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- PDB-8axh: Crystal structure of a MUC1-like glycopeptide containing the unna... -

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Basic information

Entry
Database: PDB / ID: 8axh
TitleCrystal structure of a MUC1-like glycopeptide containing the unnatural L-4-hydroxynorvaline in complex with scFv-SM3
Components
  • Mucin-1 subunit alpha
  • Single-chain variable antibody (scFv) SM3
KeywordsIMMUNE SYSTEM
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 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 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 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 1.85 Å
AuthorsBermejo, I. / Corzana, F. / Hurtado-Guerrero, R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN) Spain
CitationJournal: Jacs Au / Year: 2024
Title: Structure-Guided Approach for the Development of MUC1-Glycopeptide-Based Cancer Vaccines with Predictable Responses.
Authors: Bermejo, I.A. / Guerreiro, A. / Eguskiza, A. / Martinez-Saez, N. / Lazaris, F.S. / Asin, A. / Somovilla, V.J. / Companon, I. / Raju, T.K. / Tadic, S. / Garrido, P. / Garcia-Sanmartin, J. / ...Authors: Bermejo, I.A. / Guerreiro, A. / Eguskiza, A. / Martinez-Saez, N. / Lazaris, F.S. / Asin, A. / Somovilla, V.J. / Companon, I. / Raju, T.K. / Tadic, S. / Garrido, P. / Garcia-Sanmartin, J. / Mangini, V. / Grosso, A.S. / Marcelo, F. / Avenoza, A. / Busto, J.H. / Garcia-Martin, F. / Hurtado-Guerrero, R. / Peregrina, J.M. / Bernardes, G.J.L. / Martinez, A. / Fiammengo, R. / Corzana, F.
History
DepositionAug 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Mar 4, 2026Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Single-chain variable antibody (scFv) SM3
A: Mucin-1 subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0219
Polymers26,4272
Non-polymers5947
Water3,207178
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint15 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.501, 68.490, 90.923
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 Single-chain variable antibody (scFv) SM3


Mass: 25758.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus)
#2: Protein/peptide Mucin-1 subunit alpha / MUC1-NT / MUC1-alpha


Mass: 668.743 Da / Num. of mol.: 1 / 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.: 6 / 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: 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.: 178 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 disodium hydrogen phosphate

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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 6M / Detector: PIXEL / Date: Dec 10, 2016
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: 17900 / % possible obs: 91 % / Redundancy: 8.5 % / CC1/2: 0.999 / Rpim(I) all: 0.04 / Net I/av σ(I): 15.8 / Net I/σ(I): 15.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 8.3 % / Num. unique obs: 2199 / CC1/2: 0.768 / Rpim(I) all: 0.34 / % possible all: 77.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SM3

1sm3


Resolution: 1.85→19.21 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.218 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20597 494 2.8 %RANDOM
Rwork0.16724 ---
obs0.16832 17361 91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.344 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å2-0 Å20 Å2
2--1.3 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: 1 / Resolution: 1.85→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 24 178 1989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121867
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161646
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6892537
X-RAY DIFFRACTIONr_angle_other_deg0.7021.623834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7325233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.38558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53910275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02386
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_it1.9992.243917
X-RAY DIFFRACTIONr_mcbond_other22.243916
X-RAY DIFFRACTIONr_mcangle_it2.9293.3461143
X-RAY DIFFRACTIONr_mcangle_other2.9273.3461144
X-RAY DIFFRACTIONr_scbond_it2.7672.607950
X-RAY DIFFRACTIONr_scbond_other2.7662.607951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2713.761391
X-RAY DIFFRACTIONr_long_range_B_refined6.26836.6572048
X-RAY DIFFRACTIONr_long_range_B_other6.26736.6712049
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
Rfree0.238 38 -
Rwork0.235 1378 -
obs--99.65 %

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