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- PDB-5m5s: Clathrin heavy chain N-terminal domain bound to amphiphysin clath... -

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Basic information

Entry
Database: PDB / ID: 5m5s
TitleClathrin heavy chain N-terminal domain bound to amphiphysin clathrin-box motif
Components
  • Amphiphysin
  • Clathrin heavy chain 1
KeywordsENDOCYTOSIS
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 / RHOU GTPase cycle / RHOV GTPase cycle / Golgi Associated Vesicle Biogenesis ...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 / RHOU GTPase cycle / RHOV GTPase cycle / Golgi Associated Vesicle Biogenesis / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin coat of coated pit / clathrin coat disassembly / Cargo recognition for clathrin-mediated endocytosis / membrane coat / clathrin-coated endocytic vesicle / 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 / melanosome / mitotic cell cycle / synaptic vesicle membrane / 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: 1.88 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0669
Polymers85,7906
Non-polymers2763
Water14,466803
1
A: Clathrin heavy chain 1
E: Amphiphysin
G: Amphiphysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0795
Polymers42,8953
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-15 kcal/mol
Surface area17400 Å2
MethodPISA
2
B: Clathrin heavy chain 1
F: Amphiphysin
H: Amphiphysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9874
Polymers42,8953
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-15 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.967, 134.110, 78.012
Angle α, β, γ (deg.)90.00, 115.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-838-

HOH

21B-530-

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: 1177.258 Da / Num. of mol.: 4 / Fragment: Clathrin-box motif, UNP residues 349-358 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49418
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 803 / 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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 uL protein:peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.85 M sodium malonate pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2015 / Details: toroidal mirrors
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.88→67.1 Å / Num. obs: 99868 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.149 / Net I/σ(I): 6.5
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.092 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.568 / % possible all: 100

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Processing

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

1c9i


Resolution: 1.88→67.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.223 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23388 5291 5 %RANDOM
Rwork0.20418 ---
obs0.20565 99868 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.627 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0.25 Å2
2---0.87 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.88→67.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 18 803 6711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196273
X-RAY DIFFRACTIONr_bond_other_d0.0010.026072
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9598533
X-RAY DIFFRACTIONr_angle_other_deg0.9314018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2865806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38825.143280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.091151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9841530
X-RAY DIFFRACTIONr_chiral_restr0.090.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021402
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_it0.7321.0443136
X-RAY DIFFRACTIONr_mcbond_other0.7311.0423135
X-RAY DIFFRACTIONr_mcangle_it1.3461.5453950
X-RAY DIFFRACTIONr_mcangle_other1.3451.5473951
X-RAY DIFFRACTIONr_scbond_it0.5151.0893137
X-RAY DIFFRACTIONr_scbond_other0.5151.0913138
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9741.6254576
X-RAY DIFFRACTIONr_long_range_B_refined8.13410.3317002
X-RAY DIFFRACTIONr_long_range_B_other8.13410.3317002
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 416 -
Rwork0.365 7300 -
obs--98.8 %
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)
10.76280.19710.18640.86150.38261.05970.0557-0.04510.02290.026-0.0029-0.02960.00010.1122-0.05280.1004-0.02050.04960.1401-0.01280.02820.0310.27617.634
21.04880.2563-0.09650.8548-0.08620.77690.00120.05140.0512-0.0403-0.00260.02220.0642-0.08960.00150.116-0.0220.04020.1282-0.01160.017915.14220.58958.45
300000000000000-00.0746000.074600.0746000
400000000000000-00.0746000.074600.0746000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 363
2X-RAY DIFFRACTION2B4 - 363

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