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- PDB-5j06: Structure of the immune receptor CD33 in complex with 3'-sialyllactose -

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Basic information

Entry
Database: PDB / ID: 5j06
TitleStructure of the immune receptor CD33 in complex with 3'-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
N-acetyl-alpha-neuraminic acid / Myeloid cell surface antigen CD33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 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 27, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _chem_comp.type
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_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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_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)104,10521
Polymers100,2094
Non-polymers3,89717
Water64936
1
A: Myeloid cell surface antigen CD33
D: Myeloid cell surface antigen CD33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7419
Polymers50,1042
Non-polymers1,6377
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)52,36412
Polymers50,1042
Non-polymers2,26010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Unit cell
Length a, b, c (Å)65.050, 127.060, 142.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Sugars , 3 types, 15 molecules

#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-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/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+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.: 13
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
#5: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 38 molecules

#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.93 Å3/Da / Density % sol: 58 %
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 3'-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: 2.66→62.255 Å / Num. obs: 34631 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 58.87 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0902 / Net I/σ(I): 11.7
Reflection shellResolution: 2.66→2.755 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1.48 / % possible all: 100

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Processing

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

5ihb


Resolution: 2.66→62.255 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.48
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1707 4.93 %RANDOM
Rwork0.2088 ---
obs0.2106 34627 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.66→62.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6673 0 251 36 6960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037128
X-RAY DIFFRACTIONf_angle_d0.6039744
X-RAY DIFFRACTIONf_dihedral_angle_d9.8224213
X-RAY DIFFRACTIONf_chiral_restr0.0461122
X-RAY DIFFRACTIONf_plane_restr0.0041246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.73830.35171250.3212707X-RAY DIFFRACTION100
2.7383-2.82670.35991290.29172732X-RAY DIFFRACTION100
2.8267-2.92770.33761410.28322715X-RAY DIFFRACTION100
2.9277-3.0450.35471460.28312682X-RAY DIFFRACTION100
3.045-3.18350.33391330.25272734X-RAY DIFFRACTION100
3.1835-3.35140.26951440.24152716X-RAY DIFFRACTION100
3.3514-3.56130.27781250.22432751X-RAY DIFFRACTION100
3.5613-3.83620.25111530.21642736X-RAY DIFFRACTION100
3.8362-4.22220.19711550.18732723X-RAY DIFFRACTION100
4.2222-4.8330.18481480.14762740X-RAY DIFFRACTION99
4.833-6.08820.20961640.17372769X-RAY DIFFRACTION99
6.0882-62.27240.2331440.20142915X-RAY DIFFRACTION99
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)
11.46130.3550.21022.0168-0.54561.51850.152-0.4522-0.02680.28570.03970.1002-0.2254-0.403-0.00010.28210.01610.02190.4109-0.00630.3764-16.145139.352416.8573
22.12370.3132-1.34841.5585-0.0662.29280.1587-0.2374-0.13470.042-0.08920.30590.4837-0.88830.01540.3013-0.0201-0.00590.46690.01550.3819-19.440237.048512.4614
30.69310.1765-0.3740.75470.69711.13960.1369-0.13950.3998-0.06860.1524-0.1631-0.47090.2019-0.00570.3371-0.00340.01380.36480.05580.4368-10.116937.7632-2.3487
41.23350.0492-0.06122.19140.55080.73640.07890.3824-0.1974-0.0614-0.0706-0.0654-0.3610.09580.00660.30360.0234-0.03790.3978-0.02010.3292-10.173319.8931-19.0564
50.8424-0.41370.31210.2627-0.07930.20030.0879-0.0894-0.032-0.10890.11980.30550.0603-0.1340.64660.37180.0852-0.03570.1397-0.06090.5018-12.3497-3.57273.7356
63.0949-0.22352.55542.2988-0.09382.1198-0.05350.8755-0.006-0.2858-0.3764-0.7190.29450.9112-0.18820.43680.05390.04190.34770.05880.57871.9286-5.08692.12
71.2566-0.48660.22391.406-0.27011.0154-0.0076-0.2870.08470.3133-0.0562-0.1525-0.3157-0.0029-0.00270.32410.0267-0.09880.2044-0.02770.3592-4.5724-9.029410.0874
82.17740.53-0.17672.28530.93650.4614-0.1079-0.2655-0.2073-0.02540.1499-0.02310.0765-0.2456-0.00120.3060.02860.05390.26640.08720.26134.5251-39.554721.9027
91.57780.5565-1.05582.1351-3.00854.3560.331-0.71150.1270.6356-0.5021-0.2773-0.73810.3184-0.61370.33320.07240.06810.56260.05950.28465.5246-33.796627.9582
101.39161.317-0.34292.2596-0.28112.1645-0.0831-0.3179-0.0206-0.02290.00470.40820.1827-0.6013-0.01430.3152-0.06780.03110.49840.04990.394-19.0535-37.967314.7171
110.7050.24330.51520.1998-0.11681.2671-0.0852-0.41840.11890.2247-0.07710.1198-0.83980.7239-0.01210.4887-0.0218-0.04690.49-0.01620.4747-11.4553-26.02362.3829
121.7827-0.30570.9481.6981.3321.8619-0.020.56750.15270.03040.021-0.1375-0.15080.6516-0.07690.2983-0.119-0.04590.3880.05820.2487-11.6472-26.3978-21.9216
131.85620.66020.28921.53290.27191.3951-0.1104-0.4095-0.00530.72110.18680.60260.3641-0.3010.0080.64880.13120.19290.49150.1310.5623-38.047810.425216.4224
141.7761-0.4118-0.52121.5432-0.39911.5378-0.01350.3752-0.2970.09140.01010.1578-0.0701-0.17840.45780.27420.0399-0.04560.2505-0.02840.3934-29.592514.7388-9.9401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 149 )
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 232 )
5X-RAY DIFFRACTION5chain 'B' and (resid 18 through 56 )
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 92 )
7X-RAY DIFFRACTION7chain 'B' and (resid 93 through 149 )
8X-RAY DIFFRACTION8chain 'B' and (resid 150 through 216 )
9X-RAY DIFFRACTION9chain 'B' and (resid 217 through 232 )
10X-RAY DIFFRACTION10chain 'C' and (resid 21 through 128 )
11X-RAY DIFFRACTION11chain 'C' and (resid 129 through 149 )
12X-RAY DIFFRACTION12chain 'C' and (resid 150 through 231 )
13X-RAY DIFFRACTION13chain 'D' and (resid 21 through 102 )
14X-RAY DIFFRACTION14chain 'D' and (resid 103 through 232 )

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