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- PDB-5m5r: Clathrin heavy chain N-terminal domain bound to beta2 adaptin cla... -

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Basic information

Entry
Database: PDB / ID: 5m5r
TitleClathrin heavy chain N-terminal domain bound to beta2 adaptin clathrin box motif
Components
  • AP-2 complex subunit beta
  • Clathrin heavy chain 1
KeywordsENDOCYTOSIS / adaptor polypeptide 2 / AP2
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 / Nef Mediated CD8 Down-regulation / clathrin light chain binding / clathrin complex / negative regulation of hyaluronan biosynthetic process / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / MHC class II antigen presentation / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / clathrin coat of coated pit / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / clathrin coat disassembly / Cargo recognition for clathrin-mediated endocytosis / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / membrane coat / clathrin coat assembly / LDL clearance / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / signal sequence binding / coronary vasculature development / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / arrestin family protein binding / neurotransmitter secretion / endolysosome membrane / aorta development / ventricular septum development / clathrin binding / Recycling pathway of L1 / positive regulation of endocytosis / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / vesicle-mediated transport / MHC class II antigen presentation / receptor-mediated endocytosis / VLDLR internalisation and degradation / intracellular protein transport / kidney development / clathrin-coated endocytic vesicle membrane / autophagy / spindle / cytoplasmic side of plasma membrane / disordered domain specific binding / synaptic vesicle / endocytic vesicle membrane / melanosome / Cargo recognition for clathrin-mediated endocytosis / mitotic cell cycle / Clathrin-mediated endocytosis / Potential therapeutics for SARS / protein domain specific binding / cell division / protein-containing complex binding / glutamatergic synapse / structural molecule activity / mitochondrion / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 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. / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / 7 Propeller / Methylamine Dehydrogenase; Chain H / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Beta
Similarity search - Domain/homology
Clathrin heavy chain 1 / AP-2 complex subunit beta
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Jan 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
C: AP-2 complex subunit beta
D: AP-2 complex subunit beta


Theoretical massNumber of molelcules
Total (without water)42,6053
Polymers42,6053
Non-polymers00
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-11 kcal/mol
Surface area17100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.144, 133.177, 77.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

21A-765-

HOH

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Components

#1: Antibody Clathrin heavy chain 1


Mass: 40540.473 Da / Num. of mol.: 1
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 AP-2 complex subunit beta / AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta ...AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta / Beta-2-adaptin / Beta-adaptin / Clathrin assembly protein complex 2 beta large chain / Plasma membrane adaptor HA2/AP2 adaptin beta subunit


Mass: 1032.171 Da / Num. of mol.: 2 / Fragment: UNP Residues 629-637 / Source method: obtained synthetically
Details: N-terminal residue 'C' was added to facilitate chemical modifications (not used in this study)
Source: (synth.) Homo sapiens (human) / References: UniProt: P63010
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 1 uL protein plus peptide mix (14 mg/mL NTD and 3.4 mM peptide) plus 2 uL reservoir equilibrated against a 200 uL reservoir of 0.94 M sodium malonate pH 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2015 / Details: toroidal
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92818 Å / Relative weight: 1
ReflectionResolution: 1.76→57.1 Å / Num. obs: 52951 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.8
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 7 % / Rmerge(I) obs: 1.538 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.672 / % possible all: 100

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Processing

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

1c9i


Resolution: 1.76→57.1 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.735 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20516 2740 4.9 %RANDOM
Rwork0.17582 ---
obs0.17725 52951 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.642 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å2-0 Å2
2--0.39 Å20 Å2
3----1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.76→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 0 403 3318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193000
X-RAY DIFFRACTIONr_bond_other_d0.0020.022914
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.9564071
X-RAY DIFFRACTIONr_angle_other_deg0.97936708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.625379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74525.263133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84115528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0691513
X-RAY DIFFRACTIONr_chiral_restr0.1180.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213421
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
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_it1.6592.4561510
X-RAY DIFFRACTIONr_mcbond_other1.6572.4531509
X-RAY DIFFRACTIONr_mcangle_it2.6443.6591888
X-RAY DIFFRACTIONr_mcangle_other2.6443.6631889
X-RAY DIFFRACTIONr_scbond_it2.2142.7421490
X-RAY DIFFRACTIONr_scbond_other2.2132.7441491
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6094.0022183
X-RAY DIFFRACTIONr_long_range_B_refined8.99222.323356
X-RAY DIFFRACTIONr_long_range_B_other8.99122.3323357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 173 -
Rwork0.391 3847 -
obs--98.1 %
Refinement TLS params.Method: refined / Origin x: -20.4776 Å / Origin y: -23.3101 Å / Origin z: 3.1098 Å
111213212223313233
T0.1219 Å2-0.0206 Å2-0.0123 Å2-0.016 Å20.0106 Å2--0.0087 Å2
L0.852 °20.4136 °2-0.1285 °2-1.2155 °2-0.253 °2--1.033 °2
S0.0402 Å °0.0329 Å °0.0434 Å °-0.0901 Å °0.0297 Å °-0.0001 Å °0.0823 Å °-0.1203 Å °-0.0699 Å °

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