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- PDB-9mkg: Cryo-EM structure of human CD33 bound to 15G15.3 Fab -

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Basic information

Entry
Database: PDB / ID: 9mkg
TitleCryo-EM structure of human CD33 bound to 15G15.3 Fab
Components
  • 15G15.3 Fab heavy chain
  • 15G15.3 Fab light chain
  • Myeloid cell surface antigen CD33
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Siglec-3 / myeloid cell / antigen / transmembrane receptor / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsPuno, M.R. / Azumaya, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Rational design of oxidation-resistant antibodies through local electrostatic modulation
Authors: Lenka, S. / Stephens, N. / Mehta, S. / Seeger, F. / Jafari, N. / Liang, W.C. / Watkins, A. / Kelly, R. / Wu, S. / Puno, M.R. / Azumaya, C. / Irudayanathan, J. / Zarzar, J. / Alavattam, S. / ...Authors: Lenka, S. / Stephens, N. / Mehta, S. / Seeger, F. / Jafari, N. / Liang, W.C. / Watkins, A. / Kelly, R. / Wu, S. / Puno, M.R. / Azumaya, C. / Irudayanathan, J. / Zarzar, J. / Alavattam, S. / Kelley, B. / Izadi, S.
History
DepositionDec 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 24, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 15G15.3 Fab heavy chain
B: 15G15.3 Fab light chain
C: Myeloid cell surface antigen CD33


Theoretical massNumber of molelcules
Total (without water)78,3173
Polymers78,3173
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody 15G15.3 Fab heavy chain


Mass: 23422.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 15G15.3 Fab light chain


Mass: 23955.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Myeloid cell surface antigen CD33 / Sialic acid-binding Ig-like lectin 3 / Siglec-3 / gp67


Mass: 30939.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD33, SIGLEC3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P20138
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CD33-Fab complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 24000 nm / Nominal defocus min: 8000 nm
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2PHENIX1.21rc1_5015:model refinement
13cryoSPARC4.3.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 561118 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5IHB

5ihb


Accession code: 5IHB / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034364
ELECTRON MICROSCOPYf_angle_d0.4345938
ELECTRON MICROSCOPYf_dihedral_angle_d3.658593
ELECTRON MICROSCOPYf_chiral_restr0.043663
ELECTRON MICROSCOPYf_plane_restr0.003767

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