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- PDB-8s73: Crystal structure of Fab-antiCD43 monoclonal antibody complexed t... -

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Basic information

Entry
Database: PDB / ID: 8s73
TitleCrystal structure of Fab-antiCD43 monoclonal antibody complexed to a bis-Tn glycopeptide
Components
  • G2D11(VH-CH1)
  • antiCD43(VL-CL)
  • bis-Tn glycopeptide
KeywordsIMMUNE SYSTEM / Monoclonal antibodies / Fab-antiCD43 / antigen Tn
Function / homology2-acetamido-2-deoxy-alpha-D-galactopyranose
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHurtado-Guerrero, R. / Macias-Leon, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2022-136362NB-I00 Spain
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: Recognizing Tn and STn Epitopes in Protein Context: Structural Advances in Phage Display Libraries for Tumor-Specific Antibody Discovery
Authors: Hurtado-Guerrero, R. / Gatos, S. / Gines-Alcober, I. / Macias-Leon, J. / Manuel Gonzalez-Ramirez, A. / Kasapoglu, I. / Veloz, B. / Companon, I. / Ghirardello, M. / Merino, P. / Corzana, F. / Blixt, O.
History
DepositionFeb 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G2D11(VH-CH1)
B: antiCD43(VL-CL)
C: G2D11(VH-CH1)
D: antiCD43(VL-CL)
M: bis-Tn glycopeptide
N: bis-Tn glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,99412
Polymers94,9256
Non-polymers1,0696
Water2,576143
1
A: G2D11(VH-CH1)
B: antiCD43(VL-CL)
M: bis-Tn glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9976
Polymers47,4633
Non-polymers5353
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: G2D11(VH-CH1)
D: antiCD43(VL-CL)
N: bis-Tn glycopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9976
Polymers47,4633
Non-polymers5353
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.525, 100.525, 194.767
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-440-

HOH

21D-429-

HOH

31D-440-

HOH

41D-442-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNPROPROAA1 - 2121 - 216
21GLNGLNPROPROCC1 - 2121 - 216
12METMETARGARGBB4 - 2117 - 214
22METMETARGARGDD4 - 2117 - 214

NCS ensembles :
ID
1
2

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody G2D11(VH-CH1)


Mass: 23188.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ...Details: QVQLQQSDAELVKPGASVKISCKASGYIFADHAIHWVKRKPEQGLEWIGYISPGNDDIKYNEKFKGKATLTADKSSSTAYMQLNSLTSEDSAVYFCKRSLPGTFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody antiCD43(VL-CL)


Mass: 23699.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DYKDIQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPYTFGGGTKLEIKR ...Details: DYKDIQMTQSPASLSASVGETVTITCRASENIYSYLAWYQQKQGKSPQLLVYNAKTLAEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPYTFGGGTKLEIKR ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein/peptide / Sugars , 2 types, 6 molecules MN

#3: Protein/peptide bis-Tn glycopeptide


Mass: 575.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: 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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 2 types, 145 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: sodium malonate dibasic monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 52037 / % possible obs: 88.6 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rpim(I) all: 0.036 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6226 / CC1/2: 0.547 / Rpim(I) all: 0.738 / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.98 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.751 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 2093 4 %RANDOM
Rwork0.19544 ---
obs0.19715 49943 88.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å2-0 Å2
3----1.92 Å2
Refinement stepCycle: 1 / Resolution: 2.2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 12 144 6743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136785
X-RAY DIFFRACTIONr_bond_other_d0.0020.0156155
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6739240
X-RAY DIFFRACTIONr_angle_other_deg1.3151.61214319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2185835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61723.942274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.159151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2871516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021455
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_it4.3065.2123364
X-RAY DIFFRACTIONr_mcbond_other4.3075.2123363
X-RAY DIFFRACTIONr_mcangle_it6.1337.8044191
X-RAY DIFFRACTIONr_mcangle_other6.1337.8044192
X-RAY DIFFRACTIONr_scbond_it5.6045.8283416
X-RAY DIFFRACTIONr_scbond_other5.6035.8283417
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.468.4795046
X-RAY DIFFRACTIONr_long_range_B_refined11.31460.3426981
X-RAY DIFFRACTIONr_long_range_B_other11.31760.3366973
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A6210
12C6210
21B6414
22D6414
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 79 -
Rwork0.375 2364 -
obs--57.09 %

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