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- PDB-7bn2: Clathrin heavy chain N-terminal domain bound to Non structured pr... -

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Basic information

Entry
Database: PDB / ID: 7bn2
TitleClathrin heavy chain N-terminal domain bound to Non structured protein 3 from Eastern Equine Encephalitis Virus
Components
  • Clathrin heavy chain 1
  • Non structured protein 3 from Eastern Equine Encephalitis Virus
KeywordsTRANSPORT PROTEIN / CLTC-NTD / Clathrin-Box motif / Non structured protein 3 / Eastern Equine Encephalitis Virus
Function / homology
Function and homology information


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 / WNT5A-dependent internalization of FZD4 / Entry of Influenza Virion into Host Cell via Endocytosis / transferrin transport / amyloid-beta clearance by transcytosis ...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 / 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 / clathrin-dependent endocytosis / ALK mutants bind TKIs / endolysosome membrane / retrograde transport, endosome to Golgi / negative regulation of protein localization to plasma membrane / clathrin-coated vesicle / 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 / EPH-ephrin mediated repulsion of cells / regulation of mitotic spindle organization / MHC class II antigen presentation / VLDLR internalisation and degradation / receptor-mediated endocytosis / trans-Golgi network membrane / 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 / lysosome / endosome / cell division / focal adhesion / 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 / 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, 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
PHOSPHATE ION / Clathrin heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Eastern equine encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.965 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 / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Clathrin heavy chain 1
BBB: Clathrin heavy chain 1
CCC: Non structured protein 3 from Eastern Equine Encephalitis Virus
DDD: Non structured protein 3 from Eastern Equine Encephalitis Virus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1346
Polymers84,9434
Non-polymers1912
Water9,062503
1
AAA: Clathrin heavy chain 1
CCC: Non structured protein 3 from Eastern Equine Encephalitis Virus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5683
Polymers42,4722
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-22 kcal/mol
Surface area16640 Å2
MethodPISA
2
BBB: Clathrin heavy chain 1
DDD: Non structured protein 3 from Eastern Equine Encephalitis Virus
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5673
Polymers42,4722
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-10 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.900, 129.119, 77.881
Angle α, β, γ (deg.)90.000, 115.294, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11BBB-611-

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 Non structured protein 3 from Eastern Equine Encephalitis Virus


Mass: 1928.037 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Eastern equine encephalitis virus
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 550 MME; PEG 20K and 0.1M NPS buffer system NaN03; Na2HPO4; (NH4)2SO4, pH-6.5

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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: 1.96→89.36 Å / Num. obs: 62270 / % possible obs: 90.2 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 10
Reflection shellResolution: 1.96→2.11 Å / Num. unique obs: 3115 / CC1/2: 0.629

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1c9i

1c9i


Resolution: 1.965→89.352 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.12 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.175 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3167 5.085 %0.18
Rwork0.1815 59120 --
all0.184 ---
obs-62270 71.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.422 Å20 Å2-0.277 Å2
2---0.269 Å20 Å2
3---0.075 Å2
Refinement stepCycle: LAST / Resolution: 1.965→89.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5760 0 10 503 6273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135943
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175542
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.6378073
X-RAY DIFFRACTIONr_angle_other_deg1.3471.56912906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9745750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03323.75296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.281151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2291527
X-RAY DIFFRACTIONr_chiral_restr0.070.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021161
X-RAY DIFFRACTIONr_nbd_refined0.1940.2975
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25274
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22842
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.22678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2441
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1130.221
X-RAY DIFFRACTIONr_nbd_other0.2020.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_mcbond_it2.8923.3612962
X-RAY DIFFRACTIONr_mcbond_other2.8923.362961
X-RAY DIFFRACTIONr_mcangle_it4.4415.0233700
X-RAY DIFFRACTIONr_mcangle_other4.4415.0253701
X-RAY DIFFRACTIONr_scbond_it3.5213.7442981
X-RAY DIFFRACTIONr_scbond_other3.5173.742979
X-RAY DIFFRACTIONr_scangle_it5.4345.4544364
X-RAY DIFFRACTIONr_scangle_other5.4325.4544364
X-RAY DIFFRACTIONr_lrange_it7.6140.0056446
X-RAY DIFFRACTIONr_lrange_other7.6140.0166447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.965-2.0160.296840.27716130.27863860.8230.82926.57380.276
2.016-2.0710.286560.2819610.28162680.8380.83716.22530.28
2.071-2.1310.265430.26811130.26860610.8750.84119.07280.259
2.131-2.1970.2881660.2332470.23258840.8440.87358.00480.217
2.197-2.2690.26890.24619310.24757050.8640.85735.40750.23
2.269-2.3480.2872270.22540320.22855810.8390.87876.31250.204
2.348-2.4370.2762090.22240720.22453130.8650.88780.57590.199
2.437-2.5360.2522190.20641970.20951760.8980.90785.31680.181
2.536-2.6490.232240.243130.20248820.9070.91392.93320.174
2.649-2.7780.2462300.19644870.19847440.9080.92199.43090.169
2.778-2.9280.2232320.18242330.18444830.9260.93699.59850.163
2.928-3.1060.232080.17840530.18142660.9260.9499.88280.165
3.106-3.320.2222320.18837380.1939770.9320.94299.8240.18
3.32-3.5850.2342020.18135130.18337270.9440.95299.6780.178
3.585-3.9270.2191800.16832330.1734400.9460.95799.21510.168
3.927-4.3890.1721770.14528990.14730870.9620.96699.64370.153
4.389-5.0660.1661310.13925800.14127390.9720.97498.97770.156
5.066-6.20.1951190.16522050.16623330.9670.96799.61420.182
6.2-8.7470.194860.17217300.17318170.9530.95999.9450.192
8.747-89.3520.222530.2019700.20210270.9440.94899.61050.254

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