987 995 4.98 %
Rwork0.2553 18985 -
obs0.2575 19980 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.55 Å2
Refinement stepCycle: LAST / Resolution: 3.42→88.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 184 0 5547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01345689
X-RAY DIFFRACTIONf_angle_d1.48867748
X-RAY DIFFRACTIONf_chiral_restr0.0701903
X-RAY DIFFRACTIONf_plane_restr0.0121976
X-RAY DIFFRACTIONf_dihedral_angle_d8.1574846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.60.39291350.36992639X-RAY DIFFRACTION98.13
3.6-3.820.37521510.33842654X-RAY DIFFRACTION99.47
3.82-4.120.35421400.31582686X-RAY DIFFRACTION99.68
4.12-4.530.30511430.24872696X-RAY DIFFRACTION99.93
4.53-5.190.30681470.23812714X-RAY DIFFRACTION99.93
5.19-6.540.26911160.23852769X-RAY DIFFRACTION99.9
6.54-88.390.2321630.19322827X-RAY DIFFRACTION99.67

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