[English] 日本語
Yorodumi
- PDB-1utc: Clathrin terminal domain complexed with TLPWDLWTT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1utc
TitleClathrin terminal domain complexed with TLPWDLWTT
Components
  • AMPHIPHYSIN
  • CLATHRIN HEAVY CHAIN
KeywordsENDOCYTOSIS / CLATHRIN / CYTOSKELETON
Function / homology
Function and homology information


Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle ...Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin coat of coated pit / clathrin coat assembly / clathrin coat disassembly / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / leading edge membrane / membrane coat / Clathrin-mediated endocytosis / arrestin family protein binding / synaptic vesicle endocytosis / receptor-mediated endocytosis / intracellular protein transport / phospholipid binding / autophagy / spindle / synaptic vesicle membrane / endocytosis / disordered domain specific binding / synaptic vesicle / melanosome / mitotic cell cycle / actin cytoskeleton / Clathrin-mediated endocytosis / chemical synaptic transmission / protein domain specific binding / cell division / structural molecule activity / mitochondrion / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / Clathrin heavy-chain terminal domain / Amphiphysin / : / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Region in Clathrin and VPS ...Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / Clathrin heavy-chain terminal domain / Amphiphysin / : / 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 / BAR domain / BAR domain profile. / BAR / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / BAR domain / AH/BAR domain superfamily / 7 Propeller / Methylamine Dehydrogenase; Chain H / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Beta
Similarity search - Domain/homology
Amphiphysin / Clathrin heavy chain 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiele, A.E. / Evans, P.R. / Owen, D.J.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2004
Title: Two distinct interaction motifs in amphiphysin bind two independent sites on the clathrin terminal domain beta-propeller.
Authors: Miele, A.E. / Watson, P.J. / Evans, P.R. / Traub, L.M. / Owen, D.J.
History
DepositionDec 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Oct 16, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf
Revision 1.5Dec 13, 2023Group: 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
B: CLATHRIN HEAVY CHAIN
P: AMPHIPHYSIN
Q: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)83,0574
Polymers83,0574
Non-polymers00
Water6,431357
1
A: CLATHRIN HEAVY CHAIN
P: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)41,5292
Polymers41,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CLATHRIN HEAVY CHAIN
Q: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)41,5292
Polymers41,5292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.301, 61.301, 420.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999979, -0.005338, 0.00362), (0.004533, -0.18231, 0.983231), (-0.004588, 0.983227, 0.18233)
Vector: 51.642, 43.003, -36.089)
DetailsCLATHRIN HEAVY CHAIN IS A MONOMER BIOLOGICALLY BUTIS CLASSIFIED AS A DIMER IN THIS ENTRY SINCE EVERYMOLECULE OF CLATHRIN (CHAINS A AND B) ARE BOUND TOA PEPTIDE.

-
Components

#1: Antibody CLATHRIN HEAVY CHAIN


Mass: 40396.340 Da / Num. of mol.: 2 / Fragment: TERMINAL DOMAIN, RESIDUES 1-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Plasmid: PGEX4T2 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P49951
#2: Protein/peptide AMPHIPHYSIN


Mass: 1132.264 Da / Num. of mol.: 2 / Fragment: W-BOX, RESIDUES 379-387 / Source method: obtained synthetically / Details: PEPTIDE FROM AMPHIPHYSIN 1 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P49418
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCLATHRIN IS THE MAJOR PROTEIN OF THE POLYHEDRAL COAT OF COATED PITS & VESICLES. TWO DIFFERENT ...CLATHRIN IS THE MAJOR PROTEIN OF THE POLYHEDRAL COAT OF COATED PITS & VESICLES. TWO DIFFERENT ADAPTOR PROTEIN COMPLEXES LINK THE CLATHRIN LATTICE EITHER TO THE PLASMA MEMBRANE OR TO THE TRANS GOLGI NETWORK.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP
Crystal grow
*PLUS
pH: 9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 %(w/v)PEG80001reservoir
2200 mM1reservoirMgCl2
34 mMdithiothreitol1reservoir
4100 mMCAPS1reservoirpH9.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→24.92 Å / Num. obs: 37228 / % possible obs: 99.4 % / Redundancy: 5.84 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.3131
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.33 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.02 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 29.9 Å / Num. obs: 37078 / Redundancy: 5.8 % / Num. measured all: 495661 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.3

-
Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C9I

1c9i


Resolution: 2.3→105.41 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.03 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1856 5 %RANDOM
Rwork0.194 ---
obs0.197 35214 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5649 0 0 357 6006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225773
X-RAY DIFFRACTIONr_bond_other_d0.0010.025262
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9297834
X-RAY DIFFRACTIONr_angle_other_deg0.882312281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1945715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88224.942257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.685151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5871526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021101
X-RAY DIFFRACTIONr_nbd_refined0.1840.2888
X-RAY DIFFRACTIONr_nbd_other0.1870.24940
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.23241
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.2277
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0390.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3121.54661
X-RAY DIFFRACTIONr_mcbond_other0.17211450
X-RAY DIFFRACTIONr_mcangle_it1.50625832
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06532549
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9124.52002
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.303 115
Rwork0.23 2493
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 29.9 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

+
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