[English] 日本語
Yorodumi
- PDB-5ods: Structure of a phosphoprotein-protein complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ods
TitleStructure of a phosphoprotein-protein complex
Components
  • Clathrin heavy chain 1
  • LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU
KeywordsCELL CYCLE / Scaffolding protein / spindle association
Function / homology
Function and homology information


presynaptic endocytic zone membrane / RHOV GTPase cycle / RHOU GTPase cycle / Formation of annular gap junctions / Gap junction degradation / clathrin coat of trans-Golgi network vesicle / Myb complex / Lysosome Vesicle Biogenesis / clathrin light chain binding / LDL clearance ...presynaptic endocytic zone membrane / RHOV GTPase cycle / RHOU GTPase cycle / Formation of annular gap junctions / Gap junction degradation / clathrin coat of trans-Golgi network vesicle / Myb complex / Lysosome Vesicle Biogenesis / clathrin light chain binding / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / negative regulation of hyaluronan biosynthetic process / clathrin complex / microtubule cytoskeleton organization involved in mitosis / Retrograde neurotrophin signalling / clathrin coat / amyloid-beta clearance by transcytosis / VLDLR internalisation and degradation / Recycling pathway of L1 / clathrin coat of coated pit / photoreceptor ribbon synapse / postsynaptic endocytic zone / clathrin coat disassembly / Golgi Associated Vesicle Biogenesis / extrinsic component of synaptic vesicle membrane / metaphase/anaphase transition of mitotic cell cycle / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / membrane coat / clathrin coat assembly / mitotic spindle microtubule / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / MHC class II antigen presentation / retrograde transport, endosome to Golgi / clathrin-coated vesicle / ankyrin binding / low-density lipoprotein particle receptor binding / nuclear migration / ubiquitin-specific protease binding / Golgi organization / mitotic spindle assembly / negative regulation of protein localization to plasma membrane / synaptic vesicle endocytosis / heat shock protein binding / peptide binding / clathrin-coated pit / T-tubule / receptor-mediated endocytosis / regulation of mitotic spindle organization / mitotic spindle organization / protein serine/threonine kinase binding / NOTCH3 Activation and Transmission of Signal to the Nucleus / transferrin transport / intracellular protein transport / Negative regulation of NOTCH4 signaling / cerebral cortex development / sarcolemma / receptor internalization / microtubule cytoskeleton organization / spindle / autophagy / centriolar satellite / spindle pole / disordered domain specific binding / mitotic spindle / melanosome / myelin sheath / mitotic cell cycle / double-stranded RNA binding / lysosome / endosome / ciliary basal body / cell division / protein kinase binding / glutamatergic synapse / structural molecule activity / Golgi apparatus / protein-containing complex / mitochondrion / membrane / cytoplasm / cytosol
Similarity search - Function
Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / : / Transforming acidic coiled-coil-containing protein (TACC), C-terminal / TACC3, Aurora-A binding region / Clathrin heavy-chain terminal domain / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat ...Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / : / Transforming acidic coiled-coil-containing protein (TACC), C-terminal / TACC3, Aurora-A binding region / 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 / Transforming acidic coiled-coil-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsMukherjee, M. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L023113/1 United Kingdom
CitationJournal: Embo J. / Year: 2018
Title: Structure of a phosphoprotein-protein complex
Authors: Mukherjee, M. / Bayliss, R.
History
DepositionJul 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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
E: LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU
F: LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU
G: LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU
H: LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)266,3578
Polymers266,3578
Non-polymers00
Water00
1
A: Clathrin heavy chain 1
E: LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)66,5892
Polymers66,5892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Clathrin heavy chain 1
F: LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)66,5892
Polymers66,5892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Clathrin heavy chain 1
G: LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)66,5892
Polymers66,5892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Clathrin heavy chain 1
H: LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU


Theoretical massNumber of molelcules
Total (without water)66,5892
Polymers66,5892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.520, 120.040, 123.130
Angle α, β, γ (deg.)90.00, 95.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody
Clathrin heavy chain 1


Mass: 64355.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cltc / Production host: Escherichia coli (E. coli) / References: UniProt: Q68FD5
#2: Protein/peptide
LYS-GLU-SER-ALA-LEU-ARG-LYS-GLN-SEP-LEU-TYR-LEU-LYS-PHE-ASP-PRO-LEU-LEU


