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- PDB-3lvg: Crystal structure of a clathrin heavy chain and clathrin light ch... -

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Basic information

Entry
Database: PDB / ID: 3lvg
TitleCrystal structure of a clathrin heavy chain and clathrin light chain complex
Components
  • Clathrin heavy chain 1
  • Clathrin light chain B
KeywordsSTRUCTURAL PROTEIN / self assembly / Coated pit / Cytoplasmic vesicle / Membrane / Calcium
Function / homology
Function and homology information


postsynaptic endocytic zone cytoplasmic component / 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 ...postsynaptic endocytic zone cytoplasmic component / 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 / clathrin vesicle coat / Lysosome Vesicle Biogenesis / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin heavy chain binding / 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 / clathrin-dependent endocytosis / arrestin family protein binding / ciliary membrane / receptor-mediated endocytosis / intracellular protein transport / trans-Golgi network / synaptic vesicle membrane / spindle / autophagy / disordered domain specific binding / melanosome / mitotic cell cycle / cell division / protein domain specific binding / structural molecule activity / mitochondrion / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Clathrin light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / 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 light chain / Clathrin light chain signature 1. / Clathrin light chain signature 2. / Clathrin light chain / 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. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Clathrin light chain B / Clathrin heavy chain 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 7.94 Å
AuthorsWilbur, J.D. / Hwang, P.K. / Ybe, J.A. / Lane, M. / Sellers, B.D. / Jacobson, M.P. / Fletterick, R.J. / Brodsky, F.M.
CitationJournal: Dev.Cell / Year: 2010
Title: Conformation switching of clathrin light chain regulates clathrin lattice assembly.
Authors: Wilbur, J.D. / Hwang, P.K. / Ybe, J.A. / Lane, M. / Sellers, B.D. / Jacobson, M.P. / Fletterick, R.J. / Brodsky, F.M.
History
DepositionFeb 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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 light chain B
E: Clathrin light chain B
F: Clathrin light chain B


Theoretical massNumber of molelcules
Total (without water)273,9856
Polymers273,9856
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)228.560, 228.560, 710.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Clathrin heavy chain 1


Mass: 72180.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CLTC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49951
#2: Protein Clathrin light chain B / Lcb


Mass: 19147.379 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CLTB, CLTLB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04975
Sequence detailsFULL-LENGTH CLATHRIN LIGHT CHAIN B WAS USED IN THE CRYSTALLIZATION EXPERIMENT (UNIPROT ID P04975, ...FULL-LENGTH CLATHRIN LIGHT CHAIN B WAS USED IN THE CRYSTALLIZATION EXPERIMENT (UNIPROT ID P04975, 228 RESIDUES).

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 200mM citrate, 16-22% glycerol, 2% trifluoroethanol, vapor diffusion, hanging drop, temperature 298K
PH range: 4.0-5.0

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.017 Å
DetectorDetector: CCD / Date: Mar 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.017 Å / Relative weight: 1
ReflectionResolution: 7.9→250 Å / Num. obs: 10700 / Redundancy: 9 % / Rsym value: 0.075 / Net I/σ(I): 20
Reflection shellResolution: 7.9→8.55 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2079 / Rsym value: 0.882

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 7.94→100 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
Details: Due to the low resolution the side chain positions of UNK residues are undetermined though they were present in the phasing and refinement of the structure. Reflection data was processed ...Details: Due to the low resolution the side chain positions of UNK residues are undetermined though they were present in the phasing and refinement of the structure. Reflection data was processed using multiple resolution cutoffs. Initially, the highest resolution was 8.3A. To determine the best resolution for structure determination, maps were calculated with molecular replacement phases and manually inspected for increased structural details. For this manual determination of the resolution data was processed up to 5A resolution in an attempt to gain the highest resolution possible. The reflection data used for structure refinement was cutoff at 7.9A. Reflection data processed to a variety of other high resolution cutoffs can be obtained by sending a request to the authors.
RfactorNum. reflection% reflection
Rfree0.425 556 5.2 %
Rwork0.419 --
obs-10601 99.6 %
Solvent computationBsol: 164.754 Å2
Displacement parametersBiso max: 350.12 Å2 / Biso mean: 295.198 Å2 / Biso min: 232.2 Å2
Baniso -1Baniso -2Baniso -3
1--17.909 Å20 Å20 Å2
2---17.909 Å20 Å2
3---35.818 Å2
Refinement stepCycle: LAST / Resolution: 7.94→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16504 0 0 0 16504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_d2.853
Xplor fileSerial no: 1 / Param file: protein_rep.param

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