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- PDB-5wf9: Tepsin tENTH domain 1-153 -

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Basic information

Entry
Database: PDB / ID: 5wf9
TitleTepsin tENTH domain 1-153
ComponentsAP-4 complex accessory subunit Tepsin
KeywordsPROTEIN TRANSPORT / protein trafficking
Function / homology
Function and homology information


coated vesicle membrane / extrinsic component of organelle membrane / trans-Golgi network membrane / nuclear membrane / nuclear speck / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
Tepsin, ENTH/VHS domain / AP-4 complex accessory subunit Tepsin / ENTH domain / ENTH domain / ENTH/VHS
Similarity search - Domain/homology
AP-4 complex accessory subunit Tepsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArchuleta, T.L. / Jackson, L.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119525 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)T32MH65215-12 United States
CitationJournal: Traffic / Year: 2017
Title: Structure and evolution of ENTH and VHS/ENTH-like domains in tepsin.
Authors: Archuleta, T.L. / Frazier, M.N. / Monken, A.E. / Kendall, A.K. / Harp, J. / McCoy, A.J. / Creanza, N. / Jackson, L.P.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: AP-4 complex accessory subunit Tepsin


Theoretical massNumber of molelcules
Total (without water)16,8661
Polymers16,8661
Non-polymers00
Water99155
1
A: AP-4 complex accessory subunit Tepsin

A: AP-4 complex accessory subunit Tepsin

A: AP-4 complex accessory subunit Tepsin

A: AP-4 complex accessory subunit Tepsin


Theoretical massNumber of molelcules
Total (without water)67,4664
Polymers67,4664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Buried area4780 Å2
ΔGint-29 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.180, 90.180, 42.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-253-

HOH

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Components

#1: Protein AP-4 complex accessory subunit Tepsin / ENTH domain-containing protein 2 / Epsin for AP-4 / Tetra-epsin


Mass: 16866.463 Da / Num. of mol.: 1 / Fragment: UNP residues 1-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEPSIN, C17orf56, ENTHD2 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q96N21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 150mM MES monohydrate pH 6.0, 15% (w/v) PEG6000.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→63.8 Å / Num. obs: 16739 / % possible obs: 98.9 % / Redundancy: 26.8 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.02 / Net I/σ(I): 24.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 17.4 % / Rmerge(I) obs: 1.905 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1518 / CC1/2: 0.534 / Rpim(I) all: 0.462 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WFB

5wfb


Resolution: 1.8→45.09 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 837 5 %
Rwork0.1891 --
obs0.1907 16732 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 0 55 1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041033
X-RAY DIFFRACTIONf_angle_d0.6451398
X-RAY DIFFRACTIONf_dihedral_angle_d9.071625
X-RAY DIFFRACTIONf_chiral_restr0.036157
X-RAY DIFFRACTIONf_plane_restr0.004179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.27161300.24922468X-RAY DIFFRACTION94
1.9128-2.06050.2311380.18962611X-RAY DIFFRACTION100
2.0605-2.26790.17941390.16032637X-RAY DIFFRACTION100
2.2679-2.5960.19711390.15832645X-RAY DIFFRACTION100
2.596-3.27050.21061420.17712704X-RAY DIFFRACTION100
3.2705-45.10410.23381490.20472831X-RAY DIFFRACTION100

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