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- PDB-7zor: Crystal structure of anti-Siglec-15 Fab -

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Basic information

Entry
Database: PDB / ID: 7zor
TitleCrystal structure of anti-Siglec-15 Fab
Components
  • Anti-siglec15 FAB HC
  • Anti-siglec15 FAB LC
KeywordsIMMUNE SYSTEM / sialic acid / siglec / cancer
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.933 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 6, 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
I: Anti-siglec15 FAB HC
M: Anti-siglec15 FAB LC
H: Anti-siglec15 FAB HC
L: Anti-siglec15 FAB LC


Theoretical massNumber of molelcules
Total (without water)96,2874
Polymers96,2874
Non-polymers00
Water00
1
I: Anti-siglec15 FAB HC
M: Anti-siglec15 FAB LC


Theoretical massNumber of molelcules
Total (without water)48,1442
Polymers48,1442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-26 kcal/mol
Surface area19640 Å2
MethodPISA
2
H: Anti-siglec15 FAB HC
L: Anti-siglec15 FAB LC


Theoretical massNumber of molelcules
Total (without water)48,1442
Polymers48,1442
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-26 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.020, 60.681, 131.258
Angle α, β, γ (deg.)90.000, 107.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Anti-siglec15 FAB HC


Mass: 24378.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Anti-siglec15 FAB LC


Mass: 23765.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) PEG3350 0.1M HEPES pH7.5 0.2M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.933→62.467 Å / Num. obs: 8960 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 48.69 Å2 / CC1/2: 0.865 / Rmerge(I) obs: 0.465 / Rpim(I) all: 0.208 / Rrim(I) all: 0.511 / Net I/σ(I): 6.4
Reflection shellResolution: 3.933→4.001 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 429 / CC1/2: 0.511 / Rpim(I) all: 0.552 / Rrim(I) all: 1.09 / % possible all: 99.9

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Processing

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

5vkk


Resolution: 3.933→62.467 Å / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 422 4.89 %
Rwork0.2293 8216 -
obs0.2319 8638 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.74 Å2 / Biso mean: 51.159 Å2 / Biso min: 28.52 Å2
Refinement stepCycle: final / Resolution: 3.933→62.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6728 0 0 0 6728
Num. residues----872
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.933-4.50170.29831490.2407265498
4.5017-5.6710.24991330.21592752100
5.671-62.4670.27391400.23282810100

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