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- PDB-3htu: Crystal structure of the human VPS25-VPS20 subcomplex -

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Basic information

Entry
Database: PDB / ID: 3htu
TitleCrystal structure of the human VPS25-VPS20 subcomplex
Components
  • Vacuolar protein-sorting-associated protein 20
  • Vacuolar protein-sorting-associated protein 25
KeywordsPROTEIN TRANSPORT / ESCRT-II / ESCRT-III / VPS20 / VPS25 / MVB / Cytoplasm / Nucleus / Polymorphism / Transcription / Transcription regulation / Transport / Coiled coil / Endosome / Lipoprotein / Membrane / Myristate
Function / homology
Function and homology information


ESCRT III complex assembly / ESCRT II complex / negative regulation of epidermal growth factor-activated receptor activity / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway ...ESCRT III complex assembly / ESCRT II complex / negative regulation of epidermal growth factor-activated receptor activity / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / nuclear membrane reassembly / Sealing of the nuclear envelope (NE) by ESCRT-III / multivesicular body sorting pathway / midbody abscission / membrane fission / plasma membrane repair / vesicle budding from membrane / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / multivesicular body membrane / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / mitotic metaphase chromosome alignment / Macroautophagy / nucleus organization / viral budding via host ESCRT complex / regulation of protein catabolic process / autophagosome membrane / autophagosome maturation / Pyroptosis / nuclear pore / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / protein-containing complex binding / structural molecule activity / protein homodimerization activity / extracellular exosome / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
ESCRT-II complex, Vps25 subunit, N-terminal winged helix / ESCRT-II complex, Vps25 subunit / ESCRT-II complex subunit / Snf7 family / Snf7 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / 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
Charged multivesicular body protein 6 / Vacuolar protein-sorting-associated protein 25
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIm, Y.J. / Hurley, J.H.
CitationJournal: Dev.Cell / Year: 2009
Title: Structure and function of the ESCRT-II-III interface in multivesicular body biogenesis.
Authors: Im, Y.J. / Wollert, T. / Boura, E. / Hurley, J.H.
History
DepositionJun 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar protein-sorting-associated protein 25
B: Vacuolar protein-sorting-associated protein 20
C: Vacuolar protein-sorting-associated protein 25
D: Vacuolar protein-sorting-associated protein 20
E: Vacuolar protein-sorting-associated protein 25
F: Vacuolar protein-sorting-associated protein 20
G: Vacuolar protein-sorting-associated protein 25
H: Vacuolar protein-sorting-associated protein 20


Theoretical massNumber of molelcules
Total (without water)54,9178
Polymers54,9178
Non-polymers00
Water3,837213
1
A: Vacuolar protein-sorting-associated protein 25
B: Vacuolar protein-sorting-associated protein 20


Theoretical massNumber of molelcules
Total (without water)13,7292
Polymers13,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-2.8 kcal/mol
Surface area7380 Å2
MethodPISA
2
C: Vacuolar protein-sorting-associated protein 25
D: Vacuolar protein-sorting-associated protein 20


Theoretical massNumber of molelcules
Total (without water)13,7292
Polymers13,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-3.7 kcal/mol
Surface area7240 Å2
MethodPISA
3
E: Vacuolar protein-sorting-associated protein 25
F: Vacuolar protein-sorting-associated protein 20


Theoretical massNumber of molelcules
Total (without water)13,7292
Polymers13,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-3.5 kcal/mol
Surface area6770 Å2
MethodPISA
4
G: Vacuolar protein-sorting-associated protein 25
H: Vacuolar protein-sorting-associated protein 20


Theoretical massNumber of molelcules
Total (without water)13,7292
Polymers13,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-0.9 kcal/mol
Surface area7260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.562, 51.043, 76.987
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Vacuolar protein-sorting-associated protein 25 / hVps25 / ESCRT-II complex subunit VPS25 / ELL-associated protein of 20 kDa / Dermal papilla-derived protein 9


Mass: 9024.925 Da / Num. of mol.: 4
Fragment: The C-terminal WH2 domain of VPS25: UNP residues 102-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DERP9, EAP20, VPS25 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q9BRG1
#2: Protein/peptide
Vacuolar protein-sorting-associated protein 20 / Chromatin-modifying protein 6 / Charged multivesicular body protein 6 / Vps20 / hVps20


Mass: 4704.398 Da / Num. of mol.: 4 / Fragment: The first helix of VPS20: UNP residues 11-48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHMP6, VPS20 / Plasmid: pST39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: Q96FZ7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 35% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 6, 2008 / 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→50 Å / Num. all: 31046 / Num. obs: 30553 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.059 / Net I/σ(I): 29.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.03 / Num. unique all: 2678 / Rsym value: 0.281 / % possible all: 87.6

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Processing

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

3cuo


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.97 / SU ML: 0.142 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27261 1544 5.1 %RANDOM
Rwork0.23862 ---
obs0.24035 28995 98.38 %-
all-30553 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.521 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.05 Å2
2--1.31 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 0 213 3870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223709
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.954974
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7475431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.13424.35223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.80815719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2251541
X-RAY DIFFRACTIONr_chiral_restr0.1050.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022865
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21715
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.22474
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2121
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1931.52240
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95723472
X-RAY DIFFRACTIONr_scbond_it2.53831658
X-RAY DIFFRACTIONr_scangle_it3.6474.51502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 94 -
Rwork0.207 1843 -
obs--84.73 %

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