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- PDB-5j0b: Structure of the immune receptor CD33 in complex with 6'-sialyllactose -

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Basic information

Entry
Database: PDB / ID: 5j0b
TitleStructure of the immune receptor CD33 in complex with 6'-sialyllactose
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: 2.48 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
DepositionMar 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)104,51821
Polymers100,2094
Non-polymers4,30917
Water45025
1
A: Myeloid cell surface antigen CD33
D: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9039
Polymers50,1042
Non-polymers1,7997
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)52,61512
Polymers50,1042
Non-polymers2,51010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x+1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)64.490, 123.680, 141.600
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: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#3: 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 genetically manipulated 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
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2% PEG 20,000, 4% PEG MME 500, 100 MM BICINE/TRIS BASE PH 8.5, 1XMORPHEUS AMINO ACIDS. CRYSTALS SOAKED IN 20 MM 6'-SIALYLLACTOSE IN MOTHER LIQUOR FOR 10 DAYS.

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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 6M / Detector: PIXEL / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.48→42.57 Å / Num. obs: 39754 / % possible obs: 97.18 % / Observed criterion σ(F): 1.34 / Redundancy: 3.9 % / Biso Wilson estimate: 62.56 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.099 / Net I/σ(I): 8.05
Reflection shellResolution: 2.48→2.569 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.9263 / Mean I/σ(I) obs: 1.28 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(dev_2313: ???)refinement
xia2data reduction
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5IHB

