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- PDB-1c9i: PEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROP... -

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Basic information

Entry
Database: PDB / ID: 1c9i
TitlePEPTIDE-IN-GROOVE INTERACTIONS LINK TARGET PROTEINS TO THE B-PROPELLER OF CLATHRIN
Components
  • B-ADAPTIN 3
  • CLATHRIN
KeywordsENDOCYTOSIS/EXOCYTOSIS / BETA-PROPELLER / HELICAL HAIRPIN / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Gap junction degradation / Formation of annular gap junctions / presynaptic endocytic zone membrane / Myb complex / clathrin light chain binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance ...RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Gap junction degradation / Formation of annular gap junctions / presynaptic endocytic zone membrane / Myb complex / clathrin light chain binding / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / negative regulation of hyaluronan biosynthetic process / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / clathrin complex / clathrin coat / WNT5A-dependent internalization of FZD4 / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / amyloid-beta clearance by transcytosis / transferrin transport / MHC class II antigen presentation / extrinsic component of synaptic vesicle membrane / clathrin coat of coated pit / mitotic spindle microtubule / Recycling pathway of L1 / clathrin coat disassembly / clathrin coat assembly / photoreceptor ribbon synapse / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / Clathrin-mediated endocytosis / membrane coat / clathrin-dependent endocytosis / protein serine/threonine kinase binding / retrograde transport, endosome to Golgi / negative regulation of protein localization to plasma membrane / clathrin-coated vesicle / ankyrin binding / low-density lipoprotein particle receptor binding / ubiquitin-specific protease binding / Golgi organization / synaptic vesicle endocytosis / mitotic spindle assembly / regulation of mitotic spindle organization / clathrin-coated pit / T-tubule / heat shock protein binding / receptor-mediated endocytosis / peptide binding / intracellular protein transport / clathrin-coated endocytic vesicle membrane / sarcolemma / terminal bouton / receptor internalization / spindle / autophagy / disordered domain specific binding / melanosome / double-stranded RNA binding / mitotic cell cycle / protein kinase binding / structural molecule activity / protein-containing complex / membrane / cytosol
Similarity search - Function
Clathrin heavy-chain terminal domain / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Region in Clathrin and VPS / Clathrin heavy chain repeat homology ...Clathrin heavy-chain terminal domain / Clathrin-H-link / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Region in Clathrin and VPS / 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
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
Authorster Haar, E. / Harrison, S.C. / Kirchhausen, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Peptide-in-groove interactions link target proteins to the beta-propeller of clathrin.
Authors: ter Haar, E. / Harrison, S.C. / Kirchhausen, T.
History
DepositionAug 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLATHRIN
B: CLATHRIN
C: B-ADAPTIN 3
D: B-ADAPTIN 3


Theoretical massNumber of molelcules
Total (without water)81,7404
Polymers81,7404
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.040, 131.275, 79.010
Angle α, β, γ (deg.)90.00, 116.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CLATHRIN /


Mass: 39953.879 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PBAT4 / Production host: Escherichia coli (E. coli) / References: UniProt: P11442
#2: Protein/peptide B-ADAPTIN 3


Mass: 916.028 Da / Num. of mol.: 2 / Fragment: CLATHRIN-BOX PEPTIDE / Mutation: D815A, D823A / Source method: obtained synthetically
Details: This peptide was chemically sythesized.The sequence of this peptide naturally occurs in humans (HOMO SAPIENS).

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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: 3.9 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, KOAc, DTT, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMpeptide1drop
2100 mMTris-HCl1drop
321 %PEG40001reservoir
4350 mMpotassium acetate1reservoir
51 mMdithiothreitol1reservoir
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 27038 / Num. obs: 27038 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.3
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.207 / % possible all: 94.6
Reflection shell
*PLUS
% possible obs: 94.6 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 2.9→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 277796.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1251 4.6 %RANDOM
Rwork0.227 ---
all0.227 27038 --
obs0.227 27038 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.83 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso mean: 19.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å211.46 Å2
2--1.78 Å20 Å2
3----4.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5672 0 0 0 5672
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.9
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 194 4.5 %
Rwork0.296 4157 -
obs--94.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PA / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.268
Solvent computation
*PLUS
Displacement parameters
*PLUS

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