Mass: 2233.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6A5*PLUS
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 8 / Details: PEG 6000, sodium chloride, Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.09→61.26 Å / Num. obs: 60689 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.055 / Rrim(I) all: 0.101 / Net I/σ(I): 10.3
Reflection shellResolution: 3.09→3.14 Å / Redundancy: 3.4 % / Num. unique obs: 3053 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia20.4.0.291-ga780859-dials-1.1data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BPO

1bpo


Resolution: 3.09→61.258 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 2888 4.76 %
Rwork0.2208 --
obs0.2231 60649 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→61.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18224 0 0 0 18224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618585
X-RAY DIFFRACTIONf_angle_d1.20425225
X-RAY DIFFRACTIONf_dihedral_angle_d19.6736870
X-RAY DIFFRACTIONf_chiral_restr0.052890
X-RAY DIFFRACTIONf_plane_restr0.0053266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.14070.42531510.37362765X-RAY DIFFRACTION100
3.1407-3.19480.44021430.36072736X-RAY DIFFRACTION99
3.1948-3.25290.34631420.32662759X-RAY DIFFRACTION99
3.2529-3.31550.32531310.30322762X-RAY DIFFRACTION100
3.3155-3.38310.32021170.28512781X-RAY DIFFRACTION100
3.3831-3.45670.33941420.2742748X-RAY DIFFRACTION99
3.4567-3.53710.31261400.26572771X-RAY DIFFRACTION100
3.5371-3.62550.29231250.26332802X-RAY DIFFRACTION100
3.6255-3.72360.32871410.25632738X-RAY DIFFRACTION99
3.7236-3.83310.31581350.24292773X-RAY DIFFRACTION100
3.8331-3.95680.28131550.2392720X-RAY DIFFRACTION99
3.9568-4.09820.29471530.21952763X-RAY DIFFRACTION99
4.0982-4.26220.24231360.20482774X-RAY DIFFRACTION99
4.2622-4.45620.26461330.19142739X-RAY DIFFRACTION99
4.4562-4.6910.2381280.18692733X-RAY DIFFRACTION98
4.691-4.98480.19911350.18572759X-RAY DIFFRACTION99
4.9848-5.36950.23111230.18712785X-RAY DIFFRACTION98
5.3695-5.90940.23071190.20732744X-RAY DIFFRACTION98
5.9094-6.76360.28831500.22162715X-RAY DIFFRACTION98
6.7636-8.51780.24811510.22032705X-RAY DIFFRACTION96
8.5178-61.27050.2511380.19252689X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.60920.6946-0.60411.7778-0.79092.73460.09690.0632-0.0754-0.06020.0254-0.1154-0.18990.2809-0.04620.54670.0134-0.05740.5522-0.08240.5589129.455710.483162.4098
21.0832-1.6427-0.161.8993-0.08121.92450.16070.1665-0.16470.0504-0.14170.00930.860.51120.07910.91790.1226-0.10710.86510.01510.9071134.0827-24.1023182.321
33.2095-0.90340.19540.63990.9061.5912-0.14630.4195-0.0965-0.0855-0.0570.015-0.2473-0.53740.11391.03750.11530.04810.94810.08790.6457173.275-40.5767174.0446
42.09970.7274-1.19412.5109-1.50782.77340.1141-0.222-0.02960.1821-0.01020.4806-0.1492-0.1641-0.06840.5708-0.03410.03070.547-0.11270.899497.606-16.4455188.7777
50.6318-0.37171.01590.26220.11050.7950.42410.2133-0.3871-0.5392-0.0263-0.0498-0.1157-0.0173-0.17231.32240.2236-0.36921.4958-0.14471.722884.17980.802147.1329
62.2345-0.18610.39661.34380.3180.7425-0.3249-0.1885-0.05580.70030.3678-0.36490.46260.275-0.05591.15740.1616-0.11861.1937-0.06411.201645.1781-7.4249140.7436
7-0.0014-0.4775-0.5592-0.0485-0.9151.5749-0.1946-0.0538-0.1667-1.2601-0.598-0.61331.67010.03810.08261.8680.16320.32691.63790.03381.242878.3589-73.6264140.2779
