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- PDB-8s6v: Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycop... -

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Basic information

Entry
Database: PDB / ID: 8s6v
TitleCrystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide
Components
  • 2D9 (VL-CL)
  • G2D11 (VH-CH1)
  • Mucin-1 subunit alpha
KeywordsIMMUNE SYSTEM / Monoclonal antibody / Fab-2D9
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / mitotic G1 DNA damage checkpoint signaling ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / mitotic G1 DNA damage checkpoint signaling / transcription coregulator activity / DNA damage response, signal transduction by p53 class mediator / Golgi lumen / p53 binding / Interleukin-4 and Interleukin-13 signaling / vesicle / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleus / plasma membrane
Similarity search - Function
Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Mucin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHurtado-Guerrero, R. / Macias-Leon, J. / Gonzalez-Ramirez, A.
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 28, 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: 2D9 (VL-CL)
C: G2D11 (VH-CH1)
D: 2D9 (VL-CL)
M: Mucin-1 subunit alpha
N: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,10526
Polymers96,0576
Non-polymers2,04820
Water9,386521
1
A: G2D11 (VH-CH1)
B: 2D9 (VL-CL)
M: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,91111
Polymers48,0293
Non-polymers8838
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: G2D11 (VH-CH1)
D: 2D9 (VL-CL)
N: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,19415
Polymers48,0293
Non-polymers1,16512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.053, 111.546, 134.962
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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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 2D9 (VL-CL)


Mass: 24074.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ...Details: DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSSDQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQCYSYPFTFGSGTKLERKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR
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 Mucin-1 subunit alpha / MUC1-NT / MUC1-alpha


Mass: 765.834 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#6: 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 , 3 types, 537 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: lithium sulfate Bis-Tris PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→134.96 Å / Num. obs: 74559 / % possible obs: 100 % / Redundancy: 5.2 % / CC1/2: 0.993 / Rpim(I) all: 0.075 / Net I/σ(I): 7.1
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10735 / CC1/2: 0.599 / Rpim(I) all: 0.573 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→85.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.05 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 3113 4.2 %RANDOM
Rwork0.1994 ---
obs0.20124 71315 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.964 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å20 Å2
2---2.64 Å20 Å2
3---2.02 Å2
Refinement stepCycle: 1 / Resolution: 1.95→85.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 233 522 7337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126993
X-RAY DIFFRACTIONr_bond_other_d0.0040.0166194
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.6839517
X-RAY DIFFRACTIONr_angle_other_deg0.7821.60714558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1745860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.056518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.636101109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027679
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021317
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_it2.3333.0633434
X-RAY DIFFRACTIONr_mcbond_other2.3323.0623434
X-RAY DIFFRACTIONr_mcangle_it3.3614.5714281
X-RAY DIFFRACTIONr_mcangle_other3.3624.5724282
X-RAY DIFFRACTIONr_scbond_it3.4393.4173559
X-RAY DIFFRACTIONr_scbond_other3.3713.4043540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0734.9655202
X-RAY DIFFRACTIONr_long_range_B_refined6.78144.237547
X-RAY DIFFRACTIONr_long_range_B_other6.66843.2797433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 216 -
Rwork0.301 5207 -
obs--99.87 %

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