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- PDB-1bpo: CLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER -

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Basic information

Entry
Database: PDB / ID: 1bpo
TitleCLATHRIN HEAVY-CHAIN TERMINAL DOMAIN AND LINKER
ComponentsPROTEIN (CLATHRIN)
KeywordsMEMBRANE PROTEIN / CLATHRIN ENDOCYTOSIS BETA-PROPELLER COATED-PITS
Function / homology
Function and homology information


presynaptic endocytic zone membrane / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Myb complex / Gap junction degradation / Formation of annular gap junctions / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance ...presynaptic endocytic zone membrane / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Myb complex / Gap junction degradation / Formation of annular gap junctions / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / clathrin light chain binding / VLDLR internalisation and degradation / negative regulation of hyaluronan biosynthetic process / clathrin complex / WNT5A-dependent internalization of FZD4 / Lysosome Vesicle Biogenesis / amyloid-beta clearance by transcytosis / MHC class II antigen presentation / clathrin coat of coated pit / postsynaptic endocytic zone / Golgi Associated Vesicle Biogenesis / photoreceptor ribbon synapse / clathrin coat disassembly / extrinsic component of synaptic vesicle membrane / Recycling pathway of L1 / membrane coat / clathrin-coated endocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / mitotic spindle microtubule / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / retrograde transport, endosome to Golgi / clathrin-coated vesicle / ankyrin binding / low-density lipoprotein particle receptor binding / ubiquitin-specific protease binding / Golgi organization / mitotic spindle assembly / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / heat shock protein binding / clathrin-coated pit / T-tubule / peptide binding / receptor-mediated endocytosis / protein serine/threonine kinase binding / regulation of mitotic spindle organization / intracellular protein transport / clathrin-coated endocytic vesicle membrane / transferrin transport / sarcolemma / receptor internalization / autophagy / centriolar satellite / spindle / terminal bouton / disordered domain specific binding / mitotic spindle / melanosome / mitotic cell cycle / double-stranded RNA binding / lysosome / endosome / protein kinase binding / glutamatergic synapse / structural molecule activity / protein-containing complex / membrane / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #30 / Clathrin heavy-chain terminal domain / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #30 / Clathrin heavy-chain terminal domain / 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. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Clathrin heavy chain 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å
AuthorsHarr, E.T. / Musacchio, A. / Harrison, S.C. / Kirchhausen, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Atomic structure of clathrin: a beta propeller terminal domain joins an alpha zigzag linker.
Authors: Haar, E.T. / Musacchio, A. / Harrison, S.C. / Kirchhausen, T.
History
DepositionAug 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CLATHRIN)
B: PROTEIN (CLATHRIN)
C: PROTEIN (CLATHRIN)


Theoretical massNumber of molelcules
Total (without water)165,2713
Polymers165,2713
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PROTEIN (CLATHRIN)
B: PROTEIN (CLATHRIN)
C: PROTEIN (CLATHRIN)

A: PROTEIN (CLATHRIN)
B: PROTEIN (CLATHRIN)
C: PROTEIN (CLATHRIN)


Theoretical massNumber of molelcules
Total (without water)330,5416
Polymers330,5416
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area18820 Å2
ΔGint-69 kcal/mol
Surface area116240 Å2
MethodPISA
3
B: PROTEIN (CLATHRIN)
C: PROTEIN (CLATHRIN)


Theoretical massNumber of molelcules
Total (without water)110,1802
Polymers110,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
A: PROTEIN (CLATHRIN)

A: PROTEIN (CLATHRIN)


Theoretical massNumber of molelcules
Total (without water)110,1802
Polymers110,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)205.825, 205.825, 87.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.801226, 0.086348, 0.592106), (0.037868, -0.994863, 0.093837), (0.59717, -0.052751, -0.800383)1.92483, 160.41693, -22.44871
2given(-0.311498, 0.738452, -0.598052), (-0.888889, -0.44893, -0.091334), (-0.335928, 0.503152, 0.796238)0.78325, 159.23201, -24.33405

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Components

#1: Protein PROTEIN (CLATHRIN)


Mass: 55090.168 Da / Num. of mol.: 3 / Fragment: TERMINAL DOMAIN AND LINKER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11442
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
121-23 %PEG40001reservoir
2400-600 mM1reservoirNaCl
3100 mMPIPES1reservoirpH6.5
410 mMdithiothreitol1reservoir
50.1 mMIPTG1drop
65 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9875
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 62332 / % possible obs: 95 % / Redundancy: 3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 62848 / % possible obs: 96 % / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 70 % / Rmerge(I) obs: 0.261

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.292 -5 %RANDOM
Rwork0.226 ---
obs0.226 60345 95 %-
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11482 0 0 35 11517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.11
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINT
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM
Refinement
*PLUS
Lowest resolution: 6 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.1

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