82.5706-0.9257-0.02623.3384-0.97372.5781-0.1137-0.1880.1832-0.02780.1198-0.3455-0.21020.0542-0.01610.8124-0.0836-0.0451.0834-0.0830.687165.3416-57.5881146.8732
90.8441-1.08540.12231.8175-1.31031.4629-0.1167-0.19670.0949-0.2388-0.1502-0.07050.8793-0.02030.15871.4142-0.05720.08761.62340.0670.892372.6926-55.5953128.6419
100.60720.55440.04930.39020.41390.0151-0.2473-0.32930.8159-0.4770.48910.1205-0.5728-0.15-0.011.5456-0.18660.11952.1008-0.15672.062788.9723-19.731125.8972
111.66680.5368-0.09980.7711-0.03710.5959-0.1990.29190.09030.0724-0.1910.94430.7178-0.8681-0.02971.5323-0.28660.20181.3348-0.27111.5033126.9743-14.4841134.0834
121.04280.4433-0.44252.1265-0.76452.45980.05640.15290.3735-0.08210.21420.709-0.2752-0.349-0.09870.6580.13050.0120.95670.17111.1053157.9484-37.6859115.3222
132.0855-0.236-0.47791.14710.25430.5555-0.3004-0.3316-0.15210.11940.3621-0.13290.29380.5347-0.05211.51120.00070.37171.5208-0.20211.5361132.943-50.0072161.6425
143.11970.2046-1.23881.3291.07591.3611-0.0503-0.12530.2531-0.39310.1476-0.4527-0.0993-0.03680.14771.1179-0.17360.13540.834-0.03740.889199.1287-43.9597164.9414
151.769-2.59490.11894.0521-0.68691.0219-0.06040.62960.5335-0.85780.03060.57070.49480.02930.0321.59310.1934-0.33391.5998-0.08351.0885164.5091-31.0439164.3498
160.9857-0.09052.4225-0.0084-0.16155.9011-0.0860.1095-0.1823-0.38910.0040.05420.0750.04910.0062.69380.4778-0.58562.2117-0.04862.266363.5716-15.7419155.5092
174.07380.63621.59264.7293-2.48372.21380.08170.3588-0.1285-0.0081-0.1605-0.31470.39420.29810.05661.98490.3457-0.5822.1493-0.12742.170962.9866-16.5707143.0186
180.7231.6152-0.54693.429-1.19850.4164-0.47190.02980.54840.2025-0.16110.21160.02220.2661-0.00982.0753-0.08110.25592.2374-0.16232.238105.7438-24.1476144.698
194.01821.4486-1.16080.5167-0.33234.62050.04460.11580.0059-0.12770.17280.04950.0069-0.04590.00651.8911-0.3825-0.30152.8094-0.80793.7733106.1725-11.8008142.3777
200.98471.0551-1.71130.9663-1.72722.9157-0.29120.64260.5259-0.983-0.1597-0.3032-0.77860.2840.03912.171-0.21650.22011.42060.25821.9805121.5386-33.8619158.0571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 329 )
2X-RAY DIFFRACTION2chain 'A' and (resid 330 through 424 )
3X-RAY DIFFRACTION3chain 'A' and (resid 425 through 574 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 354 )
5X-RAY DIFFRACTION5chain 'B' and (resid 355 through 471 )
6X-RAY DIFFRACTION6chain 'B' and (resid 472 through 572 )
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 86 )
8X-RAY DIFFRACTION8chain 'C' and (resid 87 through 296 )
9X-RAY DIFFRACTION9chain 'C' and (resid 297 through 354 )
10X-RAY DIFFRACTION10chain 'C' and (resid 355 through 481 )
11X-RAY DIFFRACTION11chain 'C' and (resid 482 through 572 )
12X-RAY DIFFRACTION12chain 'D' and (resid 3 through 397 )
13X-RAY DIFFRACTION13chain 'D' and (resid 398 through 493 )
14X-RAY DIFFRACTION14chain 'D' and (resid 494 through 573 )
15X-RAY DIFFRACTION15chain 'E' and (resid 550 through 567 )
16X-RAY DIFFRACTION16chain 'F' and (resid 550 through 560 )
17X-RAY DIFFRACTION17chain 'F' and (resid 561 through 567 )
18X-RAY DIFFRACTION18chain 'G' and (resid 550 through 560 )
19X-RAY DIFFRACTION19chain 'G' and (resid 561 through 567 )
20X-RAY DIFFRACTION20chain 'H' and (resid 550 through 567 )

+
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