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- PDB-8s6t: Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide -

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Basic information

Entry
Database: PDB / ID: 8s6t
TitleCrystal structure of Fab-3F1 complexed to a bis-STn glycopeptide
Components
  • 3F1 (VH-VH1)
  • 3F1 (VL-CL)
  • Mucin-1 subunit beta
KeywordsIMMUNE SYSTEM / Monoclonal antibody / Fab-3F1
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
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHurtado-Guerrero, R. / Gines, I.
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

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Assembly

Deposited unit
A: 3F1 (VH-VH1)
B: 3F1 (VL-CL)
C: Mucin-1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5665
Polymers47,5413
Non-polymers1,0252
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-6 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.779, 74.779, 392.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody 3F1 (VH-VH1)


Mass: 23020.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: QVQLKQSDAELVKPGASVKISCKASGYTFTDHAIHWVKQKPEQGLDWIGYISPGNGDIKYNEKFKDKVTLTADKSSSTASMHLNSLTSEDSAVYFCKRSLLALDYWGQGTTLTVSS ...Details: QVQLKQSDAELVKPGASVKISCKASGYTFTDHAIHWVKQKPEQGLDWIGYISPGNGDIKYNEKFKDKVTLTADKSSSTASMHLNSLTSEDSAVYFCKRSLLALDYWGQGTTLTVSS AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 3F1 (VL-CL)


Mass: 23360.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DILMTQSHKFMSTSVGDRVSITCKASQDVGTNIAWYQQKPGRSPKVLIYSASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLTDYFCQQYSSFPLTFGVGTKLELKR ...Details: DILMTQSHKFMSTSVGDRVSITCKASQDVGTNIAWYQQKPGRSPKVLIYSASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLTDYFCQQYSSFPLTFGVGTKLELKR ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein/peptide Mucin-1 subunit beta / MUC1-beta / MUC1-CT


Mass: 1159.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P15941
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 512.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a6-b2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
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: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Magnesium chloride hexahydrate calcium chloride dihydrate NDSB sodium HEPES MOPS ethylene glycol PEG 8000

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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: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 57161 / % possible obs: 99.9 % / Redundancy: 16.1 % / CC1/2: 0.999 / Rsym value: 0.027 / Net I/σ(I): 12
Reflection shellResolution: 1.85→1.95 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 8113 / CC1/2: 0.473 / Rsym value: 0.827 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.77 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.998 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26739 2305 4 %RANDOM
Rwork0.22952 ---
obs0.23101 54692 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å2-0 Å2
3----2.02 Å2
Refinement stepCycle: 1 / Resolution: 1.85→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 79 181 3518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123416
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163100
X-RAY DIFFRACTIONr_angle_refined_deg1.761.8294659
X-RAY DIFFRACTIONr_angle_other_deg0.6161.7847214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4915424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.46459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76310546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023870
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
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_it3.9794.6981702
X-RAY DIFFRACTIONr_mcbond_other3.9784.6981702
X-RAY DIFFRACTIONr_mcangle_it5.2528.4062124
X-RAY DIFFRACTIONr_mcangle_other5.2518.4052125
X-RAY DIFFRACTIONr_scbond_it5.155.3671714
X-RAY DIFFRACTIONr_scbond_other5.1495.3651715
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3179.6012536
X-RAY DIFFRACTIONr_long_range_B_refined9.14746.483600
X-RAY DIFFRACTIONr_long_range_B_other9.12646.473587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 178 -
Rwork0.38 3891 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37130.014-0.15470.01510.01320.0891-0.0890.0595-0.0864-0.02170.040.0040.01530.01970.0490.134-0.0204-0.00520.1046-0.00430.0273-29.721544.5168-3.1613
20.457-0.2593-0.32840.44040.37720.3682-0.1398-0.0416-0.17880.05180.00140.10910.06620.00330.13840.09390.02960.05270.03050.0030.0775-30.808135.69812.4634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 212
2X-RAY DIFFRACTION2B1 - 211

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