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- PDB-5n7b: Understanding the singular conformational landscape of the Tn ant... -

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Basic information

Entry
Database: PDB / ID: 5n7b
TitleUnderstanding the singular conformational landscape of the Tn antigens: Sulfur-for- oxygen substitution in the glycosidic linkage provides new insights into molecular recognition by an antibody
Components
  • APD(CG6)RP(NH2) peptide
  • Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43
KeywordsIMMUNE SYSTEM / ANTIBODIES / ANTIGEN Tn
Function / homology
Function and homology information


immunoglobulin mediated immune response / immunoglobulin complex / antigen binding / adaptive immune response / immune response / extracellular region
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / Ig lambda-1 chain V region S43 / Ig heavy chain V-III region J606
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCompanon, I. / Martinez-Saez, N. / Castro-Lopez, J. / Jimenez-Barbero, J. / Bernardes, G.J.L. / Busto, J.H. / Avenoza, A. / Jimenez-Oses, G. / Hurtado-Guerrero, R. / Peregrina, J.M. / Corzana, F.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spain
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Structure-Based Design of Potent Tumor-Associated Antigens: Modulation of Peptide Presentation by Single-Atom O/S or O/Se Substitutions at the Glycosidic Linkage.
Authors: Companon, I. / Guerreiro, A. / Mangini, V. / Castro-Lopez, J. / Escudero-Casao, M. / Avenoza, A. / Busto, J.H. / Castillon, S. / Jimenez-Barbero, J. / Asensio, J.L. / Jimenez-Oses, G. / ...Authors: Companon, I. / Guerreiro, A. / Mangini, V. / Castro-Lopez, J. / Escudero-Casao, M. / Avenoza, A. / Busto, J.H. / Castillon, S. / Jimenez-Barbero, J. / Asensio, J.L. / Jimenez-Oses, G. / Boutureira, O. / Peregrina, J.M. / Hurtado-Guerrero, R. / Fiammengo, R. / Bernardes, G.J.L. / Corzana, F.
History
DepositionFeb 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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
H: Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43
I: APD(CG6)RP(NH2) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,08510
Polymers26,4292
Non-polymers6568
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint22 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.403, 68.648, 90.917
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: Antibody Ig heavy chain V-III region J606,Ig lambda-1 chain V region S43


Mass: 25758.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Please follow the numbering described in the PDB entry 5A2K
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pPICZalphaA / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P01801, UniProt: P01727
#2: Protein/peptide APD(CG6)RP(NH2) peptide


Mass: 670.782 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M disodium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 25141 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.867 / Rpim(I) all: 0.317 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
MOLREPMolrepphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A2I

5a2i


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.411 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21062 675 2.7 %RANDOM
Rwork0.17606 ---
obs0.17705 24415 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--1.31 Å20 Å2
3----1.7 Å2
Refinement stepCycle: 1 / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1769 0 43 179 1991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021947
X-RAY DIFFRACTIONr_bond_other_d0.0060.021793
X-RAY DIFFRACTIONr_angle_refined_deg1.541.992647
X-RAY DIFFRACTIONr_angle_other_deg1.453.0294132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0575233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68724.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09715280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.35159
X-RAY DIFFRACTIONr_chiral_restr0.1220.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2692.138919
X-RAY DIFFRACTIONr_mcbond_other1.2692.137917
X-RAY DIFFRACTIONr_mcangle_it2.0023.1951144
X-RAY DIFFRACTIONr_mcangle_other2.0013.1951144
X-RAY DIFFRACTIONr_scbond_it1.8192.5091028
X-RAY DIFFRACTIONr_scbond_other1.8152.5091028
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9283.6531499
X-RAY DIFFRACTIONr_long_range_B_refined4.97525.8512064
X-RAY DIFFRACTIONr_long_range_B_other4.97625.862065
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 40 -
Rwork0.259 1761 -
obs--100 %

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