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- PDB-7bn1: Clathrin heavy chain N-terminal domain complexed with peptide fro... -

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Basic information

Entry
Database: PDB / ID: 7bn1
TitleClathrin heavy chain N-terminal domain complexed with peptide from Protein mu-NS of Reovirus type 1
Components
  • Clathrin heavy chain 1
  • Protein mu-NS from Reovirus type 1
KeywordsTRANSPORT PROTEIN / CLTC-NTD / Clathrin-Box motif / Viral Replication protein E1 / HPV
Function / homology
Function and homology information


clathrin coat of trans-Golgi network vesicle / clathrin coat / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / amyloid-beta clearance by transcytosis / transferrin transport ...clathrin coat of trans-Golgi network vesicle / clathrin coat / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / amyloid-beta clearance by transcytosis / transferrin transport / clathrin coat of coated pit / clathrin coat assembly / clathrin coat disassembly / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / mitotic spindle microtubule / LDL clearance / Formation of annular gap junctions / Gap junction degradation / clathrin-dependent endocytosis / ALK mutants bind TKIs / endolysosome membrane / retrograde transport, endosome to Golgi / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / Lysosome Vesicle Biogenesis / RHOV GTPase cycle / Golgi Associated Vesicle Biogenesis / ubiquitin-specific protease binding / Recycling pathway of L1 / RHOU GTPase cycle / EPH-ephrin mediated repulsion of cells / negative regulation of protein localization to plasma membrane / MHC class II antigen presentation / receptor-mediated endocytosis / regulation of mitotic spindle organization / VLDLR internalisation and degradation / trans-Golgi network membrane / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / autophagy / centriolar satellite / spindle / osteoblast differentiation / disordered domain specific binding / mitotic spindle / Signaling by ALK fusions and activated point mutants / melanosome / Cargo recognition for clathrin-mediated endocytosis / extracellular vesicle / mitotic cell cycle / double-stranded RNA binding / Clathrin-mediated endocytosis / lysosome / endosome / cell division / focal adhesion / intracellular membrane-bounded organelle / protein kinase binding / structural molecule activity / protein-containing complex / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
: / 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, 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. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mammalian orthoreovirus 1 Lang
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsBadgujar, D.C. / Dobritzsch, D.
Funding support Sweden, 3items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchSB16-0039 Sweden
Swedish Research Council2016-04965 Sweden
Swedish Research Council2016-04134 Sweden
CitationJournal: Nat Commun / Year: 2023
Title: Large-scale phage-based screening reveals extensive pan-viral mimicry of host short linear motifs
Authors: Mihalic, F. / Simonetti, L. / Giudice, G. / Sander, M.R. / Lindqvist, R. / Peters, M.B.A. / Benz, C. / Kassa, E. / Badgujar, D. / Inturi, R. / Ali, M. / Krystkowiak, I. / Sayadi, A. / ...Authors: Mihalic, F. / Simonetti, L. / Giudice, G. / Sander, M.R. / Lindqvist, R. / Peters, M.B.A. / Benz, C. / Kassa, E. / Badgujar, D. / Inturi, R. / Ali, M. / Krystkowiak, I. / Sayadi, A. / Andersson, E. / Aronsson, H. / Soderberg, O. / Dobritzsch, D. / Petsalaki, E. / Overby, A.K. / Jemth, P. / Davey, N.E. / Ivarsson, Y.
History
DepositionJan 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 10, 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 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
E: Protein mu-NS from Reovirus type 1
F: Protein mu-NS from Reovirus type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9355
Polymers84,7414
Non-polymers1941
Water8,377465
1
A: Clathrin heavy chain 1
E: Protein mu-NS from Reovirus type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5653
Polymers42,3702
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4 kcal/mol
Surface area16630 Å2
MethodPISA
2
B: Clathrin heavy chain 1
F: Protein mu-NS from Reovirus type 1


Theoretical massNumber of molelcules
Total (without water)42,3702
Polymers42,3702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-8 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.533, 128.932, 78.100
Angle α, β, γ (deg.)90.000, 115.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

21A-712-

HOH

31B-485-

HOH

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Components

#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
Source: (gene. exp.) Homo sapiens (human) / Gene: CLTC, CLH17, CLTCL2, KIAA0034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00610
#2: Protein/peptide Protein mu-NS from Reovirus type 1


Mass: 1826.909 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mammalian orthoreovirus 1 Lang
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
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: 3.69 Å3/Da / Density % sol: 66.65 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 550 MME; PEG 20K, 0.12M Monosaccharides (D-Glucose; D-Mannose; D-Galactose; L-Fucose; D-Xylose; N-Acetyl-D-Glucosamine) and 0.1M Sodium HEPES; MOPS (acid) pH-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→89.43 Å / Num. obs: 61571 / % possible obs: 93.3 % / Redundancy: 3.5 % / CC1/2: 0.991 / Net I/σ(I): 9.1
Reflection shellResolution: 1.97→2.11 Å / Num. unique obs: 3080 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1c9i

1c9i


Resolution: 1.97→89.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.611 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 2950 4.8 %RANDOM
Rwork0.1839 ---
obs0.1854 58624 71.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.56 Å2 / Biso mean: 39.398 Å2 / Biso min: 21.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å2-0 Å2-0.06 Å2
2---0.28 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.97→89.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 13 470 6237
Biso mean--87.51 44.46 -
Num. residues----738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135945
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175549
X-RAY DIFFRACTIONr_angle_refined_deg1.541.6358067
X-RAY DIFFRACTIONr_angle_other_deg1.2881.56912924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9615751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48723.831295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.354151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7471526
X-RAY DIFFRACTIONr_chiral_restr0.0650.2809
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021159
LS refinement shellResolution: 1.972→2.024 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 30 -
Rwork0.323 528 -
all-558 -
obs--8.78 %

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