5ihb


Resolution: 2.48→42.57 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.76
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 1909 4.8 %RANDOM
Rwork0.2294 ---
obs0.2305 39740 97.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 79.79 Å2
Refinement stepCycle: LAST / Resolution: 2.48→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 280 25 6941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037118
X-RAY DIFFRACTIONf_angle_d0.5869725
X-RAY DIFFRACTIONf_dihedral_angle_d8.8134210
X-RAY DIFFRACTIONf_chiral_restr0.0451126
X-RAY DIFFRACTIONf_plane_restr0.0031240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.54210.43651060.4242675X-RAY DIFFRACTION98
2.5421-2.61080.43631240.40352704X-RAY DIFFRACTION98
2.6108-2.68760.37221450.36442711X-RAY DIFFRACTION98
2.6876-2.77430.3521250.31762692X-RAY DIFFRACTION99
2.7743-2.87350.35711440.31332683X-RAY DIFFRACTION98
2.8735-2.98850.32951450.30322666X-RAY DIFFRACTION97
2.9885-3.12450.32221460.31082644X-RAY DIFFRACTION97
3.1245-3.28910.36961410.28242650X-RAY DIFFRACTION96
3.2891-3.49510.30281490.26122645X-RAY DIFFRACTION96
3.4951-3.76480.24461280.24422697X-RAY DIFFRACTION96
3.7648-4.14340.22031260.20662720X-RAY DIFFRACTION97
4.1434-4.74230.16331260.15692752X-RAY DIFFRACTION98
4.7423-5.97220.17761410.17672811X-RAY DIFFRACTION99
5.9722-42.57630.23581630.19752781X-RAY DIFFRACTION94
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)
11.99810.30110.37742.73571.45133.13460.21070.4329-0.0934-0.1653-0.03130.1132-0.2965-0.0869-0.27270.46170.07810.00760.62310.04740.505115.157338.8156-17.1258
23.9174-1.5466-2.01073.54460.39365.87010.0056-0.19030.1770.16520.099-0.16960.35410.9752-0.23260.49360.0528-0.01440.622-0.04970.557421.324134.233-9.8308
32.53920.4778-0.01421.90350.45481.70540.0730.28420.3057-0.1395-0.0725-0.0512-0.45390.1680.03780.37030.046-0.00380.5062-0.08840.562414.451738.7767-7.6412
43.5371-0.5398-1.15293.5121-0.54773.56620.1511-0.3643-0.09020.24270.09620.0976-0.4257-0.4921-0.25190.5975-0.1072-0.0410.7598-0.00670.569510.627519.50519.1287
52.28342.84082.31064.62093.07922.36570.00090.0469-0.1738-0.09680.0368-0.10040.15590.15730.03970.5992-0.1051-0.06610.41040.07680.664910.5373-3.7584-3.5616
65.0089-0.74791.01855.5936-0.32366.37830.025-1.15560.52731.7223-0.54130.6517-0.7933-1.4980.44270.8782-0.16320.02290.8683-0.18741.0032-2.4993-2.020.1691
73.73490.0990.01822.7951-0.25453.0577-0.1624-1.1845-0.09240.7201-0.23820.1294-0.1162-0.55710.18650.6689-0.1698-0.06320.54320.02280.71113.4195-10.167-2.7535
81.84581.93841.17534.20112.76082.4419-0.07140.16590.5055-0.2695-0.35010.6021-0.4495-0.09160.3380.6971-0.0597-0.08740.57830.10550.70472.7688-8.6422-11.8974
94.11920.74280.50372.7302-0.54532.880.09950.3551-0.6180.25480.1661-0.43970.60360.2168-0.26590.6467-0.0168-0.0180.5091-0.08710.5764-5.2736-38.9182-21.7181
104.62950.2675-0.42324.46890.34253.6209-0.12350.79630.1128-0.0162-0.08010.4086-0.1914-0.49850.11960.7632-0.04140.05360.9309-0.04510.6133-6.2695-33.3082-27.6726
113.5315-1.528-0.11163.5316-0.14243.36530.06980.417-0.1292-0.09970.0024-0.59040.4070.9084-0.05770.47390.1265-0.01940.6598-0.00070.58318.6364-37.686-14.9319
122.2996-0.54890.03182.13460.16035.4822-0.11290.44720.04220.00920.0288-0.2780.13920.68110.09210.50790.0059-0.03520.6980.03160.666715.1273-32.5992-9.891
135.2905-0.60841.51286.31470.1915.1298-0.1096-0.59970.05360.0336-0.17380.4948-0.2391-0.88170.22970.50620.1029-0.06250.6397-0.05660.575210.7788-25.395621.5259
143.43661.3573-1.17293.2810.3363.459-0.34431.0748-0.2004-1.10480.2637-0.63940.12060.50020.05720.9152-0.13230.1350.779-0.10990.772638.34718.7578-17.2331
156.69691.0111-2.77571.7553-0.65775.4298-0.04880.95690.2414-1.12290.1687-0.4373-0.1212-0.0969-0.07561.0558-0.00840.17450.6217-0.01840.984935.983613.4275-12.7362
163.27920.858-0.88342.3873-0.54051.4262-0.0047-0.212-0.382-0.46860.0061-0.3380.06730.2537-0.0690.5119-0.0669-0.02180.44220.04520.6231.648213.885.6946
173.89040.58672.14221.80121.66478.74680.2564-1.296-0.41020.6375-0.29530.10760.785-0.88580.15770.5811-0.14940.00240.74330.14070.607623.858614.820823.1649
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 114 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 232 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 62 )
6X-RAY DIFFRACTION6chain 'B' and (resid 63 through 82 )
7X-RAY DIFFRACTION7chain 'B' and (resid 83 through 102 )
8X-RAY DIFFRACTION8chain 'B' and (resid 103 through 149 )
9X-RAY DIFFRACTION9chain 'B' and (resid 150 through 216 )
10X-RAY DIFFRACTION10chain 'B' and (resid 217 through 232 )
11X-RAY DIFFRACTION11chain 'C' and (resid 20 through 92 )
12X-RAY DIFFRACTION12chain 'C' and (resid 93 through 149 )
13X-RAY DIFFRACTION13chain 'C' and (resid 150 through 231 )
14X-RAY DIFFRACTION14chain 'D' and (resid 23 through 82 )
15X-RAY DIFFRACTION15chain 'D' and (resid 83 through 102 )
16X-RAY DIFFRACTION16chain 'D' and (resid 103 through 200 )
17X-RAY DIFFRACTION17chain 'D' and (resid 201 through 231 )

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