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- PDB-7zoz: Crystal structure of Siglec-15 in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 7zoz
TitleCrystal structure of Siglec-15 in complex with Fab
Components
  • Anti-Siglec 15 Fab HC
  • Anti-Siglec 15 Fab LC
  • Sialic acid-binding Ig-like lectin 15
KeywordsIMMUNE SYSTEM / sialic acid / siglec / cancer
Function / homology
Function and homology information


regulation of osteoclast development / regulation of bone resorption / DAP12 interactions / regulation of actin cytoskeleton organization / protein-containing complex / plasma membrane
Similarity search - Function
Sialic acid-binding Ig-like lectin 15 / 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 / Immunoglobulins ...Sialic acid-binding Ig-like lectin 15 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Sialic acid-binding Ig-like lectin 15
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 Å
AuthorsLenza, M.P. / Oyenarte, I. / Jimenez-Barbero, J. / Ereno-Orbea, J.
Funding supportEuropean Union, Spain, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionEuropean Union
Spanish Ministry of Science, Innovation, and Universities Spain
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into Siglec-15 reveal glycosylation dependency for its interaction with T cells through integrin CD11b.
Authors: Lenza, M.P. / Egia-Mendikute, L. / Antonana-Vildosola, A. / Soares, C.O. / Coelho, H. / Corzana, F. / Bosch, A. / Manisha, P. / Quintana, J.I. / Oyenarte, I. / Unione, L. / Moure, M.J. / ...Authors: Lenza, M.P. / Egia-Mendikute, L. / Antonana-Vildosola, A. / Soares, C.O. / Coelho, H. / Corzana, F. / Bosch, A. / Manisha, P. / Quintana, J.I. / Oyenarte, I. / Unione, L. / Moure, M.J. / Azkargorta, M. / Atxabal, U. / Sobczak, K. / Elortza, F. / Sutherland, J.D. / Barrio, R. / Marcelo, F. / Jimenez-Barbero, J. / Palazon, A. / Ereno-Orbea, J.
History
DepositionApr 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialic acid-binding Ig-like lectin 15
H: Anti-Siglec 15 Fab HC
L: Anti-Siglec 15 Fab LC


Theoretical massNumber of molelcules
Total (without water)81,7433
Polymers81,7433
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-26 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.534, 60.525, 53.373
Angle α, β, γ (deg.)90.000, 100.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sialic acid-binding Ig-like lectin 15 / Siglec-15 / CD33 antigen-like 3


Mass: 33598.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIGLEC15, CD33L3 / Production host: Homo sapiens (human) / References: UniProt: Q6ZMC9
#2: Antibody Anti-Siglec 15 Fab HC


Mass: 24378.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Anti-Siglec 15 Fab LC


Mass: 23765.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20 % PEG 3350 0.2 M Calcium Chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.104→106.342 Å / Num. obs: 37172 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.79 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.084 / Net I/σ(I): 15.1
Reflection shellResolution: 2.104→2.18 Å / Rmerge(I) obs: 0.633 / Num. unique obs: 1824 / CC1/2: 0.835 / Rpim(I) all: 0.307 / Rrim(I) all: 0.707

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vkk

5vkk


Resolution: 2.104→106.341 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 1898 5.11 %
Rwork0.1756 35251 -
obs0.1778 37149 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.58 Å2 / Biso mean: 40.4562 Å2 / Biso min: 17 Å2
Refinement stepCycle: final / Resolution: 2.104→106.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 0 305 4665
Biso mean---47.54 -
Num. residues----561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1045-2.15710.31411280.246245492
2.1571-2.21540.28171370.212257996
2.2154-2.28060.3392670.2212135751
2.2806-2.35420.21431530.1851265099
2.3542-2.43840.24871490.1807265699
2.4384-2.5360.2411330.18552659100
2.536-2.65140.27231470.18222661100
2.6514-2.79120.28041420.17922666100
2.7912-2.96610.22771390.18122694100
2.9661-3.19520.22481390.17392678100
3.1952-3.51670.19191430.16922692100
3.5167-4.02560.19581110.1603205476
4.0256-5.07190.1721660.14722685100
5.0719-106.340.22291440.1906276699
Refinement TLS params.Method: refined / Origin x: -37.9702 Å / Origin y: 1.4837 Å / Origin z: 14.5035 Å
111213212223313233
T0.1981 Å20.0026 Å20.0241 Å2-0.1856 Å2-0.0052 Å2--0.242 Å2
L1.5148 °2-0.1391 °20.7814 °2-0.3483 °2-0.1015 °2--1.0805 °2
S0.0029 Å °-0.1823 Å °-0.0365 Å °0.0199 Å °0.0165 Å °-0.0447 Å °0.0078 Å °0.0303 Å °-0.0365 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA42 - 166
2X-RAY DIFFRACTION1allH1 - 217
3X-RAY DIFFRACTION1allL1 - 213
4X-RAY DIFFRACTION1allD3 - 476

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