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- PDB-1utc: Clathrin terminal domain complexed with TLPWDLWTT -

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Basic information

Entry
Database: PDB / ID: 1utc
TitleClathrin terminal domain complexed with TLPWDLWTT
Components
  • AMPHIPHYSIN
  • CLATHRIN HEAVY CHAIN
KeywordsENDOCYTOSIS / CLATHRIN / CYTOSKELETON
Function / homology
Function and homology information


Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle ...Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin light chain binding / clathrin complex / negative regulation of hyaluronan biosynthetic process / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin coat of coated pit / clathrin coat disassembly / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / membrane coat / clathrin coat assembly / leading edge membrane / Clathrin-mediated endocytosis / arrestin family protein binding / synaptic vesicle endocytosis / receptor-mediated endocytosis / intracellular protein transport / phospholipid binding / autophagy / spindle / endocytosis / disordered domain specific binding / synaptic vesicle / synaptic vesicle membrane / melanosome / mitotic cell cycle / actin cytoskeleton / Clathrin-mediated endocytosis / chemical synaptic transmission / protein domain specific binding / cell division / structural molecule activity / mitochondrion / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / Clathrin heavy-chain terminal domain / Amphiphysin / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / : / Region in Clathrin and VPS ...Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / Clathrin heavy-chain terminal domain / Amphiphysin / 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 / BAR domain / BAR domain profile. / BAR / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / BAR domain / AH/BAR domain superfamily / 7 Propeller / Methylamine Dehydrogenase; Chain H / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Beta
Similarity search - Domain/homology
Amphiphysin / Clathrin heavy chain 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiele, A.E. / Evans, P.R. / Owen, D.J.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2004
Title: Two distinct interaction motifs in amphiphysin bind two independent sites on the clathrin terminal domain beta-propeller.
Authors: Miele, A.E. / Watson, P.J. / Evans, P.R. / Traub, L.M. / Owen, D.J.
History
DepositionDec 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Oct 16, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.5Dec 13, 2023Group: 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
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: CLATHRIN HEAVY CHAIN
B: CLATHRIN HEAVY CHAIN
P: AMPHIPHYSIN
Q: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)83,0574
Polymers83,0574
Non-polymers00
Water6,431357
1
A: CLATHRIN HEAVY CHAIN
P: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)41,5292
Polymers41,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CLATHRIN HEAVY CHAIN
Q: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)41,5292
Polymers41,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.301, 61.301, 420.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999979, -0.005338, 0.00362), (0.004533, -0.18231, 0.983231), (-0.004588, 0.983227, 0.18233)
Vector: 51.642, 43.003, -36.089)
DetailsCLATHRIN HEAVY CHAIN IS A MONOMER BIOLOGICALLY BUTIS CLASSIFIED AS A DIMER IN THIS ENTRY SINCE EVERYMOLECULE OF CLATHRIN (CHAINS A AND B) ARE BOUND TOA PEPTIDE.

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Components

#1: Antibody CLATHRIN HEAVY CHAIN


Mass: 40396.340 Da / Num. of mol.: 2 / Fragment: TERMINAL DOMAIN, RESIDUES 1-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Plasmid: PGEX4T2 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P49951
#2: Protein/peptide AMPHIPHYSIN


Mass: 1132.264 Da / Num. of mol.: 2 / Fragment: W-BOX, RESIDUES 379-387 / Source method: obtained synthetically / Details: PEPTIDE FROM AMPHIPHYSIN 1 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P49418
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCLATHRIN IS THE MAJOR PROTEIN OF THE POLYHEDRAL COAT OF COATED PITS & VESICLES. TWO DIFFERENT ...CLATHRIN IS THE MAJOR PROTEIN OF THE POLYHEDRAL COAT OF COATED PITS & VESICLES. TWO DIFFERENT ADAPTOR PROTEIN COMPLEXES LINK THE CLATHRIN LATTICE EITHER TO THE PLASMA MEMBRANE OR TO THE TRANS GOLGI NETWORK.

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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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %(w/v)PEG80001reservoir
2200 mM1reservoirMgCl2
34 mMdithiothreitol1reservoir
4100 mMCAPS1reservoirpH9.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→24.92 Å / Num. obs: 37228 / % possible obs: 99.4 % / Redundancy: 5.84 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.3131
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.33 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.02 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 29.9 Å / Num. obs: 37078 / Redundancy: 5.8 % / Num. measured all: 495661 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.3

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C9I

1c9i


Resolution: 2.3→105.41 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.03 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1856 5 %RANDOM
Rwork0.194 ---
obs0.197 35214 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5649 0 0 357 6006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225773
X-RAY DIFFRACTIONr_bond_other_d0.0010.025262
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9297834
X-RAY DIFFRACTIONr_angle_other_deg0.882312281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1945715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88224.942257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.685151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5871526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021101
X-RAY DIFFRACTIONr_nbd_refined0.1840.2888
X-RAY DIFFRACTIONr_nbd_other0.1870.24940
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.23241
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0390.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3121.54661
X-RAY DIFFRACTIONr_mcbond_other0.17211450
X-RAY DIFFRACTIONr_mcangle_it1.50625832
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06532549
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9124.52002
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 115
Rwork0.23 2493
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 29.9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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