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- PDB-5m5t: Clathrin heavy chain N-terminal domain bound to a non-natural cla... -

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Basic information

Entry
Database: PDB / ID: 5m5t
TitleClathrin heavy chain N-terminal domain bound to a non-natural clathrin-box motif peptide (Amph4T1)
Components
  • Amphiphysin
  • Clathrin heavy chain 1
KeywordsENDOCYTOSIS
Function / homology
Function and homology information


presynaptic endocytic zone / 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 ...presynaptic endocytic zone / 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 / postsynaptic endocytic zone / photoreceptor ribbon synapse / clathrin coat disassembly / Cargo recognition for clathrin-mediated endocytosis / extrinsic component of synaptic vesicle membrane / clathrin-coated endocytic vesicle / membrane coat / clathrin coat assembly / leading edge membrane / Clathrin-mediated endocytosis / Clathrin-mediated endocytosis / arrestin family protein binding / positive regulation of endocytosis / synaptic vesicle endocytosis / phosphatase binding / axon terminus / receptor-mediated endocytosis / learning / intracellular protein transport / phospholipid binding / autophagy / spindle / terminal bouton / disordered domain specific binding / synaptic vesicle / melanosome / mitotic cell cycle / presynapse / cytoskeleton / protein domain specific binding / cell division / protein-containing complex binding / glutamatergic synapse / structural molecule activity / mitochondrion / identical protein binding / plasma membrane
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)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMuenzner, J. / Graham, S.C.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome Trust and Royal Society098406/Z/12/Z United Kingdom
Wellcome Trust090909/Z/09/Z United Kingdom
National Institutes of HealthGM106963 United States
CitationJournal: Traffic / Year: 2017
Title: Cellular and viral peptides bind multiple sites on the N-terminal domain of clathrin.
Authors: Muenzner, J. / Traub, L.M. / Kelly, B.T. / Graham, S.C.
History
DepositionOct 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: 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 1
B: Clathrin heavy chain 1
E: Amphiphysin
F: Amphiphysin
G: Amphiphysin
H: Amphiphysin
I: Amphiphysin
J: Amphiphysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4179
Polymers88,3258
Non-polymers921
Water18,3571019
1
A: Clathrin heavy chain 1
E: Amphiphysin
G: Amphiphysin
I: Amphiphysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2555
Polymers44,1624
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-19 kcal/mol
Surface area17000 Å2
MethodPISA
2
B: Clathrin heavy chain 1
F: Amphiphysin
H: Amphiphysin
J: Amphiphysin


Theoretical massNumber of molelcules
Total (without water)44,1624
Polymers44,1624
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-19 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.810, 130.970, 79.120
Angle α, β, γ (deg.)90.00, 116.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-616-

HOH

21B-717-

HOH

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Components

#1: Antibody Clathrin heavy chain 1


Mass: 40540.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal residues 'GS' are residual following cleavage of the purification tag
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CLTC / Plasmid: pOPT3G / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P49951
#2: Protein/peptide
Amphiphysin


Mass: 1207.327 Da / Num. of mol.: 6 / Fragment: UNP residues 349-358 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: O08838
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 1 uL reservoir equilibrated against a 200 uL reservoir of 1.1 M sodium malonate pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91742 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 24, 2015 / Details: toroidal mirrors
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91742 Å / Relative weight: 1
ReflectionResolution: 1.7→33.6 Å / Num. obs: 128743 / % possible obs: 98.2 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.564 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C9I

1c9i


Resolution: 1.7→33.59 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.358 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18507 6564 4.9 %RANDOM
Rwork0.15799 ---
obs0.15927 128743 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.305 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.46 Å2
2--0.64 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.7→33.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5962 0 6 1019 6987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196274
X-RAY DIFFRACTIONr_bond_other_d0.0020.026094
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9598528
X-RAY DIFFRACTIONr_angle_other_deg0.929314041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86225.143280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.659151116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9331530
X-RAY DIFFRACTIONr_chiral_restr0.1010.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217185
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021401
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_it1.4591.9173143
X-RAY DIFFRACTIONr_mcbond_other1.4581.9153142
X-RAY DIFFRACTIONr_mcangle_it2.3982.8483949
X-RAY DIFFRACTIONr_mcangle_other2.3982.853950
X-RAY DIFFRACTIONr_scbond_it1.8372.1463131
X-RAY DIFFRACTIONr_scbond_other1.8372.1423129
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0383.1384577
X-RAY DIFFRACTIONr_long_range_B_refined8.47518.2197728
X-RAY DIFFRACTIONr_long_range_B_other8.47418.2287729
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
Rfree0.319 493 -
Rwork0.295 9062 -
obs--94.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.58540.15240.22820.7750.33140.85480.0218-0.0890.06170.02950.0212-0.0743-0.0010.0859-0.0430.0585-0.01070.00740.0655-0.0280.087719.39260.53417.9801
20.36380.1216-0.04350.2556-0.0290.2740.01780.00020.0211-0.03230.0039-0.00610.0554-0.047-0.02170.0564-0.0205-0.01830.0110.0080.011812.549519.824358.6839
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 363
2X-RAY DIFFRACTION2B4 - 363

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