[English] 日本語
Yorodumi
- PDB-9c0z: Clathrin terminal domain complexed with pitstop 2d -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c0z
TitleClathrin terminal domain complexed with pitstop 2d
ComponentsClathrin heavy chain 1
KeywordsENDOCYTOSIS / Clathrin heavy chain 1
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 / clathrin coat of coated pit ...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 / 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 / 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
: / ACETATE ION / DI(HYDROXYETHYL)ETHER / Clathrin heavy chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsBulut, H. / Horatscheck, A. / Krauss, M. / Santos, K.F. / McCluskey, A. / Wahl, C.W. / Nazare, M. / Haucke, V.
Funding support Germany, 1items
OrganizationGrant numberCountry
Leibniz Association Germany
CitationJournal: Structure / Year: 2025
Title: Next-generation small molecule inhibitors of clathrin function acutely inhibit endocytosis.
Authors: Horatscheck, A. / Krauss, M. / Bulut, H. / Chambon, V. / Zadah, M.S. / Dransart, E. / Peloza, K. / Santos, K.F. / Robertson, M.J. / Prichard, K. / Miksche, S. / Radetzki, S. / von Kries, J.P. ...Authors: Horatscheck, A. / Krauss, M. / Bulut, H. / Chambon, V. / Zadah, M.S. / Dransart, E. / Peloza, K. / Santos, K.F. / Robertson, M.J. / Prichard, K. / Miksche, S. / Radetzki, S. / von Kries, J.P. / Wahl, M.C. / McCluskey, A. / Johannes, L. / Haucke, V. / Nazare, M.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2May 14, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Clathrin heavy chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,77413
Polymers40,4121
Non-polymers1,36212
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.826, 74.486, 82.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Antibody , 1 types, 1 molecules A

#1: Antibody Clathrin heavy chain 1 / Clathrin heavy chain on chromosome 17 / CLH-17


Mass: 40412.320 Da / Num. of mol.: 1
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

-
Non-polymers , 8 types, 421 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-A1ATQ / ~{N}-[4-oxidanylidene-5-[(2-phenoxyphenyl)methylidene]-1,3-thiazol-2-yl]naphthalene-1-sulfonamide


Mass: 486.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C26H18N2O4S2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 150 MM POTASSIUM ACETATE, 0.1 M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.509→41.18 Å / Num. obs: 68885 / % possible obs: 99.89 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.07239 / Net I/σ(I): 16.23
Reflection shellResolution: 1.509→1.564 Å / Num. unique obs: 6782 / CC1/2: 0.652

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→41.18 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.246 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18571 3514 5.1 %RANDOM
Rwork0.16172 ---
obs0.16293 65389 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 1.51→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 87 409 3332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162937
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.8214150
X-RAY DIFFRACTIONr_angle_other_deg0.6281.7566754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.997514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.47210520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5931.1711489
X-RAY DIFFRACTIONr_mcbond_other1.5031.171486
X-RAY DIFFRACTIONr_mcangle_it2.3962.0991866
X-RAY DIFFRACTIONr_mcangle_other2.42.1011867
X-RAY DIFFRACTIONr_scbond_it2.7731.4461564
X-RAY DIFFRACTIONr_scbond_other2.7741.4461563
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0742.5082275
X-RAY DIFFRACTIONr_long_range_B_refined5.27715.043380
X-RAY DIFFRACTIONr_long_range_B_other5.27615.043381
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.548 Å
RfactorNum. reflection% reflection
Rfree0.258 248 -
Rwork0.262 4715 -
obs--98.2 %

+
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