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- PDB-7aw6: The extracellular region of CD33 with bound sialoside analogue P22 -

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Basic information

Entry
Database: PDB / ID: 7aw6
TitleThe extracellular region of CD33 with bound sialoside analogue P22
ComponentsMyeloid cell surface antigen CD33
KeywordsIMMUNE SYSTEM / receptor / Siglec / Ig-like / sialic acid / Alzheimer's disease / lectin / cell surface antigen
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-FVP / PHOSPHATE ION / Myeloid cell surface antigen CD33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Thompson, A.P. / Arrowsmith, C.H. / Edwards, A.M. / von Delft, F. / Bountra, C. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1RF1AG057443 United States
CitationJournal: To Be Published
Title: The extracellular region of CD33 with bound sialoside analogue P22
Authors: Bradshaw, W.J. / Katis, V.L. / Thompson, A.P. / Arrowsmith, C.H. / Edwards, A.M. / von Delft, F. / Bountra, C. / Gileadi, O.
History
DepositionNov 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)59,99216
Polymers55,8362
Non-polymers4,15614
Water4,270237
1
A: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7766
Polymers27,9181
Non-polymers1,8585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
2
B: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,21610
Polymers27,9181
Non-polymers2,2989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
Unit cell
Length a, b, c (Å)59.641, 103.230, 84.495
Angle α, β, γ (deg.)90.000, 110.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 11 molecules AB

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


Mass: 27917.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD33, SIGLEC3 / Plasmid: pHL-sec / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P20138
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 242 molecules

#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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.1M citrate/phosphate, 6.5% PEG 400, 6.5% PEG 500 MME, 6.5% PEG 600, 6.5% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→79.19 Å / Num. obs: 33360 / % possible obs: 95.5 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.06 / Rrim(I) all: 0.155 / Χ2: 0.94 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.795 / Mean I/σ(I) obs: 1 / Num. unique obs: 1742 / CC1/2: 0.497 / Rpim(I) all: 0.954 / Rrim(I) all: 2.047 / Χ2: 0.86 / % possible all: 69.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IHB

5ihb


Resolution: 1.95→79.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.677 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.192 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1705 5.1 %RANDOM
Rwork0.1936 ---
obs0.1962 31641 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.45 Å2 / Biso mean: 33.442 Å2 / Biso min: 17.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0.99 Å2
2---0.08 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 1.95→79.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 275 237 3869
Biso mean--47.14 38.95 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133772
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173402
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.7165179
X-RAY DIFFRACTIONr_angle_other_deg1.2431.6157909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15620.753186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0115556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.191528
X-RAY DIFFRACTIONr_chiral_restr0.0650.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024732
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02839
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 112 -
Rwork0.322 1718 -
all-1830 -
obs--70.06 %

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