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- PDB-6qnn: CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF -

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Basic information

Entry
Database: PDB / ID: 6qnn
TitleCLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF
Components
  • Clathrin heavy chain 1
  • G2 and S phase-expressed protein 1
KeywordsCELL CYCLE / BETA-PROPELLER / CLATHRIN-BOX / LIDL-MOTIF
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 / cytoplasmic microtubule / microtubule-based process / RHOU GTPase cycle / EPH-ephrin mediated repulsion of cells / regulation of mitotic spindle organization / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / MHC class II antigen presentation / VLDLR internalisation and degradation / receptor-mediated endocytosis / trans-Golgi network membrane / G2/M Checkpoints / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / mitotic spindle / autophagy / spindle / osteoblast differentiation / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / extracellular vesicle / disordered domain specific binding / 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 / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Proline/serine-rich coiled-coil protein 1/G2 and S phase-expressed protein 1 / G2 and S phase-expressed protein 1 / G2 and S phase-expressed protein 1, N-terminal / G-2 and S-phase expressed 1 / Clathrin heavy-chain terminal domain / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat ...Proline/serine-rich coiled-coil protein 1/G2 and S phase-expressed protein 1 / G2 and S phase-expressed protein 1 / G2 and S phase-expressed protein 1, N-terminal / G-2 and S-phase expressed 1 / Clathrin heavy-chain terminal domain / Clathrin-H-link / 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 / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Beta
Similarity search - Domain/homology
Clathrin heavy chain 1 / G2 and S phase-expressed protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.03 Å
AuthorsPorfetye, A.T. / Lin, Y. / Vetter, I.R.
CitationJournal: J.Cell Biol. / Year: 2020
Title: Clathrin's adaptor interaction sites are repurposed to stabilize microtubules during mitosis.
Authors: Rondelet, A. / Lin, Y.C. / Singh, D. / Porfetye, A.T. / Thakur, H.C. / Hecker, A. / Brinkert, P. / Schmidt, N. / Bendre, S. / Muller, F. / Mazul, L. / Widlund, P.O. / Bange, T. / Hiller, M. ...Authors: Rondelet, A. / Lin, Y.C. / Singh, D. / Porfetye, A.T. / Thakur, H.C. / Hecker, A. / Brinkert, P. / Schmidt, N. / Bendre, S. / Muller, F. / Mazul, L. / Widlund, P.O. / Bange, T. / Hiller, M. / Vetter, I.R. / Bird, A.W.
History
DepositionFeb 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clathrin heavy chain 1
B: G2 and S phase-expressed protein 1


Theoretical massNumber of molelcules
Total (without water)47,6272
Polymers47,6272
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-8 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.987, 51.987, 154.094
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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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.: 1
Fragment: LIDL motifs A-E, REFSEQ RESIDUES 661-726, N-TERMINAL 'GPLG' ARE NON-NATURAL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLTC, CLH17, CLTCL2, KIAA0034 / Plasmid: pGEX6p1 variant pGEX-2rbs / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q00610
#2: Protein G2 and S phase-expressed protein 1 / GTSE-1 / Protein B99 homolog


Mass: 7083.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GTSE1 peptide corresponds to residues 706-724 of the NCBI reference seq. NP_057510.5 (739 residues)
Source: (gene. exp.) Homo sapiens (human) / Gene: GTSE1 / Plasmid: pGEX-2rbs modified pGEX6p1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NYZ3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.51 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 20% PEG 6000, 0.1M TRIS pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99993 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 2.03→49.259 Å / Num. obs: 26009 / % possible obs: 98.8 % / Redundancy: 13.639 % / Biso Wilson estimate: 56.489 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Χ2: 1.143 / Net I/σ(I): 18.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.03-2.0813.4322.0341.7319290.8392.11498.2
2.08-2.1413.0491.4032.4218230.9161.4698
2.14-2.212.9120.9963.2818030.9511.03798.4
2.2-2.2714.2840.9073.8617910.9730.9498.2
2.27-2.3414.3930.674.9416800.9820.69498
2.34-2.4314.2280.5595.6116470.9860.5898.2
2.43-2.5214.1920.417.2415820.9910.42598.6
2.52-2.6213.9470.2849.5115670.9940.29598.9
2.62-2.7413.2290.21211.3814790.9960.22198.8
2.74-2.8713.1450.16414.2913910.9970.17198.9
2.87-3.0314.5080.11720.2713490.9980.12198.8
3.03-3.2114.310.09126.112820.9990.09499.5
3.21-3.4313.9630.06833.5912090.9990.0799.3
3.43-3.7113.4340.05839.8811300.9990.0699.7
3.71-4.0612.0680.04843.8210370.9990.05100
4.06-4.5413.1780.04151.569190.9990.04399.8
4.54-5.2413.8450.03955.3485010.041100
5.24-6.4213.2320.0455.076940.9990.04199.9
6.42-9.0812.0290.03554.485460.9990.037100
9.08-49.25914.2230.02862.583010.9990.02999.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UTC

1utc


Resolution: 2.03→49.259 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 43.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2839 1054 4.06 %
Rwork0.2401 24878 -
obs0.2418 25932 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.14 Å2 / Biso mean: 66.1852 Å2 / Biso min: 41.08 Å2
Refinement stepCycle: final / Resolution: 2.03→49.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 0 21 2925
Biso mean---67.22 -
Num. residues----373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.12240.43361280.40453062319098
2.1224-2.23430.4031300.34943084321498
2.2343-2.37430.37441320.32273097322998
2.3743-2.55760.38371290.31263053318298
2.5576-2.8150.34691330.31663113324699
2.815-3.22220.35031330.29033150328399
3.2222-4.05940.28651340.238531433277100
4.0594-49.27370.21231350.179831763311100

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