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- PDB-2zme: Integrated structural and functional model of the human ESCRT-II ... -

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Basic information

Entry
Database: PDB / ID: 2zme
TitleIntegrated structural and functional model of the human ESCRT-II complex
Components
  • Vacuolar protein-sorting-associated protein 25
  • Vacuolar protein-sorting-associated protein 36
  • Vacuolar-sorting protein SNF8
KeywordsPROTEIN TRANSPORT / ESCRT / Sorting / MBV / vps / Nucleus / Transcription / Transcription regulation / Transport / Endosome / Lipid-binding
Function / homology
Function and homology information


ESCRT II complex / negative regulation of epidermal growth factor-activated receptor activity / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of protein complex stability / multivesicular body sorting pathway / membrane fission / early endosome to late endosome transport / positive regulation of exosomal secretion / multivesicular body assembly / endocytic recycling ...ESCRT II complex / negative regulation of epidermal growth factor-activated receptor activity / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / regulation of protein complex stability / multivesicular body sorting pathway / membrane fission / early endosome to late endosome transport / positive regulation of exosomal secretion / multivesicular body assembly / endocytic recycling / phosphatidylinositol-3-phosphate binding / regulation of protein catabolic process / channel regulator activity / Endosomal Sorting Complex Required For Transport (ESCRT) / HCMV Late Events / ubiquitin binding / macroautophagy / recycling endosome / positive regulation of protein catabolic process / late endosome membrane / transcription regulator complex / lysosome / endosome membrane / endosome / intracellular membrane-bounded organelle / lipid binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / structural molecule activity / protein homodimerization activity / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #260 / ESCRT-2 complex, Snf8 / "Winged helix" DNA-binding domain. Chain C. Domain 1 / ESCRT-II complex, Vps25 subunit, N-terminal winged helix / ESCRT-II complex, Vps25 subunit / ESCRT-II complex subunit / Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family ...Helix Hairpins - #260 / ESCRT-2 complex, Snf8 / "Winged helix" DNA-binding domain. Chain C. Domain 1 / ESCRT-II complex, Vps25 subunit, N-terminal winged helix / ESCRT-II complex, Vps25 subunit / ESCRT-II complex subunit / Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein-sorting-associated protein 36 / Vacuolar-sorting protein SNF8 / Vacuolar protein-sorting-associated protein 25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsIm, Y.J. / Hurley, J.H.
CitationJournal: Dev.Cell / Year: 2008
Title: Integrated structural model and membrane targeting mechanism of the human ESCRT-II complex
Authors: Im, Y.J. / Hurley, J.H.
History
DepositionApr 17, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 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

Downloads & links

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Assembly

Deposited unit
A: Vacuolar-sorting protein SNF8
B: Vacuolar protein-sorting-associated protein 36
C: Vacuolar protein-sorting-associated protein 25
D: Vacuolar protein-sorting-associated protein 25


Theoretical massNumber of molelcules
Total (without water)80,1334
Polymers80,1334
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-59.7 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.480, 81.480, 226.244
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein Vacuolar-sorting protein SNF8 / ELL-associated protein of 30 kDa


Mass: 28903.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNF8, EAP30 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q96H20
#2: Protein Vacuolar protein-sorting-associated protein 36 / ELL-associated protein of 45 kDa


Mass: 26753.189 Da / Num. of mol.: 1 / Fragment: UNP residues 149-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS36, C13orf9, EAP45 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q86VN1
#3: Protein Vacuolar protein-sorting-associated protein 25 / hVps25 / ELL-associated protein of 20 kDa / Dermal papilla-derived protein 9


Mass: 12238.329 Da / Num. of mol.: 2 / Fragment: UNP residues 1-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS25, DERP9, EAP20 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q9BRG1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 40% PEG300, 0.1M Tris-HCl, pH8.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 19966 / Num. obs: 19408 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 100.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 41.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.25 / Num. unique all: 1915 / Rsym value: 0.429 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CUQ

3cuq


Resolution: 2.9→40.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.883 / SU B: 46.029 / SU ML: 0.423 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31277 990 5.1 %RANDOM
Rwork0.21423 ---
obs0.21928 18368 99.54 %-
all-19408 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.362 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.9→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 0 72 5127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225155
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.9716946
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1915624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9724.652230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.49715991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1131528
X-RAY DIFFRACTIONr_chiral_restr0.1150.2773
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023781
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2710.22761
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.23536
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.53201
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31725038
X-RAY DIFFRACTIONr_scbond_it1.74932212
X-RAY DIFFRACTIONr_scangle_it2.9814.51908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 82 -
Rwork0.3 1306 -
obs--98.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9722-3.086-1.54665.54643.41314.9478-0.26890.36091.4182-0.71260.1688-0.3138-0.58170.34740.10020.3583-0.3857-0.32940.13080.36070.0867-2.2571.013-16.443
22.64030.93781.20552.94111.38691.5809-0.15350.20580.2026-0.04360.23450.3075-0.13820.1106-0.0810.0864-0.2042-0.16790.17350.2041-0.008-16.522-17.806-13.995
31.0934-0.21821.03790.6749-0.96382.43110.04560.16990.03170.0576-0.1630.0716-0.1140.14820.11740.0331-0.0604-0.13490.1150.0630.0709-32.344-33.449-26.169
414.32283.1016-5.35931.3093-2.71225.7810.71050.8714-0.8227-1.2672-0.1736-1.55760.86380.1156-0.53690.2393-0.413-0.07390.236-0.08970.69314.136-15.701-21.125
53.3621.62330.35566.82421.19552.90740.0351-0.0182-0.41820.68580.3883-0.7146-0.00910.3998-0.42340.0111-0.0832-0.350.22060.0102-0.0003-0.06-28.785-8.359
64.89940.83042.92075.66413.88683.8240.06550.2513-0.02380.64040.2113-0.63210.58340.3403-0.27680.08980.0118-0.17020.05470.07720.0674-12.515-50.489-15.977
71.68262.1153-1.02972.9421-1.31593.10290.18050.0832-0.08240.4624-0.36180.42760.0235-0.12440.18130.1343-0.18030.09160.07490.05340.1238-42.292-43.39-5.182
81.27851.10990.45533.99193.21697.0787-0.20111.17560.259-0.19720.4353-0.17210.3095-0.1771-0.23420.0327-0.0919-0.02960.4937-0.0717-0.0872-21.228-59.077-39.661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 74
2X-RAY DIFFRACTION1B172 - 201
3X-RAY DIFFRACTION2A75 - 173
4X-RAY DIFFRACTION3A174 - 250
5X-RAY DIFFRACTION4B202 - 236
6X-RAY DIFFRACTION5B237 - 316
7X-RAY DIFFRACTION6B317 - 385
8X-RAY DIFFRACTION7C4 - 102
9X-RAY DIFFRACTION8D6 - 101

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