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- EMDB-48326: Cryo-EM structure of human CD33 bound to 15G15.3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-48326
TitleCryo-EM structure of human CD33 bound to 15G15.3 Fab
Map datalocal resolution map 1 used for model building of Fab and CD33 IgV domain
Sample
  • Complex: CD33-Fab complex
    • Protein or peptide: 15G15.3 Fab heavy chain
    • Protein or peptide: 15G15.3 Fab light chain
    • Protein or peptide: Myeloid cell surface antigen CD33
KeywordsSiglec-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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsPuno MR / Azumaya C
Funding support1 items
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 WC / Watkins A / Kelly R / Wu S / Puno MR / Azumaya C / Irudayanathan J / Zarzar J / Alavattam S / Kelley B / Izadi S
History
DepositionDec 17, 2024-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48326.png

Downloads & links

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Map

FileDownload / File: emd_48326.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal resolution map 1 used for model building of Fab and CD33 IgV domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 256 pix.
= 351.96 Å		1.37 Å/pix.
x 256 pix.
= 351.96 Å		1.37 Å/pix.
x 256 pix.
= 351.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37484 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.44
Minimum - Maximum-3.7952223 - 4.150014
Average (Standard dev.)0.00024278238 (±0.048329905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 351.96005 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48326_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_48326_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_48326_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_48326_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CD33-Fab complex

EntireName: CD33-Fab complex
Components
  • Complex: CD33-Fab complex
    • Protein or peptide: 15G15.3 Fab heavy chain
    • Protein or peptide: 15G15.3 Fab light chain
    • Protein or peptide: Myeloid cell surface antigen CD33

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Supramolecule #1: CD33-Fab complex

SupramoleculeName: CD33-Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 15G15.3 Fab heavy chain

MacromoleculeName: 15G15.3 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.422328 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGIFS NHAISWVRQA PGQGLEWMGG IIPIFGTANY AQKFQGRVTI TADESTSTAF MELSSLRSE DTAVYYCARE WADVFDIWGQ GTMVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGIFS NHAISWVRQA PGQGLEWMGG IIPIFGTANY AQKFQGRVTI TADESTSTAF MELSSLRSE DTAVYYCARE WADVFDIWGQ GTMVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCDK

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Macromolecule #2: 15G15.3 Fab light chain

MacromoleculeName: 15G15.3 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.955686 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EIVLTQSPLS LPVTPGEPAS ISCRSSQSLL HSNGYNYLDW YLQKPGQSPQ LLIYLGVNSV SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
EIVLTQSPLS LPVTPGEPAS ISCRSSQSLL HSNGYNYLDW YLQKPGQSPQ LLIYLGVNSV SGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PWTFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #3: Myeloid cell surface antigen CD33

MacromoleculeName: Myeloid cell surface antigen CD33 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.939438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSMDPNFWLQ VQESVTVQEG LCVLVPCTFF HPIPYYDKNS PVHGYWFREG AIISRDSPVA TNKLDQEVQE ETQGRFRLLG DPSRNNCSL SIVDARRRDN GSYFFRMERG STKYSYKSPQ LSVHVTDLTH RPKILIPGTL EPGHSKNLTC SVSWACEQGT P PIFSWLSA ...String:
GSMDPNFWLQ VQESVTVQEG LCVLVPCTFF HPIPYYDKNS PVHGYWFREG AIISRDSPVA TNKLDQEVQE ETQGRFRLLG DPSRNNCSL SIVDARRRDN GSYFFRMERG STKYSYKSPQ LSVHVTDLTH RPKILIPGTL EPGHSKNLTC SVSWACEQGT P PIFSWLSA APTSLGPRTT HSSVLIITPR PQDHGTNLTC QVKFAGAGVT TERTIQLNVT YVPQNPTTGI FPGDGSGKQE TR AGVVHGN SGLNDIFEAQ KIEWHENLYF QGDYKDDDDK

UniProtKB: Myeloid cell surface antigen CD33

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 24.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab Initio model from data
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.0) / Number images used: 561118
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5ihb


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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