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- PDB-7zx4: Clathrin N-terminal domain in complex with a HURP phospho-peptide -

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Basic information

Entry
Database: PDB / ID: 7zx4
TitleClathrin N-terminal domain in complex with a HURP phospho-peptide
Components
  • Clathrin heavy chain 1
  • Disks large-associated protein 5
KeywordsENDOCYTOSIS / complex / phospho-regulated SLiM-based interactions / HURP / DLGAP5
Function / homology
Function and homology information


mitotic chromosome movement towards spindle pole / clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / signaling / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis ...mitotic chromosome movement towards spindle pole / clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / signaling / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / transferrin transport / amyloid-beta clearance by transcytosis / mitotic spindle microtubule / clathrin coat of coated pit / clathrin coat disassembly / clathrin coat assembly / Retrograde neurotrophin signalling / Formation of annular gap junctions / clathrin-coated endocytic vesicle / Gap junction degradation / LDL clearance / kinetochore assembly / clathrin-dependent endocytosis / positive regulation of mitotic metaphase/anaphase transition / ALK mutants bind TKIs / spindle pole centrosome / endolysosome membrane / retrograde transport, endosome to Golgi / negative regulation of protein localization to plasma membrane / NOTCH3 Intracellular Domain Regulates Transcription / clathrin-coated vesicle / centrosome localization / Lysosome Vesicle Biogenesis / RHOV GTPase cycle / low-density lipoprotein particle receptor binding / Golgi Associated Vesicle Biogenesis / ubiquitin-specific protease binding / Recycling pathway of L1 / RHOU GTPase cycle / centriolar satellite / EPH-ephrin mediated repulsion of cells / regulation of mitotic spindle organization / regulation of mitotic cell cycle / MHC class II antigen presentation / VLDLR internalisation and degradation / receptor-mediated endocytosis / mitotic spindle organization / trans-Golgi network membrane / chromosome segregation / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / mitotic spindle / autophagy / spindle / osteoblast differentiation / double-stranded RNA binding / disordered domain specific binding / extracellular vesicle / Signaling by ALK fusions and activated point mutants / melanosome / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / mitotic cell cycle / microtubule binding / lysosome / endosome / cell division / focal adhesion / protein kinase binding / structural molecule activity / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS ...SAPAP family / Guanylate-kinase-associated protein (GKAP) protein / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin heavy chain 1 / Disks large-associated protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsKliche, J. / Badgujar, D. / Dobritzsch, D. / Ivarsson, Y.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2020-03380 Sweden
Other private Sweden
CitationJournal: Mol.Syst.Biol. / Year: 2023
Title: Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions.
Authors: Kliche, J. / Garvanska, D.H. / Simonetti, L. / Badgujar, D. / Dobritzsch, D. / Nilsson, J. / Davey, N.E. / Ivarsson, Y.
History
DepositionMay 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Disks large-associated protein 5
D: Disks large-associated protein 5
E: Disks large-associated protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7189
Polymers88,4755
Non-polymers2434
Water5,891327
1
A: Clathrin heavy chain 1
C: Disks large-associated protein 5
E: Disks large-associated protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7117
Polymers45,4693
Non-polymers2434
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-21 kcal/mol
Surface area17570 Å2
MethodPISA
2
B: Clathrin heavy chain 1
D: Disks large-associated protein 5


Theoretical massNumber of molelcules
Total (without water)43,0062
Polymers43,0062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-6 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.774, 94.242, 88.981
Angle α, β, γ (deg.)90.000, 103.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody / Protein/peptide , 2 types, 5 molecules ABCDE

#1: Antibody Clathrin heavy chain 1 / Clathrin heavy chain on chromosome 17 / CLH-17


Mass: 40543.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the entry corresponds to the N-terminal domain of human clathrin
Source: (gene. exp.) Homo sapiens (human) / Gene: CLTC, CLH17, CLTCL2, KIAA0034 / Plasmid: pETM33 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: Q00610
#2: Protein/peptide Disks large-associated protein 5 / DAP-5 / Discs large homolog 7 / Disks large-associated protein DLG7 / Hepatoma up-regulated protein / HURP


Mass: 2462.651 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15398

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Non-polymers , 4 types, 331 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 50 mM Tris pH 7.5, 30 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.08→43.2 Å / Num. obs: 45105 / % possible obs: 96 % / Redundancy: 2.7 % / CC1/2: 0.909 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.071 / Rrim(I) all: 0.123 / Net I/σ(I): 6.9
Reflection shellResolution: 2.08→2.12 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2302 / CC1/2: 0.716 / Rpim(I) all: 0.268 / Rrim(I) all: 0.475 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C9I

1c9i


Resolution: 2.08→43.2 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.537 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.258 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2286 5.1 %RANDOM
Rwork0.2061 ---
obs0.2084 42817 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.61 Å2 / Biso mean: 28.039 Å2 / Biso min: 6.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.27 Å2
2--0.38 Å20 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 2.08→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5791 0 14 328 6133
Biso mean--33.57 31.99 -
Num. residues----741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135955
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175551
X-RAY DIFFRACTIONr_angle_refined_deg1.441.6388083
X-RAY DIFFRACTIONr_angle_other_deg1.2331.56912931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7365748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57423.724290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.963151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7641526
X-RAY DIFFRACTIONr_chiral_restr0.0620.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026605
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021161
LS refinement shellResolution: 2.08→2.134 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 140 -
Rwork0.271 3230 -
all-3370 -
obs--97.43 %

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