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- PDB-9bet: Structure of the human CD33 transmembrane domain -

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Basic information

Entry
Database: PDB / ID: 9bet
TitleStructure of the human CD33 transmembrane domain
ComponentsMyeloid cell surface antigen CD33
KeywordsSUGAR BINDING PROTEIN / Siglec / lectin / receptor / CD33
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 / signaling receptor activity / carbohydrate binding / protein phosphatase binding / cell adhesion / negative regulation of cell population proliferation / external side of plasma membrane / 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)
MethodSOLUTION NMR / simulated annealing
AuthorsUlmer, T.S. / Vu, H.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG072442 United States
CitationJournal: Biochemistry / Year: 2025
Title: Structure of the CD33 Receptor and Implications for the Siglec Family.
Authors: Vu, H.N. / Situ, A.J. / Dai, X. / Ulmer, T.S.
History
DepositionApr 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myeloid cell surface antigen CD33


Theoretical massNumber of molelcules
Total (without water)4,3841
Polymers4,3841
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR relaxation study, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 21all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

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


Mass: 4384.272 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD33, SIGLEC3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P20138
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCA
131isotropic13D HN(CA)CB
141isotropic13D 1H-15N NOESY
151isotropic13D HN(CA)CO

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Sample preparation

DetailsType: bicelle
Contents: 350 mM 1,2-dihexanoyl-sn-glycero-3-phosphocholine, 105 mM 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 25 mM HEPES, 1.0 mM [U-100% 13C; U-100% 15N; U-80% 2H] CD33(Gln251-Arg291), 93% H2O/7% D2O
Label: 2H13C15N_sample / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 mM1,2-dihexanoyl-sn-glycero-3-phosphocholinenone1
105 mM1,2-dimyristoyl-sn-glycero-3-phosphocholinenone1
25 mMHEPESnone1
1.0 mMCD33(Gln251-Arg291)[U-100% 13C; U-100% 15N; U-80% 2H]1
Sample conditionsIonic strength: 25 mM / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 308.2 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 21 / Conformers submitted total number: 21

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