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- PDB-2xzg: Clathrin Terminal Domain Complexed with Pitstop 1 -

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Basic information

Entry
Database: PDB / ID: 2xzg
TitleClathrin Terminal Domain Complexed with Pitstop 1
ComponentsCLATHRIN HEAVY CHAIN 1
KeywordsENDOCYTOSIS / ENDOCYTOSIS INHIBITION
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 / disordered domain specific binding / extracellular vesicle / 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, 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 / DI(HYDROXYETHYL)ETHER / Chem-VH1 / Clathrin heavy chain 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 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. / Tomlin, N. / Pechstein, A. / Chau, N. / Chircop, M. / Sakoff, J. / Von Kries, ...Authors: Von Kleist, L. / Stahlschmidt, W. / Bulut, H. / Gromova, K. / Puchkov, D. / Robertson, M.J. / Macgregor, K.A. / Tomlin, N. / Pechstein, A. / Chau, N. / Chircop, M. / Sakoff, J. / Von Kries, J.P. / Saenger, W. / Krausslich, H. / Shupliakov, O. / Robinson, P.J. / Mccluskey, A. / Haucke, V.
History
DepositionNov 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)41,4366
Polymers40,6911
Non-polymers7465
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.340, 73.915, 84.384
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: 40690.688 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q00610

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Non-polymers , 5 types, 463 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-VH1 / 2-(4-AMINOBENZYL)-1,3-DIOXO-2,3-DIHYDRO-1H-BENZO[DE]ISOQUINOLINE-5-SULFONATE


Mass: 382.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H13N2O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPITSTOP 1 COMPOUND IS RESIDUE VH1, 2-(4-AMINOBENZYL)- 1,3-DIOXO-2,3-DIHYDRO-1H-BENZO[DE] ...PITSTOP 1 COMPOUND IS RESIDUE VH1, 2-(4-AMINOBENZYL)- 1,3-DIOXO-2,3-DIHYDRO-1H-BENZO[DE]ISOQUINOLINE-5-SULFONATE.

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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: 2.72 Å3/Da / Density % sol: 54.75 % / Description: NONE
Crystal growpH: 8
Details: 20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, PH 8.0.

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→33.85 Å / Num. obs: 47297 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.34
Reflection shellHighest resolution: 1.7 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.19 / % possible all: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1C9I

1c9i


Resolution: 1.7→33.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.679 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19973 2366 5 %RANDOM
Rwork0.15864 ---
obs0.16071 44946 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.556 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2803 0 51 458 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222945
X-RAY DIFFRACTIONr_bond_other_d0.0010.021971
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.9633996
X-RAY DIFFRACTIONr_angle_other_deg1.0063.0014825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49825128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39815507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2981513
X-RAY DIFFRACTIONr_chiral_restr0.1220.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213252
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
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_it1.2751.51813
X-RAY DIFFRACTIONr_mcbond_other0.3741.5726
X-RAY DIFFRACTIONr_mcangle_it2.11622951
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.97731132
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6634.51045
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 126 -
Rwork0.221 2404 -
obs--100 %

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