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- PDB-6d49: Cell Surface Receptor in Complex with Ligand at 1.80-A Resolution -

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Basic information

Entry
Database: PDB / ID: 6d49
TitleCell Surface Receptor in Complex with Ligand at 1.80-A Resolution
ComponentsMyeloid cell surface antigen CD33
KeywordsIMMUNE SYSTEM / Sialic Acid Binding / Transmembrane / Receptor / Siglec
Function / homology
Function and homology information


immune response-inhibiting signal transduction / protein tyrosine phosphatase activator activity / negative regulation of monocyte activation / sialic acid binding / negative regulation of interleukin-8 production / Fc-gamma receptor signaling pathway / 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 / negative regulation of interleukin-8 production / Fc-gamma receptor signaling pathway / 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 / Golgi apparatus / cell surface / signal transduction / nucleoplasm / 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 / Immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-FVP / Myeloid cell surface antigen CD33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsHermans, S.J. / Miles, L.A. / Parker, M.W.
CitationJournal: Iscience / Year: 2019
Title: Small Molecule Binding to Alzheimer Risk Factor CD33 Promotes A beta Phagocytosis.
Authors: Miles, L.A. / Hermans, S.J. / Crespi, G.A.N. / Gooi, J.H. / Doughty, L. / Nero, T.L. / Markulic, J. / Ebneth, A. / Wroblowski, B. / Oehlrich, D. / Trabanco, A.A. / Rives, M.L. / Royaux, I. / ...Authors: Miles, L.A. / Hermans, S.J. / Crespi, G.A.N. / Gooi, J.H. / Doughty, L. / Nero, T.L. / Markulic, J. / Ebneth, A. / Wroblowski, B. / Oehlrich, D. / Trabanco, A.A. / Rives, M.L. / Royaux, I. / Hancock, N.C. / Parker, M.W.
History
DepositionApr 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myeloid cell surface antigen CD33
B: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,07113
Polymers29,2972
Non-polymers2,77511
Water4,558253
1
A: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9906
Polymers14,6481
Non-polymers1,3415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0827
Polymers14,6481
Non-polymers1,4336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.369, 68.765, 73.468
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14648.298 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD33, SIGLEC3 / Production host: Escherichia coli (E. coli) / References: UniProt: P20138
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FVP / 2-aminoethyl 5-{[(4-cyclohexyl-1H-1,2,3-triazol-1-yl)acetyl]amino}-3,5,9-trideoxy-9-[(4-hydroxy-3,5-dimethylbenzene-1-carbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->6)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside


Mass: 972.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H64N6O20 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.16 % / Description: Cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 0.6 M NaCl 18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→36.462 Å / Num. obs: 26760 / % possible obs: 99.4 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.035 / Rrim(I) all: 0.081 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1534 / CC1/2: 0.877 / Rpim(I) all: 0.284 / Rrim(I) all: 0.664 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_1496refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D48

6d48


Resolution: 1.801→36.462 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.35
RfactorNum. reflection% reflection
Rfree0.2108 1296 4.85 %
Rwork0.1835 --
obs0.1848 26728 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→36.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2040 0 190 253 2483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072306
X-RAY DIFFRACTIONf_angle_d1.1543134
X-RAY DIFFRACTIONf_dihedral_angle_d14.5851793
X-RAY DIFFRACTIONf_chiral_restr0.065334
X-RAY DIFFRACTIONf_plane_restr0.006392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8008-1.87290.24221460.2282748X-RAY DIFFRACTION97
1.8729-1.95820.23111730.20492782X-RAY DIFFRACTION98
1.9582-2.06140.25231380.19372800X-RAY DIFFRACTION100
2.0614-2.19050.23991400.1932812X-RAY DIFFRACTION99
2.1905-2.35960.22121190.19012835X-RAY DIFFRACTION99
2.3596-2.5970.25511420.19392844X-RAY DIFFRACTION100
2.597-2.97270.22381550.19032847X-RAY DIFFRACTION100
2.9727-3.74470.18671400.17092862X-RAY DIFFRACTION100
3.7447-36.46980.18141430.17062902X-RAY DIFFRACTION100

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