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- PDB-5onf: The ENTH domain from epsin-1 -

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Basic information

Entry
Database: PDB / ID: 5onf
TitleThe ENTH domain from epsin-1
ComponentsEpsin-1
KeywordsENDOCYTOSIS / adaptor protein complex
Function / homology
Function and homology information


Cargo recognition for clathrin-mediated endocytosis / actin cortical patch assembly / clathrin vesicle coat / cellular bud tip / cellular bud neck / mating projection tip / K63-linked polyubiquitin modification-dependent protein binding / clathrin binding / actin filament organization / ubiquitin binding ...Cargo recognition for clathrin-mediated endocytosis / actin cortical patch assembly / clathrin vesicle coat / cellular bud tip / cellular bud neck / mating projection tip / K63-linked polyubiquitin modification-dependent protein binding / clathrin binding / actin filament organization / ubiquitin binding / phospholipid binding / endocytosis / early endosome / endosome / plasma membrane / cytoplasm
Similarity search - Function
ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / ENTH domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #90 / ENTH/VHS / Ubiquitin-interacting motif. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGarcia-Alai, M. / GIeras, A. / Meijers, R.
CitationJournal: Nat Commun / Year: 2018
Title: Epsin and Sla2 form assemblies through phospholipid interfaces.
Authors: Garcia-Alai, M.M. / Heidemann, J. / Skruzny, M. / Gieras, A. / Mertens, H.D.T. / Svergun, D.I. / Kaksonen, M. / Uetrecht, C. / Meijers, R.
History
DepositionAug 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epsin-1
B: Epsin-1
C: Epsin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1354
Polymers54,0163
Non-polymers1181
Water00
1
A: Epsin-1
C: Epsin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1293
Polymers36,0112
Non-polymers1181
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epsin-1


Theoretical massNumber of molelcules
Total (without water)18,0051
Polymers18,0051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.929, 119.363, 129.542
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYHISHISAA15 - 11015 - 110
21GLYGLYHISHISBB15 - 11015 - 110
31GLYGLYHISHISCC15 - 11015 - 110
12GLNGLNILEILEAA120 - 147120 - 147
22GLNGLNILEILEBB120 - 147120 - 147
32GLNGLNILEILECC120 - 147120 - 147

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.497313, -0.867503, -0.010853), (-0.867536, 0.497367, -0.002759), (0.007791, 0.008043, -0.999937)-51.40252, -29.88401, 0.31751
3given(-0.494268, -0.869305, -0.002808), (0.869304, -0.494252, -0.005022), (0.002978, -0.004924, 0.999983)-86.08505, -29.37409, -0.24016

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Components

#1: Protein Epsin-1


Mass: 18005.471 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ENT1, YDL161W / Production host: Escherichia coli (E. coli) / References: UniProt: Q12518
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M CaCl2, 25 % PEG 3350 and 0.1 M Tris pH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.127 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.322
111/2H-1/2K, -3/2H-1/2K, -L20.285
111/2H+1/2K, 3/2H-1/2K, -L30.393
ReflectionResolution: 2.75→27 Å / Num. obs: 13379 / % possible obs: 99.1 % / Redundancy: 5.3 % / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→27.11 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 28.878 / SU ML: 0.55 / Cross valid method: THROUGHOUT / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2847 651 4.9 %RANDOM
Rwork0.27168 ---
obs0.27236 12691 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 126.471 Å2
Baniso -1Baniso -2Baniso -3
1-69.83 Å20 Å20 Å2
2--20.66 Å20 Å2
3----90.48 Å2
Refinement stepCycle: 1 / Resolution: 2.8→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 8 0 3623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193670
X-RAY DIFFRACTIONr_bond_other_d0.0020.023454
X-RAY DIFFRACTIONr_angle_refined_deg1.051.9554924
X-RAY DIFFRACTIONr_angle_other_deg0.91438007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2495438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.424.615195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53115729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5711530
X-RAY DIFFRACTIONr_chiral_restr0.0520.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024035
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02747
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.18812.6831761
X-RAY DIFFRACTIONr_mcbond_other6.18712.6821760
X-RAY DIFFRACTIONr_mcangle_it9.3219.0082196
X-RAY DIFFRACTIONr_mcangle_other9.31819.0092197
X-RAY DIFFRACTIONr_scbond_it5.13613.2151909
X-RAY DIFFRACTIONr_scbond_other5.13513.2171910
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.10919.6712729
X-RAY DIFFRACTIONr_long_range_B_refined12.264318
X-RAY DIFFRACTIONr_long_range_B_other12.2594319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1544medium positional0.790.5
11B1544medium positional0.80.5
11C1544medium positional0.710.5
22A457medium positional0.660.5
22B457medium positional1.020.5
22C457medium positional0.770.5
11A1544medium thermal9.922
11B1544medium thermal8.922
11C1544medium thermal7.172
22A457medium thermal8.482
22B457medium thermal9.742
22C457medium thermal9.422
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 46 -
Rwork0.401 928 -
obs--97.3 %

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