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- PDB-6fzq: Crystal structure of scFv-SM3 in complex with compound 3 -

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Basic information

Entry
Database: PDB / ID: 6fzq
TitleCrystal structure of scFv-SM3 in complex with compound 3
Components
  • Mucin-1
  • scFv-1SM3,scFv-1SM3
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 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBermejo, I.A. / Usabiaga, I. / Companon, I. / Castro-Lopez, J. / Insausti, A. / Fernandez, J.A. / Avenoza, A. / Busto, J.H. / Jimenez-Barbero, J. / Asensio, J.L. ...Bermejo, I.A. / Usabiaga, I. / Companon, I. / Castro-Lopez, J. / Insausti, A. / Fernandez, J.A. / Avenoza, A. / Busto, J.H. / Jimenez-Barbero, J. / Asensio, J.L. / Jimenez-Oses, G. / Peregrina, J.M. / Hurtado-Guerrero, R. / Cocinero, E.J. / Corzana, F.
Funding support Spain, 2items
OrganizationGrant numberCountry
MICINNCTQ2013-44367-C2-2-P Spain
MICINNBFU2016-75633-P Spain
CitationJournal: J.Am.Chem.Soc. / Year: 2018
Title: Water Sculpts the Distinctive Shapes and Dynamics of the Tumor-Associated Carbohydrate Tn Antigens: Implications for Their Molecular Recognition.
Authors: Bermejo, I.A. / Usabiaga, I. / Companon, I. / Castro-Lopez, J. / Insausti, A. / Fernandez, J.A. / Avenoza, A. / Busto, J.H. / Jimenez-Barbero, J. / Asensio, J.L. / Peregrina, J.M. / Jimenez- ...Authors: Bermejo, I.A. / Usabiaga, I. / Companon, I. / Castro-Lopez, J. / Insausti, A. / Fernandez, J.A. / Avenoza, A. / Busto, J.H. / Jimenez-Barbero, J. / Asensio, J.L. / Peregrina, J.M. / Jimenez-Oses, G. / Hurtado-Guerrero, R. / Cocinero, E.J. / Corzana, F.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: scFv-1SM3,scFv-1SM3
P: Mucin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,29313
Polymers26,4152
Non-polymers87811
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint21 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.324, 69.639, 90.590
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 scFv-1SM3,scFv-1SM3


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 / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-EEN / 2-deoxy-2-[(difluoroacetyl)amino]-alpha-D-galactopyranose / N-DIFLUOROACETYL-D-GALACTOSAMINE / 2-deoxy-2-[(difluoroacetyl)amino]-alpha-D-galactose / 2-deoxy-2-[(difluoroacetyl)amino]-D-galactose / 2-deoxy-2-[(difluoroacetyl)amino]-galactose


Type: D-saccharide, alpha linking / Mass: 257.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13F2NO6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.68 %
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
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→90.59 Å / Num. obs: 24914 / % possible obs: 98.1 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rpim(I) all: 0.028 / Net I/σ(I): 16.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.769 / Rpim(I) all: 0.409 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OWP

5owp


Resolution: 1.7→55.21 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 5.061 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.11 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22521 705 2.8 %RANDOM
Rwork0.1751 ---
obs0.17653 24153 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--1.71 Å20 Å2
3----2.07 Å2
Refinement stepCycle: 1 / Resolution: 1.7→55.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 56 115 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021857
X-RAY DIFFRACTIONr_bond_other_d0.0030.021708
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9432508
X-RAY DIFFRACTIONr_angle_other_deg1.0653.0043920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4375230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90524.02677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43315274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.044159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022087
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02434
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_it1.4452.33926
X-RAY DIFFRACTIONr_mcbond_other1.4452.327925
X-RAY DIFFRACTIONr_mcangle_it2.3613.4771151
X-RAY DIFFRACTIONr_mcangle_other2.363.4811152
X-RAY DIFFRACTIONr_scbond_it2.1892.749931
X-RAY DIFFRACTIONr_scbond_other2.1772.749931
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4443.9471357
X-RAY DIFFRACTIONr_long_range_B_refined7.91829.12055
X-RAY DIFFRACTIONr_long_range_B_other7.91629.1192056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 43 -
Rwork0.294 1476 -
obs--82.78 %
Refinement TLS params.Method: refined / Origin x: 11.1419 Å / Origin y: 1.2837 Å / Origin z: 12.9105 Å
111213212223313233
T0.0027 Å20.0006 Å2-0.0028 Å2-0.0036 Å2-0.0065 Å2--0.0406 Å2
L0.2991 °2-0.1343 °2-0.038 °2-0.471 °20.5418 °2--0.6771 °2
S0.0113 Å °-0.0244 Å °-0.0092 Å °-0.0325 Å °0.0076 Å °-0.0205 Å °-0.0387 Å °-0.0065 Å °-0.0189 Å °

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