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- PDB-3cuq: Integrated structural and functional model of the human ESCRT-II ... -

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Basic information

Entry
Database: PDB / ID: 3cuq
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 / channel regulator activity ...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 / channel regulator activity / phosphatidylinositol-3-phosphate binding / endocytic recycling / regulation of protein catabolic process / localization / 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 / structural molecule activity / perinuclear region of cytoplasm / protein homodimerization activity / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / MIR / Resolution: 2.61 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 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 20, 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

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)92,2434
Polymers92,2434
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-61.6 kcal/mol
Surface area36170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.162, 89.153, 91.437
Angle α, β, γ (deg.)90.00, 101.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26243.051 Da / Num. of mol.: 1 / Fragment: UNP residues 25-258
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: 24456.402 Da / Num. of mol.: 1 / Fragment: UNP residues 169-386
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: 20771.682 Da / Num. of mol.: 2
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.: 38 / 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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5% PEG4000, 15% Glycerol, 100mM Na-Acetate, pH4.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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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: Apr 8, 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: 2.6→50 Å / Num. all: 31993 / Num. obs: 30680 / % possible obs: 91.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Biso Wilson estimate: 38.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 33.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.13 / Num. unique all: 2343 / Rsym value: 0.302 / % possible all: 61.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.61→44.8 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.89 / SU B: 29.042 / SU ML: 0.294 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.601 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29804 1532 5 %RANDOM
Rwork0.23773 ---
obs0.24074 29133 90.95 %-
all-30665 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.494 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.46 Å2
2---3.45 Å20 Å2
3---3.95 Å2
Refinement stepCycle: LAST / Resolution: 2.61→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5592 0 0 38 5630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225704
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9667689
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.065688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25224.659264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.387151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2851532
X-RAY DIFFRACTIONr_chiral_restr0.1110.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024217
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.22704
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23913
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7661.53550
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31625548
X-RAY DIFFRACTIONr_scbond_it1.83532457
X-RAY DIFFRACTIONr_scangle_it2.9914.52141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 63 -
Rwork0.417 1319 -
obs--55.88 %
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)
112.5653-1.85553.07435.14491.04493.4044-0.4653-1.2449-1.27851.55980.27470.6111.3054-0.40810.19061.3177-0.11070.30890.2580.45040.0554-48.6717.44734.233
21.6836-0.4173-0.44797.72631.0374.233-0.15290.0429-0.14281.44620.3161-0.1621-0.00920.0785-0.16320.33360.0793-0.077-0.21620.05130.2281-36.8225.66815.371
33.66192.844-1.128910.0430.99643.6827-0.0239-0.27020.2895-0.31850.06550.28880.0785-0.0982-0.04160.0716-0.0336-0.0483-0.1859-0.0010.2511-34.36322.496-8.583
434.43647.832620.158213.25753.497711.90320.6735-0.2481-2.64310.1931.35812.12072.0877-1.8463-2.03151.08930.2561.11640.28210.2960.6017-61.64531.8627.896
52.3552-0.2504-0.38868.9744-0.27444.7948-0.25710.18840.08621.93430.40630.7339-0.0605-0.2845-0.14920.48860.16190.2093-0.28910.01490.2351-46.29543.70517.818
62.4854-1.2166-0.17244.34090.97644.197-0.05220.1444-0.0749-0.21310.03950.448-0.119-0.25610.01270.0774-0.0234-0.1621-0.10220.02750.4307-42.75348.126-8.432
75.10564.785-0.72567.2635-0.91880.9709-0.28230.0404-0.3623-0.3628-0.0496-1.45880.06440.20060.3320.25680.00910.1046-0.15480.07330.6693-13.19535.613-13.026
89.94623.17561.827912.09660.368812.7569-0.4039-0.25630.61230.51420.81680.0491-0.7516-0.7562-0.4129-0.6047-0.10280.0606-0.29190.04570.94933.4957.143-3.25
94.45540.34322.72829.2249-0.10086.52550.65391.3919-1.3965-2.1665-0.3911.65780.8771-0.4522-0.26290.83370.0164-0.90270.4153-0.50660.4678-52.29137.157-30.797
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 - 252
5X-RAY DIFFRACTION4B212 - 236
6X-RAY DIFFRACTION5B237 - 316
7X-RAY DIFFRACTION6B317 - 385
8X-RAY DIFFRACTION7C4 - 103
9X-RAY DIFFRACTION8C104 - 176
10X-RAY DIFFRACTION9D6 - 101

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