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- PDB-2qy7: Crystal structure of human epsinR ENTH domain -

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Basic information

Entry
Database: PDB / ID: 2qy7
TitleCrystal structure of human epsinR ENTH domain
ComponentsClathrin interactor 1
KeywordsPROTEIN BINDING / ENTH domain / epsin / Alternative splicing / Cytoplasm / Cytoplasmic vesicle / Endocytosis / Lipid-binding / Membrane / Phosphorylation
Function / homology
Function and homology information


clathrin vesicle coat / clathrin coat assembly / clathrin binding / Golgi Associated Vesicle Biogenesis / phospholipid binding / endocytosis / endosome / cadherin binding / intracellular membrane-bounded organelle / perinuclear region of cytoplasm ...clathrin vesicle coat / clathrin coat assembly / clathrin binding / Golgi Associated Vesicle Biogenesis / phospholipid binding / endocytosis / endosome / cadherin binding / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / membrane / plasma membrane / cytosol
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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Clathrin interactor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiller, S.E. / Collins, B.M. / McCoy, A.J. / Robinson, M.S. / Owen, D.J.
CitationJournal: Nature / Year: 2007
Title: A SNARE-adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles.
Authors: Miller, S.E. / Collins, B.M. / McCoy, A.J. / Robinson, M.S. / Owen, D.J.
History
DepositionAug 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

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Assembly

Deposited unit
A: Clathrin interactor 1
B: Clathrin interactor 1
C: Clathrin interactor 1


Theoretical massNumber of molelcules
Total (without water)52,3043
Polymers52,3043
Non-polymers00
Water5,783321
1
A: Clathrin interactor 1


Theoretical massNumber of molelcules
Total (without water)17,4351
Polymers17,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Clathrin interactor 1


Theoretical massNumber of molelcules
Total (without water)17,4351
Polymers17,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Clathrin interactor 1


Theoretical massNumber of molelcules
Total (without water)17,4351
Polymers17,4351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.455, 91.122, 52.893
Angle α, β, γ (deg.)90.00, 107.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Clathrin interactor 1 / Epsin-4 / Epsin-related protein / EpsinR / Enthoprotin / Clathrin-interacting protein localized in ...Epsin-4 / Epsin-related protein / EpsinR / Enthoprotin / Clathrin-interacting protein localized in the trans- Golgi region / Clint


Mass: 17434.732 Da / Num. of mol.: 3 / Fragment: epsinR ENTH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLINT1, ENTH, EPN4, EPNR, KIAA0171 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q14677
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 39.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 30% (w/v) PEG3000, 100 mM CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9816 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9816 Å / Relative weight: 1
ReflectionResolution: 2→36.4 Å / Num. obs: 28679 / % possible obs: 99.1 % / Observed criterion σ(F): 3.5 / Redundancy: 4.4 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.5 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.263 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25465 1439 5 %RANDOM
Rwork0.20369 ---
obs0.20628 27096 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.049 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.1 Å2
2--0.06 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 0 321 3747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223489
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9534674
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4755405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20523.846195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65315693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4661536
X-RAY DIFFRACTIONr_chiral_restr0.0890.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022652
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21835
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22364
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.2116
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.871.52111
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38523255
X-RAY DIFFRACTIONr_scbond_it2.06631596
X-RAY DIFFRACTIONr_scangle_it3.3624.51419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 111 -
Rwork0.219 1928 -
obs--95.82 %

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