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- PDB-6tgg: scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar -

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Basic information

Entry
Database: PDB / ID: 6tgg
TitlescFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar
Components
  • Mucin-1
  • ScFv_SM3
KeywordsANTITUMOR PROTEIN / Antibody / ScFv / antigen Tn / iminosugar / anti cancer vaccine / conformational analysis
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 / DNA damage response, signal transduction by p53 class mediator ...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 / DNA damage response, signal transduction by p53 class mediator / localization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / 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
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBermejo, I.A. / Navo, C.D. / Castro-Lopez, J. / Samchez-Fernandez, E.M. / Guerreiro, A. / Avenoza, A. / Busto, J.H. / Garcia-Martin, F. / Nishimura, S.I. / Garcia-Fernandez, J.M. ...Bermejo, I.A. / Navo, C.D. / Castro-Lopez, J. / Samchez-Fernandez, E.M. / Guerreiro, A. / Avenoza, A. / Busto, J.H. / Garcia-Martin, F. / Nishimura, S.I. / Garcia-Fernandez, J.M. / Ortiz-Mellet, C. / Bernardes, G.J.L. / Hurtado-Guerrero, R. / Peregrina, J.M. / Corzana, F.
CitationJournal: Chem Sci / Year: 2020
Title: Synthesis, conformational analysis and in vivo assays of an anti-cancer vaccine that features an unnatural antigen based on an sp 2 -iminosugar fragment.
Authors: Bermejo, I.A. / Navo, C.D. / Castro-Lopez, J. / Guerreiro, A. / Jimenez-Moreno, E. / Sanchez Fernandez, E.M. / Garcia-Martin, F. / Hinou, H. / Nishimura, S.I. / Garcia Fernandez, J.M. / ...Authors: Bermejo, I.A. / Navo, C.D. / Castro-Lopez, J. / Guerreiro, A. / Jimenez-Moreno, E. / Sanchez Fernandez, E.M. / Garcia-Martin, F. / Hinou, H. / Nishimura, S.I. / Garcia Fernandez, J.M. / Mellet, C.O. / Avenoza, A. / Busto, J.H. / Bernardes, G.J.L. / Hurtado-Guerrero, R. / Peregrina, J.M. / Corzana, F.
History
DepositionNov 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: ScFv_SM3
P: Mucin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8947
Polymers26,4152
Non-polymers4785
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer under a gel filtration column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint7 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.271, 68.689, 90.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: 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 / MUC-1 / Breast carcinoma-associated antigen DF3 / Cancer antigen 15-3 / CA 15-3 / Carcinoma- ...MUC-1 / Breast carcinoma-associated antigen DF3 / Cancer antigen 15-3 / CA 15-3 / Carcinoma-associated mucin / Episialin / H23AG / Krebs von den Lungen-6 / KL-6 / PEMT / Peanut-reactive urinary mucin / PUM / Polymorphic epithelial mucin / PEM / Tumor-associated epithelial membrane antigen / EMA / Tumor-associated mucin


Mass: 656.708 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Note that this is a modified glycopeptide containing an sp2-imino sugar. In addition, the Thr residue is covalently bound to the sp2-imino sugar (it is found in the pdb as A2G).
Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-N8W / ~{N}-[(6~{S},7~{R},8~{S},8~{a}~{R})-7,8-bis(oxidanyl)-3-oxidanylidene-1,5,6,7,8,8~{a}-hexahydro-[1,3]oxazolo[3,4-a]pyridin-6-yl]ethanamide


Mass: 230.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H14N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 disodium hydrogen phosphate

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 15528 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.987 / Rpim(I) all: 0.076 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.11 Å / Mean I/σ(I) obs: 4.8 / Num. unique obs: 2229 / CC1/2: 0.758 / Rpim(I) all: 0.342 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OWP

5owp


Resolution: 2→19.21 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.993 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.174
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 441 2.8 %RANDOM
Rwork0.1754 ---
obs0.177 15042 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.39 Å2 / Biso mean: 24.33 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--2.15 Å20 Å2
3----2.23 Å2
Refinement stepCycle: final / Resolution: 2→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 32 167 1956
Biso mean--48.36 31.97 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0141847
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181600
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.6712506
X-RAY DIFFRACTIONr_angle_other_deg1.0251.6733739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4655232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16522.55886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1515275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.601159
X-RAY DIFFRACTIONr_chiral_restr0.070.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.254 32 -
Rwork0.206 1095 -
obs--99.73 %

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