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- PDB-7pee: Crystal structure of extracellular part of human Trop2 -

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Basic information

Entry
Database: PDB / ID: 7pee
TitleCrystal structure of extracellular part of human Trop2
ComponentsTumor-associated calcium signal transducer 2
KeywordsMEMBRANE PROTEIN / extracellular part / dimer
Function / homology
Function and homology information


negative regulation of branching involved in ureteric bud morphogenesis / ureteric bud morphogenesis / negative regulation of ruffle assembly / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of epithelial cell migration / positive regulation of stem cell differentiation / regulation of epithelial cell proliferation / negative regulation of cell motility / negative regulation of stress fiber assembly / lateral plasma membrane ...negative regulation of branching involved in ureteric bud morphogenesis / ureteric bud morphogenesis / negative regulation of ruffle assembly / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of epithelial cell migration / positive regulation of stem cell differentiation / regulation of epithelial cell proliferation / negative regulation of cell motility / negative regulation of stress fiber assembly / lateral plasma membrane / visual perception / basal plasma membrane / extracellular space / extracellular exosome / nucleus / membrane / cytosol
Similarity search - Function
Epithelial cell adhesion molecule N-terminal domain / Transmembrane glycoprotein EPCAM/Trop-2 / : / Epithelial cell adhesion molecule, N-terminal domain / EPCAM/Trop-2, C-terminal / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats.
Similarity search - Domain/homology
Tumor-associated calcium signal transducer 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsPavsic, M.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyJ1-7119 Slovenia
Slovenian Research AgencyP1-0207 Slovenia
CitationJournal: Int J Mol Sci / Year: 2021
Title: Trop2 Forms a Stable Dimer with Significant Structural Differences within the Membrane-Distal Region as Compared to EpCAM.
Authors: Pavsic, M.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor-associated calcium signal transducer 2
B: Tumor-associated calcium signal transducer 2
C: Tumor-associated calcium signal transducer 2
D: Tumor-associated calcium signal transducer 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,30110
Polymers113,5254
Non-polymers1,7766
Water54030
1
A: Tumor-associated calcium signal transducer 2
D: Tumor-associated calcium signal transducer 2
hetero molecules


  • defined by author&software
  • Evidence: homology, Extracelluar region of human EpCAM (paralogue) forms a stable dimer in solution at physiological pH and ionic strength., gel filtration, Extracelullar region of Trop2 migrates on ...Evidence: homology, Extracelluar region of human EpCAM (paralogue) forms a stable dimer in solution at physiological pH and ionic strength., gel filtration, Extracelullar region of Trop2 migrates on size exclusion chromatography column as a dimeric species (at physiological pH)., cross-linking, Chemical cross-linking of extracellular region of Trop2 in solution at physiological pH using cross-linker BS3 results in formation of covalently-bonded species with a molecular mass coresponding to a dimer.
  • 57.7 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)57,6505
Polymers56,7632
Non-polymers8883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-14 kcal/mol
Surface area22960 Å2
MethodPISA
2
B: Tumor-associated calcium signal transducer 2
C: Tumor-associated calcium signal transducer 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6505
Polymers56,7632
Non-polymers8883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-18 kcal/mol
Surface area23070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.080, 145.080, 217.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: Protein
Tumor-associated calcium signal transducer 2 / Cell surface glycoprotein Trop-2 / Membrane component chromosome 1 surface marker 1 / Pancreatic ...Cell surface glycoprotein Trop-2 / Membrane component chromosome 1 surface marker 1 / Pancreatic carcinoma marker protein GA733-1 / Trop2EX


Mass: 28381.301 Da / Num. of mol.: 4 / Mutation: N120Q,N208Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TACSTD2, GA733-1, M1S1, TROP2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P09758
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 5.05 Å3/Da / Density % sol: 75.63 % / Description: rod
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 1.6 M ammonium sulfate, 0.5 M NaCl, 0.0133 M EDTA, 0.1 M MES pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.81→48.38 Å / Num. obs: 57322 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 64.21 Å2 / CC1/2: 0.998 / Rsym value: 0.1157 / Net I/σ(I): 15.14
Reflection shellResolution: 2.81→2.98 Å / Mean I/σ(I) obs: 1.85 / Num. unique obs: 9084 / CC1/2: 0.717 / Rsym value: 1.19 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MZV

4mzv


Resolution: 2.81→48.37 Å / SU ML: 0.4202 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.8396
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2633 2865 5 %
Rwork0.2396 54435 -
obs0.2408 57300 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.8 Å2
Refinement stepCycle: LAST / Resolution: 2.81→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7476 0 114 30 7620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00747728
X-RAY DIFFRACTIONf_angle_d1.074910442
X-RAY DIFFRACTIONf_chiral_restr0.06721158
X-RAY DIFFRACTIONf_plane_restr0.01281384
X-RAY DIFFRACTIONf_dihedral_angle_d14.5632982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.850.42691390.35522659X-RAY DIFFRACTION99.08
2.85-2.910.31121420.32852692X-RAY DIFFRACTION99.37
2.91-2.960.37261400.33332666X-RAY DIFFRACTION99.68
2.96-3.020.45961420.35042691X-RAY DIFFRACTION99.47
3.02-3.090.40271410.34242668X-RAY DIFFRACTION99.72
3.09-3.160.32811410.3132683X-RAY DIFFRACTION99.61
3.16-3.240.35551410.28442680X-RAY DIFFRACTION99.79
3.24-3.330.30521420.25862687X-RAY DIFFRACTION99.68
3.33-3.420.27981420.26662710X-RAY DIFFRACTION99.76
3.42-3.530.30731420.26662702X-RAY DIFFRACTION99.72
3.53-3.660.26271420.26272696X-RAY DIFFRACTION99.79
3.66-3.810.27041430.23532709X-RAY DIFFRACTION99.86
3.81-3.980.25471420.22642692X-RAY DIFFRACTION99.33
3.98-4.190.25361440.20752737X-RAY DIFFRACTION99.83
4.19-4.450.23981440.20082733X-RAY DIFFRACTION99.9
4.45-4.80.21371440.19352741X-RAY DIFFRACTION100
4.8-5.280.20721450.19822758X-RAY DIFFRACTION99.69
5.28-6.040.2131470.22072790X-RAY DIFFRACTION99.76
6.04-7.610.26671480.24582810X-RAY DIFFRACTION99.8
7.61-48.370.21841540.21512931X-RAY DIFFRACTION98.31

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