[English] 日本語
Yorodumi
- PDB-6qnp: CLATHRIN HEAVY CHAIN N-TERMINAL DOMAIN BOUND TO GTSE1 LIDL MOTIF -

+
Open data


ID or keywords:

Loading...

-
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 / Entry of Influenza Virion into Host Cell via Endocytosis / WNT5A-dependent internalization of FZD4 / 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 / Entry of Influenza Virion into Host Cell via Endocytosis / WNT5A-dependent internalization of FZD4 / amyloid-beta clearance by transcytosis / clathrin coat of coated pit / clathrin coat disassembly / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / clathrin coat assembly / mitotic spindle microtubule / LDL clearance / Formation of annular gap junctions / clathrin-dependent endocytosis / Gap junction degradation / ALK mutants bind TKIs / endolysosome membrane / retrograde transport, endosome to Golgi / clathrin-coated vesicle / low-density lipoprotein particle receptor binding / RHOV GTPase cycle / Lysosome Vesicle Biogenesis / 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 / VLDLR internalisation and degradation / regulation of mitotic spindle organization / trans-Golgi network membrane / transferrin transport / DNA damage response, signal transduction by p53 class mediator / intracellular protein transport / G2/M Checkpoints / clathrin-coated endocytic vesicle membrane / receptor internalization / autophagy / centriolar satellite / spindle / disordered domain specific binding / osteoblast differentiation / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Signaling by ALK fusions and activated point mutants / melanosome / Cargo recognition for clathrin-mediated endocytosis / mitotic cell cycle / extracellular vesicle / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more