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- PDB-8s6k: Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide -

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Basic information

Entry
Database: PDB / ID: 8s6k
TitleCrystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide
Components
  • Mucin-1 subunit alpha
  • ScFv-G2D11
KeywordsIMMUNE SYSTEM / Monoclonal antibody / ScFv-G2D11
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 / DNA damage response, signal transduction by p53 class mediator / transcription coregulator activity / 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: 1.75 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 27, 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: ScFv-G2D11
H: ScFv-G2D11
M: Mucin-1 subunit alpha
N: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,69320
Polymers55,0634
Non-polymers1,63016
Water8,197455
1
A: ScFv-G2D11
M: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,40811
Polymers27,5312
Non-polymers8779
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: ScFv-G2D11
N: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2849
Polymers27,5312
Non-polymers7537
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.992, 69.667, 87.367
Angle α, β, γ (deg.)90.00, 102.99, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12A
22H

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
11GLNGLNSERSERAA1 - 1121 - 116
21GLNGLNSERSERHB1 - 1121 - 116
12GLYGLYMETMETAA122 - 1106126 - 240
22GLYGLYMETMETHB122 - 1106126 - 240

NCS ensembles :
ID
1
2

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Components

#1: Antibody ScFv-G2D11


Mass: 26933.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SSGGGGSGGGGGSSGSSDVVMTQSHKFMSTSVGDRVSITCKASQDVGTAVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGGGTKLEMKRGGHHHHHH
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus)
#2: Protein/peptide Mucin-1 subunit alpha / MUC1-NT / MUC1-alpha


Mass: 597.642 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / 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.: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: lithium chloride Tris PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 52287 / % possible obs: 96.5 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.3
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6651 / CC1/2: 0.778 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.487 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22142 2094 4 %RANDOM
Rwork0.18236 ---
obs0.18396 50086 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.741 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å2-0 Å2-0.81 Å2
2---0.17 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 1.75→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 48 456 4192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133842
X-RAY DIFFRACTIONr_bond_other_d0.0040.0183507
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.6995190
X-RAY DIFFRACTIONr_angle_other_deg1.6111.6568137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.555469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1523.497163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89615608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6281512
X-RAY DIFFRACTIONr_chiral_restr0.1020.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024289
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02855
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_it1.3681.6771870
X-RAY DIFFRACTIONr_mcbond_other1.3671.6761869
X-RAY DIFFRACTIONr_mcangle_it2.1392.5062329
X-RAY DIFFRACTIONr_mcangle_other2.1392.5072330
X-RAY DIFFRACTIONr_scbond_it2.0521.871972
X-RAY DIFFRACTIONr_scbond_other2.0511.8721973
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1482.6922858
X-RAY DIFFRACTIONr_long_range_B_refined5.84320.9554337
X-RAY DIFFRACTIONr_long_range_B_other5.8420.9594337
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35540.1
12H35540.1
21A34040.07
22H34040.07
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 120 -
Rwork0.257 2867 -
obs--74.66 %
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)
10.2445-0.10940.08850.3813-0.06360.65360.03910.00960.00070.0183-0.02050.02960.05620.0561-0.01870.0163-0.0022-0.00890.09760.01030.042219.547-6.296330.9222
20.6960.34460.48130.3947-0.01710.6446-0.012-0.0572-0.0541-0.04930.0425-0.0530.0348-0.0957-0.03060.0124-0.02950.01080.1034-0.01660.0372-0.3958-7.412124.6951
30.0221-0.04380.04650.3085-0.64671.64910.0320.0164-0.03180.0868-0.0980.0167-0.31840.13080.06590.13410.0013-0.06260.0915-0.00740.059212.519423.36946.041
40.3533-0.2410.01040.27470.34911.1580.0185-0.02970.0225-0.0504-0.0157-0.0115-0.0977-0.0924-0.00270.07070.0164-0.03710.0689-0.01420.0263-0.752224.51222.0105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 112
2X-RAY DIFFRACTION2A121 - 1107
3X-RAY DIFFRACTION3H1 - 112
4X-RAY DIFFRACTION4H122 - 1107

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