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- PDB-9c0y: Clathrin terminal domain complexed with Pitstop 2c -

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Basic information

Entry
Database: PDB / ID: 9c0y
TitleClathrin terminal domain complexed with Pitstop 2c
ComponentsClathrin heavy chain 1
KeywordsENDOCYTOSIS / Clathrin heavy chain 1
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / clathrin coat / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / amyloid-beta clearance by transcytosis / clathrin coat of coated pit ...clathrin coat of trans-Golgi network vesicle / clathrin coat / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / amyloid-beta clearance by transcytosis / clathrin coat of coated pit / transferrin transport / clathrin coat assembly / clathrin coat disassembly / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / mitotic spindle microtubule / LDL clearance / Formation of annular gap junctions / Gap junction degradation / clathrin-dependent endocytosis / ALK mutants bind TKIs / endolysosome membrane / retrograde transport, endosome to Golgi / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / Lysosome Vesicle Biogenesis / RHOV GTPase cycle / Golgi Associated Vesicle Biogenesis / ubiquitin-specific protease binding / Recycling pathway of L1 / RHOU GTPase cycle / EPH-ephrin mediated repulsion of cells / negative regulation of protein localization to plasma membrane / MHC class II antigen presentation / receptor-mediated endocytosis / regulation of mitotic spindle organization / VLDLR internalisation and degradation / trans-Golgi network membrane / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / autophagy / centriolar satellite / spindle / osteoblast differentiation / disordered domain specific binding / mitotic spindle / Signaling by ALK fusions and activated point mutants / melanosome / Cargo recognition for clathrin-mediated endocytosis / extracellular vesicle / mitotic cell cycle / double-stranded RNA binding / Clathrin-mediated endocytosis / lysosome / endosome / cell division / focal adhesion / intracellular membrane-bounded organelle / protein kinase binding / structural molecule activity / protein-containing complex / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / : / Region in Clathrin and VPS / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Clathrin heavy chain repeat homology ...Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / : / Region in Clathrin and VPS / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
: / ACETATE ION / DI(HYDROXYETHYL)ETHER / Clathrin heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBulut, H. / Horatscheck, A. / Krauss, M. / Santos, K.F. / McCluskey, A. / Wahl, C.W. / Nazare, M. / Haucke, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
Leibniz Association Germany
CitationJournal: Structure / Year: 2025
Title: Next-generation small molecule inhibitors of clathrin function acutely inhibit endocytosis.
Authors: Horatscheck, A. / Krauss, M. / Bulut, H. / Chambon, V. / Zadah, M.S. / Dransart, E. / Peloza, K. / Santos, K.F. / Robertson, M.J. / Prichard, K. / Miksche, S. / Radetzki, S. / von Kries, J.P. ...Authors: Horatscheck, A. / Krauss, M. / Bulut, H. / Chambon, V. / Zadah, M.S. / Dransart, E. / Peloza, K. / Santos, K.F. / Robertson, M.J. / Prichard, K. / Miksche, S. / Radetzki, S. / von Kries, J.P. / Wahl, M.C. / McCluskey, A. / Johannes, L. / Haucke, V. / Nazare, M.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2May 14, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clathrin heavy chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,45314
Polymers41,0611
Non-polymers1,39213
Water5,098283
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.562, 73.674, 85.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 1 types, 1 molecules A

#1: Antibody Clathrin heavy chain 1 / Clathrin heavy chain on chromosome 17 / CLH-17


Mass: 41061.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLTC, CLH17, CLTCL2, KIAA0034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00610

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Non-polymers , 7 types, 296 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-A1ATR / N-{(5Z)-4-oxo-5-[(2-phenoxyphenyl)methylidene]-4,5-dihydro-1,3-thiazol-2-yl}naphthalene-2-sulfonamide


Mass: 486.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H18N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.4→42.59 Å / Num. obs: 88731 / % possible obs: 99.52 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.06984 / Net I/σ(I): 15.86
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 1.217 / Num. unique obs: 8546

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→42.59 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.166 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20584 4528 5.1 %RANDOM
Rwork0.18416 ---
obs0.18525 84203 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.251 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.78 Å20 Å2
3---1.14 Å2
Refinement stepCycle: 1 / Resolution: 1.4→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 91 283 3178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123005
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162876
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.8044073
X-RAY DIFFRACTIONr_angle_other_deg0.6771.7466625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.9226.90521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3710512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02678
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_it1.9111.571462
X-RAY DIFFRACTIONr_mcbond_other1.8631.5681460
X-RAY DIFFRACTIONr_mcangle_it2.822.8091832
X-RAY DIFFRACTIONr_mcangle_other2.822.8131833
X-RAY DIFFRACTIONr_scbond_it3.2571.9161543
X-RAY DIFFRACTIONr_scbond_other3.2571.9161542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8213.3382235
X-RAY DIFFRACTIONr_long_range_B_refined5.77616.393234
X-RAY DIFFRACTIONr_long_range_B_other5.77516.393235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.435 Å
RfactorNum. reflection% reflection
Rfree0.363 304 -
Rwork0.361 5847 -
obs--94.33 %

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