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- PDB-6d4a: Cell Surface Receptor with Bound Ligand at 1.75-A Resolution -

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Basic information

Entry
Database: PDB / ID: 6d4a
TitleCell Surface Receptor with Bound Ligand at 1.75-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 / positive regulation of protein tyrosine phosphatase activity / negative regulation of monocyte activation / sialic acid binding / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of calcium ion transport / negative regulation of tumor necrosis factor production / specific granule membrane ...immune response-inhibiting signal transduction / positive regulation of protein tyrosine phosphatase activity / negative regulation of monocyte activation / sialic acid binding / negative regulation of interleukin-8 production / negative regulation of interleukin-1 beta production / tertiary granule membrane / negative regulation of calcium ion transport / negative regulation of tumor necrosis factor production / specific granule membrane / positive regulation of protein secretion / cell-cell adhesion / peroxisome / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / Immunoglobulins ...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: 1.751 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5197
Polymers29,2972
Non-polymers2,2225
Water5,999333
1
A: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8054
Polymers14,6481
Non-polymers1,1573
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)15,7133
Polymers14,6481
Non-polymers1,0652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.391, 68.339, 73.618
Angle α, β, γ (deg.)90.00, 97.45, 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.94 % / 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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→34.17 Å / Num. obs: 28662 / % possible obs: 98.4 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.042 / Rrim(I) all: 0.083 / Net I/σ(I): 13.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2 / Num. unique obs: 1477 / CC1/2: 0.756 / Rpim(I) all: 0.397 / Rrim(I) all: 0.785 / % possible all: 94.2

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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: 1.751→34.17 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.23
RfactorNum. reflection% reflection
Rfree0.2022 1530 5.34 %
Rwork0.1765 --
obs0.1779 28638 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.751→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 154 333 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072242
X-RAY DIFFRACTIONf_angle_d1.0013057
X-RAY DIFFRACTIONf_dihedral_angle_d13.5121769
X-RAY DIFFRACTIONf_chiral_restr0.061331
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7509-1.80740.31981340.26972372X-RAY DIFFRACTION95
1.8074-1.8720.26821530.22222397X-RAY DIFFRACTION97
1.872-1.9470.21591580.19052448X-RAY DIFFRACTION98
1.947-2.03560.19131330.18232416X-RAY DIFFRACTION98
2.0356-2.14290.21321480.17912467X-RAY DIFFRACTION98
2.1429-2.27710.23751210.16962498X-RAY DIFFRACTION98
2.2771-2.45290.19991420.17582476X-RAY DIFFRACTION99
2.4529-2.69960.21361320.18432469X-RAY DIFFRACTION99
2.6996-3.09010.20541430.17892476X-RAY DIFFRACTION99
3.0901-3.89230.16821310.15422518X-RAY DIFFRACTION99
3.8923-34.1760.18041350.16682571X-RAY DIFFRACTION100

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