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- PDB-9r9b: Crystal structure of clathrin heavy chain in complex with a pepti... -

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Basic information

Entry
Database: PDB / ID: 9r9b
TitleCrystal structure of clathrin heavy chain in complex with a peptidomimetic inhibitor of the TACC3 interaction
Components
  • Clathrin heavy chain 1
  • SP-TACC3
KeywordsCELL CYCLE / Mitotic spindle Hydrocarbon stapled peptide Microtubule-binding
Function / homology
Function and homology information


presynaptic endocytic zone membrane / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Myb complex / Gap junction degradation / Formation of annular gap junctions / clathrin light chain binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance ...presynaptic endocytic zone membrane / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Myb complex / Gap junction degradation / Formation of annular gap junctions / clathrin light chain binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / negative regulation of hyaluronan biosynthetic process / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / clathrin complex / Lysosome Vesicle Biogenesis / WNT5A-dependent internalization of FZD4 / clathrin coat / amyloid-beta clearance by transcytosis / MHC class II antigen presentation / clathrin coat of coated pit / Golgi Associated Vesicle Biogenesis / photoreceptor ribbon synapse / postsynaptic endocytic zone / clathrin coat disassembly / extrinsic component of synaptic vesicle membrane / Recycling pathway of L1 / clathrin-coated endocytic vesicle / membrane coat / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / mitotic spindle microtubule / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / retrograde transport, endosome to Golgi / clathrin-coated vesicle / ankyrin binding / low-density lipoprotein particle receptor binding / 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 / protein serine/threonine kinase binding / clathrin-coated endocytic vesicle membrane / transferrin transport / intracellular protein transport / receptor internalization / sarcolemma / autophagy / spindle / centriolar satellite / disordered domain specific binding / terminal bouton / mitotic spindle / melanosome / mitotic cell cycle / double-stranded RNA binding / lysosome / endosome / protein kinase binding / glutamatergic synapse / structural molecule activity / protein-containing complex / 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
Clathrin heavy chain 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.146 Å
AuthorsBayliss, R. / Gunning, V.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003577/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003577/2 United Kingdom
Cancer Research UKC25425/A27718 United Kingdom
Cancer Research UKC24461/A23302 United Kingdom
CitationJournal: To Be Published
Title: Development of a peptidomimetic inhibitor of the TACC3/clathrin interaction on the mitotic spindle
Authors: Gunning, V. / Bayliss, R.
History
DepositionMay 19, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clathrin heavy chain 1
B: SP-TACC3


Theoretical massNumber of molelcules
Total (without water)66,9082
Polymers66,9082
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-8 kcal/mol
Surface area28070 Å2
Unit cell
Length a, b, c (Å)111.218, 111.218, 212.862
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-655-

HOH

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Components

#1: Antibody Clathrin heavy chain 1


Mass: 64355.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cltc / Production host: Escherichia coli (E. coli) / References: UniProt: P11442
#2: Protein/peptide SP-TACC3


Mass: 2551.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 20% w/v polyethylene glycol 3350 200 mM tri-potassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.146→96.318 Å / Num. obs: 24209 / % possible obs: 96.1 % / Redundancy: 39.5 % / CC1/2: 0.984 / Net I/σ(I): 23
Reflection shellResolution: 2.146→2.419 Å / Num. unique obs: 1210 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.146→96.318 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 23.142 / SU ML: 0.257 / Cross valid method: FREE R-VALUE / ESU R: 0.569 / ESU R Free: 0.321 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2684 1204 4.973 %
Rwork0.2036 23005 -
all0.207 --
obs-24209 55.9 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.272 Å2
Baniso -1Baniso -2Baniso -3
1-0.011 Å20.005 Å20 Å2
2--0.011 Å2-0 Å2
3----0.035 Å2
Refinement stepCycle: LAST / Resolution: 2.146→96.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 0 67 4696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124722
X-RAY DIFFRACTIONr_angle_refined_deg2.2841.8146391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.468523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83910831
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.35810213
X-RAY DIFFRACTIONr_chiral_restr0.1340.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023546
X-RAY DIFFRACTIONr_nbd_refined0.240.21959
X-RAY DIFFRACTIONr_nbtor_refined0.3150.23248
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2147
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.22
X-RAY DIFFRACTIONr_mcbond_it4.042.9722354
X-RAY DIFFRACTIONr_mcangle_it6.3295.3342927
X-RAY DIFFRACTIONr_scbond_it5.6393.2252368
X-RAY DIFFRACTIONr_scangle_it8.3325.7383464
X-RAY DIFFRACTIONr_lrange_it11.43535.60119244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc work% reflection obs (%)WRfactor RworkFsc free
2.146-2.20200.331910.33131310.882.90640.322
2.202-2.26200.3682020.36830650.8626.59050.372
2.262-2.3280.45870.3492690.35129710.8759.28980.3450.961
2.328-2.3990.536150.3414760.34728900.90416.98960.330.783
2.399-2.4780.348310.3255640.32628230.91221.07690.3030.912
2.478-2.5650.388310.3216830.32427160.92126.28870.2840.879
2.565-2.6610.426440.328610.32526210.92634.52880.2910.893
2.661-2.770.334830.31211100.31325560.93146.67450.2820.915
2.77-2.8930.377730.29416190.29824380.93569.40120.2540.881
2.893-3.0340.3221050.28221760.28423300.94197.8970.2480.933
3.034-3.1980.3661170.28121240.28522410.9431000.250.909
3.198-3.3920.338970.23420200.23821170.9631000.2110.92
3.392-3.6260.28840.21219120.21519960.971000.2020.947
3.626-3.9160.293940.18917810.19418750.9761000.1860.945
3.916-4.2890.251040.16816460.17317500.9821000.1730.96
4.289-4.7940.228770.14514970.14915740.9861000.1620.966
4.794-5.5330.221810.15513320.15914130.9851000.1820.969
5.533-6.7710.253700.18211440.18712140.9781000.2190.96
6.771-9.5520.191610.169230.1629840.9821000.2110.975
9.552-96.3180.228300.1995740.26040.9461000.3570.962
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)
10.67280.0008-0.57030.55140.27862.73150.0991-0.26440.13580.0503-0.20630.02420.00730.17640.10720.0532-0.0502-0.05190.2224-0.03730.281221.9729.338-19.45
25.37895.0101-4.611713.7589-0.411814.3066-0.1553-0.03850.13870.22110.1357-1.07630.11010.61790.01960.1984-0.02560.02450.0848-0.02510.275231.73829.008-50.259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp1 - 572
2X-RAY DIFFRACTION2ALLBp550 - 569

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