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- PDB-6e4l: The structure of the N-terminal domain of human clathrin heavy ch... -

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Basic information

Entry
Database: PDB / ID: 6e4l
TitleThe structure of the N-terminal domain of human clathrin heavy chain 1 (nTD) in complex with ES9
ComponentsClathrin heavy chain 1
KeywordsENDOCYTOSIS / Clathrin-mediated endocytosis (CME) / Clathrin N-terminal domain (nTD) / chemical inhibition
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / negative regulation of hyaluronan biosynthetic process / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Entry of Influenza Virion into Host Cell via Endocytosis / transferrin transport / WNT5A-dependent internalization of FZD4 / amyloid-beta clearance by transcytosis ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / negative regulation of hyaluronan biosynthetic process / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Entry of Influenza Virion into Host Cell via Endocytosis / transferrin transport / WNT5A-dependent internalization of FZD4 / amyloid-beta clearance by transcytosis / clathrin coat of coated pit / LDL clearance / mitotic spindle microtubule / clathrin coat disassembly / clathrin coat assembly / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / Formation of annular gap junctions / Gap junction degradation / clathrin-dependent endocytosis / endolysosome membrane / ALK mutants bind TKIs / 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 / regulation of mitotic spindle organization / MHC class II antigen presentation / VLDLR internalisation and degradation / receptor-mediated endocytosis / trans-Golgi network membrane / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / mitotic spindle / autophagy / spindle / osteoblast differentiation / disordered domain specific binding / double-stranded RNA binding / Signaling by ALK fusions and activated point mutants / extracellular vesicle / melanosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / mitotic cell cycle / lysosome / endosome / cell division / focal adhesion / protein kinase binding / structural molecule activity / protein-containing complex / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Clathrin heavy-chain terminal domain / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS / Clathrin heavy chain repeat homology ...Clathrin heavy-chain terminal domain / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / 5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide / Clathrin heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDejonghe, W. / Sharma, I. / Denoo, B. / Munck, S.D. / Bulut, H. / Mylle, E. / Vasileva, M. / Lu, Q. / Savatin, D.V. / Mishev, K. ...Dejonghe, W. / Sharma, I. / Denoo, B. / Munck, S.D. / Bulut, H. / Mylle, E. / Vasileva, M. / Lu, Q. / Savatin, D.V. / Mishev, K. / Nerinckx, W. / Staes, A. / Drozdzecki, A. / Audenaert, D. / Madder, A. / Friml, J. / Damme, D.V. / Gevaert, K. / Haucke, V. / Savvides, S. / Winne, J. / Russinova, E.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Disruption of endocytosis through chemical inhibition of clathrin heavy chain function.
Authors: Dejonghe, W. / Sharma, I. / Denoo, B. / De Munck, S. / Lu, Q. / Mishev, K. / Bulut, H. / Mylle, E. / De Rycke, R. / Vasileva, M. / Savatin, D.V. / Nerinckx, W. / Staes, A. / Drozdzecki, A. / ...Authors: Dejonghe, W. / Sharma, I. / Denoo, B. / De Munck, S. / Lu, Q. / Mishev, K. / Bulut, H. / Mylle, E. / De Rycke, R. / Vasileva, M. / Savatin, D.V. / Nerinckx, W. / Staes, A. / Drozdzecki, A. / Audenaert, D. / Yperman, K. / Madder, A. / Friml, J. / Van Damme, D. / Gevaert, K. / Haucke, V. / Savvides, S.N. / Winne, J. / Russinova, E.
History
DepositionJul 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
A: Clathrin heavy chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,97410
Polymers41,0611
Non-polymers9139
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint10 kcal/mol
Surface area16530 Å2
Unit cell
Length a, b, c (Å)71.210, 74.340, 84.230
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 , 6 types, 189 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-HRS / 5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide


Mass: 363.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7BrN2O4S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→51.424 Å / Num. obs: 58329 / % possible obs: 97.75 % / Redundancy: 4.3 % / Net I/σ(I): 17.53
Reflection shellResolution: 1.6→1.657 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G55

4g55


Resolution: 1.6→51.424 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.93
RfactorNum. reflection% reflection
Rfree0.2143 2014 3.45 %
Rwork0.1879 --
obs0.1888 58324 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→51.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 53 180 3036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082945
X-RAY DIFFRACTIONf_angle_d0.9083990
X-RAY DIFFRACTIONf_dihedral_angle_d10.881776
X-RAY DIFFRACTIONf_chiral_restr0.058447
X-RAY DIFFRACTIONf_plane_restr0.005518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.64010.33011410.29563714X-RAY DIFFRACTION92
1.6401-1.68440.31751380.27034026X-RAY DIFFRACTION98
1.6844-1.7340.29361340.24793977X-RAY DIFFRACTION98
1.734-1.790.26841440.2353962X-RAY DIFFRACTION98
1.79-1.85390.24961470.21434011X-RAY DIFFRACTION98
1.8539-1.92820.28221460.21134015X-RAY DIFFRACTION98
1.9282-2.01590.20351410.19363993X-RAY DIFFRACTION98
2.0159-2.12220.22891440.19163996X-RAY DIFFRACTION98
2.1222-2.25520.20081450.18034042X-RAY DIFFRACTION99
2.2552-2.42930.23411460.18484025X-RAY DIFFRACTION98
2.4293-2.67380.21491440.18654063X-RAY DIFFRACTION98
2.6738-3.06060.22361440.18754096X-RAY DIFFRACTION99
3.0606-3.85590.1971490.17674134X-RAY DIFFRACTION99
3.8559-51.45060.17341510.16524256X-RAY DIFFRACTION98

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