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

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Basic information

Entry
Database: PDB / ID: 6qnp
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 coat / clathrin light chain binding / clathrin complex / negative regulation of hyaluronan biosynthetic process / 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 / clathrin coat of coated pit ...clathrin coat of trans-Golgi network vesicle / clathrin coat / clathrin light chain binding / clathrin complex / negative regulation of hyaluronan biosynthetic process / 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 / clathrin coat of coated pit / transferrin transport / 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 / microtubule-based process / cytoplasmic microtubule / MHC class II antigen presentation / receptor-mediated endocytosis / regulation of mitotic spindle organization / VLDLR internalisation and degradation / DNA damage response, signal transduction by p53 class mediator / trans-Golgi network membrane / intracellular protein transport / G2/M Checkpoints / clathrin-coated endocytic vesicle membrane / receptor internalization / autophagy / centriolar satellite / spindle / osteoblast differentiation / disordered domain specific binding / mitotic spindle / The role of GTSE1 in G2/M progression after G2 checkpoint / 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 / microtubule cytoskeleton / microtubule binding / lysosome / endosome / cell division / focal adhesion / intracellular membrane-bounded organelle / 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, N-terminal / G-2 and S-phase expressed 1 / 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 ...Proline/serine-rich coiled-coil 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, 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. / 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: 2.7 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 2.0Oct 2, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / refine / struct_asym / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _refine.pdbx_diffrn_id / _struct_asym.entity_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end
Revision 2.1Jan 29, 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 2.2Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clathrin heavy chain 1
B: Clathrin heavy chain 1
C: Clathrin heavy chain 1
D: Clathrin heavy chain 1
H: G2 and S phase-expressed protein 1
I: G2 and S phase-expressed protein 1
J: G2 and S phase-expressed protein 1
K: G2 and S phase-expressed protein 1


Theoretical massNumber of molelcules
Total (without water)190,3388
Polymers190,3388
Non-polymers00
Water4,432246
1
A: Clathrin heavy chain 1
H: G2 and S phase-expressed protein 1


Theoretical massNumber of molelcules
Total (without water)47,5852
Polymers47,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-17 kcal/mol
Surface area17320 Å2
MethodPISA
2
B: Clathrin heavy chain 1
I: G2 and S phase-expressed protein 1


Theoretical massNumber of molelcules
Total (without water)47,5852
Polymers47,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-17 kcal/mol
Surface area17030 Å2
MethodPISA
3
C: Clathrin heavy chain 1
J: G2 and S phase-expressed protein 1


Theoretical massNumber of molelcules
Total (without water)47,5852
Polymers47,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-19 kcal/mol
Surface area17220 Å2
MethodPISA
4
D: Clathrin heavy chain 1
K: G2 and S phase-expressed protein 1


Theoretical massNumber of molelcules
Total (without water)47,5852
Polymers47,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-18 kcal/mol
Surface area17060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.090, 90.150, 100.230
Angle α, β, γ (deg.)90.000, 110.120, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4
Fragment: LIDL motifs A-D, REFSEQ RESIDUES 653-719, N-TERMINAL 'GPLGS' ARE NON-NATURAL
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
G2 and S phase-expressed protein 1 / GTSE-1 / Protein B99 homolog


Mass: 7040.994 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTSE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYZ3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 12% PEG 4000, 0.1M SODIUM ACETATE, 0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 2.7→49.19 Å / Num. obs: 43602 / % possible obs: 99.2 % / Redundancy: 6.876 % / Biso Wilson estimate: 65.226 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.141 / Rrim(I) all: 0.153 / Χ2: 1.002 / Net I/σ(I): 10.39 / Num. measured all: 299788 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.7-2.776.6091.891.0532010.452.05299
2.77-2.856.4561.4971.2831100.5641.6398.6
2.85-2.937.0931.121.9130450.791.20798.9
2.93-3.027.1950.8452.5129480.8430.9199.2
3.02-3.127.1780.6833.0528730.8880.73699
3.12-3.237.1250.5054.0627680.9480.54499.2
3.23-3.357.0680.3685.4426690.9640.39799.4
3.35-3.496.850.2767.2625650.9790.29999.1
3.49-3.646.4620.199.2224840.990.20799.2
3.64-3.826.6450.15911.0623520.9930.17398.8
3.82-4.027.1680.13213.8722450.9960.14399.5
4.02-4.277.1670.09517.321330.9980.10299.7
4.27-4.567.0150.07920.4220320.9980.08699.3
4.56-4.936.8580.0721.4418670.9990.07699.7
4.93-5.46.3080.06721.3117260.9980.07399.1
5.4-6.046.8180.07120.7615640.9990.07799.2
6.04-6.977.1310.06722.1413900.9990.07299.6
6.97-8.546.8020.04925.7411820.9990.05499.5
8.54-12.076.140.0334.249280.9990.03399
12.07-49.197.0190.02635.9252010.02898.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XFITdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M5T

5m5t


Resolution: 2.7→49.19 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.12
RfactorNum. reflection% reflection
Rfree0.2914 2171 4.99 %
Rwork0.2409 --
obs0.2434 43479 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.64 Å2 / Biso mean: 71.1235 Å2 / Biso min: 29.26 Å2
Refinement stepCycle: final / Resolution: 2.7→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11839 0 0 246 12085
Biso mean---59.22 -
Num. residues----1519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.75870.44251360.37162580271699
2.7587-2.82290.43441350.35432552268799
2.8229-2.89340.37211330.32092529266299
2.8934-2.97170.36951370.29762605274299
2.9717-3.05910.30811350.28725662701100
3.0591-3.15780.35151350.28942560269599
3.1578-3.27070.33231360.28732580271699
3.2707-3.40160.36341350.27112578271399
3.4016-3.55640.30761350.24652575271099
3.5564-3.74380.30611370.23952598273599
3.7438-3.97830.23751340.23682578271299
3.9783-4.28530.29611350.21522572270799
4.2853-4.71620.25891370.197526072744100
4.7162-5.39790.25441370.20952590272799
5.3979-6.79790.27131380.23172625276399
6.7979-49.19770.23751360.21022613274997

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