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- PDB-4g55: Clathrin terminal domain complexed with pitstop 2 -

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Basic information

Entry
Database: PDB / ID: 4g55
TitleClathrin terminal domain complexed with pitstop 2
ComponentsClathrin heavy chain 1
KeywordsENDOCYTOSIS / Beta-Propeller
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / transferrin transport / amyloid-beta clearance by transcytosis ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / transferrin transport / amyloid-beta clearance by transcytosis / mitotic spindle microtubule / clathrin coat of coated pit / clathrin coat disassembly / clathrin coat assembly / Retrograde neurotrophin signalling / Formation of annular gap junctions / clathrin-coated endocytic vesicle / Gap junction degradation / LDL clearance / clathrin-dependent endocytosis / ALK mutants bind TKIs / endolysosome membrane / retrograde transport, endosome to Golgi / negative regulation of protein localization to plasma membrane / clathrin-coated vesicle / Lysosome Vesicle Biogenesis / RHOV GTPase cycle / low-density lipoprotein particle receptor binding / Golgi Associated Vesicle Biogenesis / ubiquitin-specific protease binding / Recycling pathway of L1 / RHOU GTPase cycle / EPH-ephrin mediated repulsion of cells / 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 / double-stranded RNA binding / extracellular vesicle / disordered domain specific binding / Signaling by ALK fusions and activated point mutants / 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-H-link / 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 / Region in Clathrin and VPS / Clathrin heavy chain repeat homology ...Clathrin heavy-chain terminal domain / Clathrin-H-link / 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 / 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 / DI(HYDROXYETHYL)ETHER / Chem-VH2 / Clathrin heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.69 Å
AuthorsBulut, H. / Von Kleist, L. / Saenger, W. / Haucke, V.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Role of the clathrin terminal domain in regulating coated pit dynamics revealed by small molecule inhibition.
Authors: von Kleist, L. / Stahlschmidt, W. / Bulut, H. / Gromova, K. / Puchkov, D. / Robertson, M.J. / MacGregor, K.A. / Tomilin, N. / Tomlin, N. / Pechstein, A. / Chau, N. / Chircop, M. / Sakoff, J. ...Authors: von Kleist, L. / Stahlschmidt, W. / Bulut, H. / Gromova, K. / Puchkov, D. / Robertson, M.J. / MacGregor, K.A. / Tomilin, N. / Tomlin, N. / Pechstein, A. / Chau, N. / Chircop, M. / Sakoff, J. / von Kries, J.P. / Saenger, W. / Krausslich, H.G. / Shupliakov, O. / Robinson, P.J. / McCluskey, A. / Haucke, V.
History
DepositionJul 17, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionAug 1, 2012ID: 2XZH
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Other
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)42,72919
Polymers41,0611
Non-polymers1,66818
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.899, 74.019, 82.118
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 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLH17, CLTC, CLTCL2, KIAA0034 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q00610

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Non-polymers , 6 types, 425 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-VH2 / N-[5-[(4-BROMOPHENYL)METHYL]-4-HYDROXY-1,3-THIAZOL-2-YL]NAPHTHALENE-1-SULFONAMIDE / PITSTOP 2


Mass: 475.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15BrN2O3S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 12, 2010
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.69→33.74 Å / Num. all: 49091 / Num. obs: 49069 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Net I/σ(I): 3.94
Reflection shellResolution: 1.69→1.73 Å / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 1.69→33.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.901 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21458 2454 5 %RANDOM
Rwork0.17215 ---
obs0.17429 46613 99.96 %-
all-49091 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.977 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å20 Å2
2---1.09 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.69→33.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 102 407 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023019
X-RAY DIFFRACTIONr_bond_other_d0.0020.022027
X-RAY DIFFRACTIONr_angle_refined_deg2.1031.9714079
X-RAY DIFFRACTIONr_angle_other_deg1.0693.0024965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6155373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90724.962131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76515514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2291514
X-RAY DIFFRACTIONr_chiral_restr0.3420.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213345
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02583
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 166 -
Rwork0.204 3177 -
obs--99.97 %

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