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- PDB-5m61: Clathrin heavy chain N-terminal domain bound to an extended amphi... -

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Basic information

Entry
Database: PDB / ID: 5m61
TitleClathrin heavy chain N-terminal domain bound to an extended 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 / 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: 1.84 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 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9877
Polymers86,8956
Non-polymers921
Water14,142785
1
A: Clathrin heavy chain 1
E: Amphiphysin
G: Amphiphysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5404
Polymers43,4483
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-13 kcal/mol
Surface area17400 Å2
MethodPISA
2
B: Clathrin heavy chain 1
F: Amphiphysin
H: Amphiphysin


Theoretical massNumber of molelcules
Total (without water)43,4483
Polymers43,4483
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-12 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.120, 131.150, 77.830
Angle α, β, γ (deg.)90.00, 115.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

21A-826-

HOH

31B-557-

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: 1453.612 Da / Num. of mol.: 4 / Fragment: extended Clathrin-box motif, UNP residues 349-360 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 785 / 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 % sol: 66.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 1 uL protein:peptide mix (14 mg/mL protein, 3.4 mM peptide) plus 2 uL of 1.04 M sodium malonate pH 7.1, 0.2 M sodium perchlorate equilibrated against a 200 uL reservoir of 1.15 M sodium malonate pH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2015 / Details: KB mirrors
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→39.7 Å / Num. obs: 102809 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Net I/σ(I): 12.8
Reflection shellResolution: 1.84→1.89 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.232 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.528 / % possible all: 99.5

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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: 1.84→39.66 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.542 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18153 5312 4.9 %RANDOM
Rwork0.16149 ---
obs0.16247 102809 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0.31 Å2
2--0.3 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.84→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5958 0 6 785 6749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196252
X-RAY DIFFRACTIONr_bond_other_d0.0020.026020
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.9558498
X-RAY DIFFRACTIONr_angle_other_deg0.915313868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51324.982281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.644151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2511530
X-RAY DIFFRACTIONr_chiral_restr0.0920.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217173
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021417
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_it1.282.1743132
X-RAY DIFFRACTIONr_mcbond_other1.2792.1723131
X-RAY DIFFRACTIONr_mcangle_it2.133.2393936
X-RAY DIFFRACTIONr_mcangle_other2.133.2413937
X-RAY DIFFRACTIONr_scbond_it1.6312.4123120
X-RAY DIFFRACTIONr_scbond_other1.6312.4143121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7293.5344562
X-RAY DIFFRACTIONr_long_range_B_refined8.36719.8127366
X-RAY DIFFRACTIONr_long_range_B_other8.36919.7817362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 402 -
Rwork0.295 7533 -
obs--99.5 %
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)
10.64920.18960.24980.87540.38050.92030.0214-0.08320.05090.03040.0517-0.09670.00490.1131-0.07310.1-0.0030.01550.0858-0.0370.071319.69680.430117.6839
20.79430.2669-0.00850.6713-0.03260.59870.01480.02970.0253-0.05530.01560.03740.1042-0.0808-0.03040.1156-0.0402-0.01130.02840.00430.004214.172719.985858.1349
300000000000000-00.0879000.087900.0879000
41.20081.3520.80286.1077.729610.70470.1639-0.13070.0795-0.1379-0.17270.0789-0.3943-0.09550.00870.21510.01280.03230.1148-0.0910.08562.627716.95727.7857
510.86711.4234-7.158912.4225-7.17775.0155-0.1903-0.2402-0.31980.0638-0.2123-0.11160.38940.15230.40260.3315-0.06980.1090.14480.04670.146217.86343.237277.4594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 363
2X-RAY DIFFRACTION2B4 - 363
3X-RAY DIFFRACTION4G1 - 12
4X-RAY DIFFRACTION5H1 - 12

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