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- PDB-5ihb: Structure of the immune receptor CD33 -

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Basic information

Entry
Database: PDB / ID: 5ihb
TitleStructure of the immune receptor CD33
ComponentsMyeloid cell surface antigen CD33
KeywordsIMMUNE SYSTEM / Immune receptor / Siglec / Ig-like / sialic-acid binding
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
Myeloid cell surface antigen CD33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsDodd, R.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustRG47376 United Kingdom
CitationJournal: To Be Published
Title: Structure of ligand bound CD33 receptor associated with Alzheimer's disease
Authors: Dodd, R.B. / Meadows, W. / Qamar, S. / Johnson, C.M. / Kronenberg-Versteeg, D. / St George-Hyslop, P.
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Myeloid cell surface antigen CD33
D: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,86316
Polymers100,2094
Non-polymers2,65412
Water4,179232
1
A: Myeloid cell surface antigen CD33
D: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4328
Polymers50,1042
Non-polymers1,3276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Myeloid cell surface antigen CD33
hetero molecules

B: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4328
Polymers50,1042
Non-polymers1,3276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)64.960, 127.040, 143.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 25052.139 Da / Num. of mol.: 4 / Fragment: UNP residues 21-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD33, SIGLEC3 / Plasmid: pHLSec / Cell line (production host): HEK 293-F / 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.: 12 / Source method: isolated from a natural source / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2% PEG 20,000, 4% PEG MME 500, 100 mM Bicine/Tris base pH 8.5, 1xMorpheus amino acids

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.24→62.32 Å / Num. obs: 56518 / % possible obs: 98.1 % / Redundancy: 4.7 % / Biso Wilson estimate: 48.3786782344 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0696 / Net I/σ(I): 11.92
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.9 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(dev_2313)refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model derived from 2ZG2 by Sculptor

2zg2


Resolution: 2.24→62.32 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.78 / Phase error: 24.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 2792 4.94 %RANDOM
Rwork0.1984 ---
obs0.2003 56515 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.33 Å2
Refinement stepCycle: LAST / Resolution: 2.24→62.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6639 0 168 232 7039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087008
X-RAY DIFFRACTIONf_angle_d0.7799583
X-RAY DIFFRACTIONf_dihedral_angle_d9.7394172
X-RAY DIFFRACTIONf_chiral_restr0.0531098
X-RAY DIFFRACTIONf_plane_restr0.0061234
LS refinement shellResolution: 2.24→2.2786 Å
RfactorNum. reflection% reflection
Rfree0.3483 121 4.56 %
Rwork0.3088 2652 -
obs--98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5166-0.4295-0.2450.660.43992.0630.18140.35080.0552-0.03060.0950.0724-0.0251-0.1904-0.1590.372-0.00430.00840.45680.04430.398243.6547103.207855.2625
22.90090.87820.15682.2192-0.63532.92030.19970.36140.25890.0449-0.2067-0.08610.03480.34370.03130.3429-0.00210.0310.4932-0.01710.415755.3643102.422953.8423
34.81780.2591-1.46193.0107-0.77896.0497-0.1241-0.5263-0.63880.0947-0.0272-0.60280.45341.22490.09230.50070.0879-0.03760.58380.00050.554257.838797.657362.8226
42.2635-0.28660.3462.1724-0.44886.05250.09610.1185-0.12530.14470.0227-0.16040.66410.2541-0.11430.3780.01750.01910.4563-0.0070.495548.196498.785362.9163
51.65190.0921-0.5531.1310.29263.89140.0830.45260.1564-0.20630.0903-0.0302-0.19090.3334-0.12840.33640.0110.02090.5309-0.00720.460351.5997105.419850.4231
61.6337-0.46230.24451.7228-1.27782.27860.099-0.31770.00410.40030.18040.2293-0.324-0.4342-0.18820.3579-0.0309-0.01380.4949-0.0490.443640.181491.285981.2577
73.2152-0.3244-0.94562.2231-0.08292.59720.1201-0.586-0.12980.1269-0.01150.0378-0.15740.0354-0.10530.4056-0.0698-0.03230.50790.01920.375144.162784.921990.0731
81.74221.94091.84034.35432.7032.59530.133-0.26630.06560.1513-0.23820.01120.0499-0.35780.03920.4613-0.0746-0.03330.35920.01970.518438.759858.481868.9239
91.61520.82750.75882.94591.40781.942-0.04340.18880.3159-0.3266-0.23640.1393-0.4229-0.16360.25760.387-0.0662-0.05360.40.0620.451135.543954.583159.4579
104.79110.63870.61092.3052-0.22092.19820.04150.4574-0.49360.15660.0734-0.17020.30780.1366-0.07950.4657-0.01330.02930.3966-0.11690.437827.609925.150948.4134
112.3208-0.43960.23912.44390.4322.3338-0.05390.5445-0.2990.2758-0.2260.11990.51980.18590.32750.43720.05010.02720.5258-0.10420.437944.559725.542954.9595
123.70910.26190.34412.9465-0.36853.57120.08710.1809-0.1915-0.2851-0.0997-0.51740.32110.93640.0460.53780.06520.01770.7455-0.08190.622357.552324.049655.1679
134.5187-0.68682.30752.94792.33786.291-0.01920.4206-0.10991.1230.3858-0.78450.83731.2036-0.07990.62440.096-0.15340.6581-0.05010.649654.709926.660965.1958
142.0956-0.1411-0.28322.74791.74763.7504-0.10220.3612-0.13820.3920.2696-0.46220.41240.6322-0.13110.46180.0324-0.02350.5235-0.07150.508250.932826.656757.0396
151.27280.11790.51231.9668-0.30285.6049-0.10750.16630.0013-0.1082-0.0886-0.1097-1.35620.00640.21960.36960.0226-0.05180.44320.01430.510643.837637.491669.1371
163.4929-0.98410.95243.7908-0.35473.13340.0058-0.54470.22760.00080.09330.1563-0.2988-0.4767-0.10890.40910.0802-0.03280.4621-0.08630.388443.722536.9893.6204
173.51760.4541-0.9381.9183-0.62073.95230.01960.7215-0.1164-0.92040.2108-0.40120.18080.4014-0.20740.9568-0.09210.19990.7148-0.15310.793370.21374.10755.3183
182.1970.2808-0.90491.68620.69053.42930.0016-0.3485-0.3847-0.21030.0431-0.2622-0.04940.2143-0.02380.3764-0.0552-0.02970.37420.02270.480762.202578.178381.3167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 128 )
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 232 )
8X-RAY DIFFRACTION8chain 'B' and (resid 19 through 102 )
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 149 )
10X-RAY DIFFRACTION10chain 'B' and (resid 150 through 232 )
11X-RAY DIFFRACTION11chain 'C' and (resid 21 through 51 )
12X-RAY DIFFRACTION12chain 'C' and (resid 52 through 83 )
13X-RAY DIFFRACTION13chain 'C' and (resid 84 through 95 )
14X-RAY DIFFRACTION14chain 'C' and (resid 96 through 128 )
15X-RAY DIFFRACTION15chain 'C' and (resid 129 through 149 )
16X-RAY DIFFRACTION16chain 'C' and (resid 150 through 232 )
17X-RAY DIFFRACTION17chain 'D' and (resid 23 through 102 )
18X-RAY DIFFRACTION18chain 'D' and (resid 103 through 231 )

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