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- PDB-3qil: Crystal structure analysis of the clathrin trimerization domain -

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Basic information

Entry
Database: PDB / ID: 3qil
TitleCrystal structure analysis of the clathrin trimerization domain
ComponentsClathrin heavy chain 1
KeywordsSTRUCTURAL PROTEIN / clathrin trimerization domain / ENDOCYTOSIS
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 / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / arrestin family protein binding / receptor-mediated endocytosis / intracellular protein transport / spindle / autophagy / disordered domain specific binding / melanosome / mitotic cell cycle / cell division / protein domain specific binding / structural molecule activity / mitochondrion / identical protein binding
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #730 / 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 ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #730 / 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. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Clathrin heavy chain 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.92 Å
AuthorsYbe, J.A. / Mishra, S. / Nix, J.
CitationJournal: Febs Lett. / Year: 2013
Title: Nuclear localization of clathrin involves a labile helix outside the trimerization domain.
Authors: Ybe, J.A. / Fontaine, S.N. / Stone, T. / Nix, J. / Lin, X. / Mishra, S.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Clathrin heavy chain 1
F: Clathrin heavy chain 1
G: Clathrin heavy chain 1
H: Clathrin heavy chain 1
I: Clathrin heavy chain 1
J: Clathrin heavy chain 1
K: Clathrin heavy chain 1
L: Clathrin heavy chain 1
M: Clathrin heavy chain 1
N: Clathrin heavy chain 1
O: Clathrin heavy chain 1
P: Clathrin heavy chain 1
Q: Clathrin heavy chain 1
R: Clathrin heavy chain 1
S: Clathrin heavy chain 1
T: Clathrin heavy chain 1
U: Clathrin heavy chain 1
V: Clathrin heavy chain 1
W: Clathrin heavy chain 1
X: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)354,21124
Polymers354,21124
Non-polymers00
Water0
1
A: Clathrin heavy chain 1
B: Clathrin heavy chain 1
C: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)44,2763
Polymers44,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Clathrin heavy chain 1
E: Clathrin heavy chain 1
F: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)44,2763
Polymers44,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Clathrin heavy chain 1
H: Clathrin heavy chain 1
I: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)44,2763
Polymers44,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Clathrin heavy chain 1
K: Clathrin heavy chain 1
L: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)44,2763
Polymers44,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Clathrin heavy chain 1
N: Clathrin heavy chain 1
O: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)44,2763
Polymers44,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Clathrin heavy chain 1
Q: Clathrin heavy chain 1
R: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)44,2763
Polymers44,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: Clathrin heavy chain 1
T: Clathrin heavy chain 1
U: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)44,2763
Polymers44,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
V: Clathrin heavy chain 1
W: Clathrin heavy chain 1
X: Clathrin heavy chain 1


Theoretical massNumber of molelcules
Total (without water)44,2763
Polymers44,2763
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)255.780, 255.780, 312.990
Angle α, β, γ (deg.)90.000, 90.000, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ...
Clathrin heavy chain 1


Mass: 14758.777 Da / Num. of mol.: 24 / Fragment: CLATHRIN TRIMERIZATION DOMAIN / Mutation: C1528A, T1585L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CLTC / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: P49951

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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: 5.56 Å3/Da / Density % sol: 77.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: NaCl, Imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 3.75→500 Å / Num. obs: 61002 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.75-3.887.350.5812.31100
3.88-4.047.270.4932.91100
4.04-4.227.390.3683.71100
4.22-4.457.360.2455.31100
4.45-4.727.380.1856.61100
4.72-5.097.380.1538.11100
5.09-5.67.40.1378.71100
5.6-6.417.330.10611.11100
6.41-8.077.320.05917.81100
8.07-54.586.810.03931.5199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.75 Å54.56 Å
Translation3.75 Å54.56 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7LDzdata scaling
PHASER1.3.2phasing
CNSrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.92→54.58 Å / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.386 5828 8.5 %
Rwork0.339 --
obs0.339 58944 86.1 %
Solvent computationBsol: 635.08 Å2
Displacement parametersBiso mean: 277.85 Å2
Refinement stepCycle: LAST / Resolution: 3.92→54.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23032 0 0 0 23032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it71.40975
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it93.712100
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.92→4.06 Å
RfactorNum. reflection% reflection
Rfree0.4271 433 -
Rwork0.4134 3706 -
obs--60.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param

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