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- PDB-6fzr: Crystal structure of scFv-SM3 in complex with compound 2 -

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Basic information

Entry
Database: PDB / ID: 6fzr
TitleCrystal structure of scFv-SM3 in complex with compound 2
Components
  • Mucin-1
  • 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 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 / 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: 1.8 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
MICINN, CTQ2013-44367-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 1.1Jul 31, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_symm_contact / struct_conn
Revision 1.2Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,15111
Polymers26,4152
Non-polymers7369
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint15 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.274, 69.431, 90.778
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-SM3


Mass: 25758.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Special processing instructions: Although this structure is a ScFv, please follow the same numbering as shown in PDB entry 5OWP.
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 / Fragment: UNP residues 141-146 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15941
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-EEQ / 2-deoxy-2-[(fluoroacetyl)amino]-alpha-D-galactopyranose / 2-fluoranyl-~{N}-[(2~{S},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide / 2-deoxy-2-[(fluoroacetyl)amino]-alpha-D-galactose / 2-deoxy-2-[(fluoroacetyl)amino]-D-galactose / 2-deoxy-2-[(fluoroacetyl)amino]-galactose


Type: D-saccharide, alpha linking / Mass: 239.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14FNO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.54 %
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: 1.8→55.15 Å / Num. obs: 20522 / % possible obs: 95.7 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rpim(I) all: 0.044 / Net I/σ(I): 12.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.793 / Rpim(I) all: 0.543 / % possible all: 99.9

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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: 1.8→55.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.648 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23201 560 2.7 %RANDOM
Rwork0.18665 ---
obs0.18795 19913 95.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.901 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--1.9 Å20 Å2
3----1.98 Å2
Refinement stepCycle: 1 / Resolution: 1.8→55.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 47 99 1911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021855
X-RAY DIFFRACTIONr_bond_other_d0.0020.021706
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9412511
X-RAY DIFFRACTIONr_angle_other_deg1.0973.0043916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77324.02677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99915275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.505159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022094
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
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_it1.2932.364928
X-RAY DIFFRACTIONr_mcbond_other1.2942.361927
X-RAY DIFFRACTIONr_mcangle_it2.1513.5271154
X-RAY DIFFRACTIONr_mcangle_other2.153.5311155
X-RAY DIFFRACTIONr_scbond_it1.6812.764927
X-RAY DIFFRACTIONr_scbond_other1.6762.764927
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6973.9731356
X-RAY DIFFRACTIONr_long_range_B_refined7.1429.3332028
X-RAY DIFFRACTIONr_long_range_B_other7.13929.3512029
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 40 -
Rwork0.282 1525 -
obs--99.94 %
Refinement TLS params.Method: refined / Origin x: -11.1251 Å / Origin y: 1.3676 Å / Origin z: -12.9258 Å
111213212223313233
T0.0466 Å2-0.0074 Å2-0.0092 Å2-0.0985 Å20.0094 Å2--0.0068 Å2
L0.3142 °20.1694 °2-0.1103 °2-0.6836 °2-0.7442 °2--0.8581 °2
S0.0163 Å °0.0113 Å °-0.0195 Å °0.0246 Å °0.0136 Å °0.0311 Å °-0.0543 Å °0.0249 Å °-0.0299 Å °

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