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- PDB-5ods: Structure of a phosphoprotein-protein complex -

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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 / Retrograde neurotrophin signalling / microtubule cytoskeleton organization involved in mitosis / clathrin coat / amyloid-beta clearance by transcytosis / VLDLR internalisation and degradation / clathrin coat of coated pit / Recycling pathway of L1 / 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 / membrane coat / clathrin-coated endocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / mitotic spindle microtubule / Clathrin-mediated endocytosis / astral microtubule organization / MHC class II antigen presentation / clathrin-dependent endocytosis / retrograde transport, endosome to Golgi / clathrin-coated vesicle / nuclear migration / low-density lipoprotein particle receptor binding / ankyrin binding / centriolar satellite / 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 / receptor-mediated endocytosis / T-tubule / sperm midpiece / mitotic spindle organization / regulation of mitotic spindle organization / protein serine/threonine kinase binding / myelin sheath / NOTCH3 Activation and Transmission of Signal to the Nucleus / transferrin transport / receptor internalization / cerebral cortex development / intracellular protein transport / sarcolemma / Negative regulation of NOTCH4 signaling / mitotic spindle / spindle / autophagy / spindle pole / disordered domain specific binding / melanosome / mitotic cell cycle / double-stranded RNA binding / ciliary basal body / lysosome / endosome / cell division / centrosome / protein kinase binding / glutamatergic synapse / structural molecule activity / protein-containing complex / mitochondrion / membrane / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
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

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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

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Experimental details

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Experiment

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

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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

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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

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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 )

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