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- PDB-9vl2: Structure of CD33 complexed with its mAb-10C8 -

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Basic information

Entry
Database: PDB / ID: 9vl2
TitleStructure of CD33 complexed with its mAb-10C8
Components
  • Myeloid cell surface antigen CD33
  • heavy chain of Fab-10C8
  • light chain of Fab-10C8
KeywordsIMMUNE SYSTEM / CD33 Siglec-3 HBV infection immune checkpoint
Function / homology
Function and homology information


immune response-inhibiting signal transduction / protein tyrosine phosphatase activator activity / negative regulation of monocyte activation / sialic acid binding / Fc-gamma receptor signaling pathway / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of tumor necrosis factor production / specific granule membrane ...immune response-inhibiting signal transduction / protein tyrosine phosphatase activator activity / negative regulation of monocyte activation / sialic acid binding / Fc-gamma receptor signaling pathway / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of tumor necrosis factor production / specific granule membrane / positive regulation of protein secretion / cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / peroxisome / cell-cell signaling / carbohydrate binding / signaling receptor activity / protein phosphatase binding / cell adhesion / external side of plasma membrane / negative regulation of cell population proliferation / Neutrophil degranulation / cell surface / Golgi apparatus / signal transduction / plasma membrane
Similarity search - Function
: / Immunoglobulin / Immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Myeloid cell surface antigen CD33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsYeh, Y.H. / Sung, P.S. / Hsieh, S.L. / Hsiao, C.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: J.Biomed.Sci. / Year: 2026
Title: Crystal structure of the CD33/Fab-10C8 complex elucidates the mechanism of antibody antagonism in HBV-induced immunosuppression.
Authors: Yeh, Y.H. / Lin, M.G. / Sung, P.S. / Hsieh, S.L. / Hsiao, C.D.
History
DepositionJun 24, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloid cell surface antigen CD33
B: light chain of Fab-10C8
C: heavy chain of Fab-10C8
D: Myeloid cell surface antigen CD33
E: light chain of Fab-10C8
F: heavy chain of Fab-10C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,84712
Polymers141,1146
Non-polymers1,7346
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)71.408, 71.156, 86.765
Angle α, β, γ (deg.)95.89, 94.16, 111.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Myeloid cell surface antigen CD33 / Sialic acid-binding Ig-like lectin 3 / Siglec-3 / gp67


Mass: 23990.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD33, SIGLEC3 / Cell line (production host): expi293F / Production host: Homo sapiens (human) / References: UniProt: P20138
#2: Antibody light chain of Fab-10C8


Mass: 23439.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi-CHO-s / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody heavy chain of Fab-10C8


Mass: 23127.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi-CHO-s / Production host: Cricetulus griseus (Chinese hamster)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}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.: 4 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl pH 8.5, 15% PEG 4000 / PH range: 8.0-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 23442 / % possible obs: 92.7 % / Redundancy: 1.9 % / CC1/2: 0.97 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.5
Reflection shellResolution: 3.37→3.4 Å / Rmerge(I) obs: 0.095 / Num. unique obs: 881 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX("2.0_5885": ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→28.35 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 2010 8.57 %
Rwork0.2047 --
obs0.2088 23442 88.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.18→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9840 0 112 0 9952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210227
X-RAY DIFFRACTIONf_angle_d0.52713948
X-RAY DIFFRACTIONf_dihedral_angle_d12.2893766
X-RAY DIFFRACTIONf_chiral_restr0.0421570
X-RAY DIFFRACTIONf_plane_restr0.0051776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.260.37231060.30861064X-RAY DIFFRACTION61
3.26-3.340.37191150.27971265X-RAY DIFFRACTION73
3.34-3.440.33951300.26231389X-RAY DIFFRACTION80
3.44-3.550.34381360.25991475X-RAY DIFFRACTION84
3.55-3.680.38611280.29371382X-RAY DIFFRACTION81
3.68-3.830.34511340.25451554X-RAY DIFFRACTION90
3.83-40.28091690.22141658X-RAY DIFFRACTION96
4-4.210.25511570.19341716X-RAY DIFFRACTION98
4.21-4.470.21421570.17951691X-RAY DIFFRACTION98
4.47-4.820.22061590.15931650X-RAY DIFFRACTION97
4.82-5.30.20261580.16881674X-RAY DIFFRACTION97
5.3-6.060.23581580.19051670X-RAY DIFFRACTION97
6.06-7.610.23171530.21391681X-RAY DIFFRACTION97
7.61-28.350.1991500.1741563X-RAY DIFFRACTION90

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