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- PDB-2f66: Structure of the ESCRT-I endosomal trafficking complex -

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Basic information

Entry
Database: PDB / ID: 2f66
TitleStructure of the ESCRT-I endosomal trafficking complex
Components
  • Protein SRN2
  • Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
  • Vacuolar protein sorting-associated protein VPS28Vacuole
KeywordsTRANSPORT PROTEIN / Endosome / Trafficking complex / Vps23 / Vps28 / Vps37 / Vacuolar Protein Sorting / ESCRT protein complexes / Endosomal Sorting Complex Required for Transport / ESCRT-I / ubiquitin / Tsg101
Function / homology
Function and homology information


negative regulation of protein polyubiquitination / ESCRT I complex / ATP export / endosome transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / vacuolar transport / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / reticulophagy ...negative regulation of protein polyubiquitination / ESCRT I complex / ATP export / endosome transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / vacuolar transport / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / reticulophagy / protein targeting to membrane / endosome to lysosome transport / ubiquitin binding / protein modification process / cytoplasmic side of plasma membrane / protein transport / late endosome membrane / endosome / protein-containing complex binding / nucleus / cytosol
Similarity search - Function
ESCRT-1 complex, Vps37, fungi / Vps28 N-terminal domain / Helix Hairpins - #820 / Modifier of rudimentary, Modr / Modifier of rudimentary (Mod(r)) protein / VPS37 C-terminal domain profile. / Vacuolar protein sorting-associated Vps28 / Vacuolar protein sorting-associated, VPS28, N-terminal / Vacuolar protein sorting-associated, VPS28, C-terminal / VPS28, C-terminal domain superfamily ...ESCRT-1 complex, Vps37, fungi / Vps28 N-terminal domain / Helix Hairpins - #820 / Modifier of rudimentary, Modr / Modifier of rudimentary (Mod(r)) protein / VPS37 C-terminal domain profile. / Vacuolar protein sorting-associated Vps28 / Vacuolar protein sorting-associated, VPS28, N-terminal / Vacuolar protein sorting-associated, VPS28, C-terminal / VPS28, C-terminal domain superfamily / VPS28, N-terminal domain superfamily / VPS28 protein / VPS28 C-terminal domain profile. / VPS28 N-terminal domain profile. / Helix hairpin bin / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / UEV domain / UEV domain profile. / ESCRT assembly domain / Helix hairpin bin domain superfamily / de novo design (two linked rop proteins) / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Helix Hairpins / Ubiquitin-conjugating enzyme/RWD-like / Helix non-globular / Special / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease / Vacuolar protein sorting-associated protein 28 / Protein SRN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKostelansky, M.S. / Lee, S. / Kim, J. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Structural and functional organization of the ESCRT-I trafficking complex.
Authors: Kostelansky, M.S. / Sun, J. / Lee, S. / Kim, J. / Ghirlando, R. / Hierro, A. / Emr, S.D. / Hurley, J.H.
History
DepositionNov 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein VPS28
C: Protein SRN2
D: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
E: Vacuolar protein sorting-associated protein VPS28
F: Protein SRN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5558
Polymers61,3636
Non-polymers1922
Water41423
1
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein VPS28
C: Protein SRN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8735
Polymers30,6813
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-54 kcal/mol
Surface area15030 Å2
MethodPISA
2
D: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
E: Vacuolar protein sorting-associated protein VPS28
F: Protein SRN2


Theoretical massNumber of molelcules
Total (without water)30,6813
Polymers30,6813
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-31 kcal/mol
Surface area14810 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-133 kcal/mol
Surface area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.003, 144.644, 119.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease / Vacuolar protein sorting-associated protein VPS23


Mass: 7550.657 Da / Num. of mol.: 2 / Fragment: Vps23C-Terminal Domain (322-385) / Mutation: C344A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: STP22, VPS23 / Plasmid: pST39 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: P25604
#2: Protein Vacuolar protein sorting-associated protein VPS28 / Vacuole


Mass: 13296.793 Da / Num. of mol.: 2 / Fragment: Vps28N-Terminal Domain (13-125) / Mutation: C101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS28, VPT28 / Plasmid: pST39 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: Q02767
#3: Protein Protein SRN2


Mass: 9833.885 Da / Num. of mol.: 2 / Fragment: Vps37C-Terminal Domain (132-213)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SRN2, VPS37 / Plasmid: pST39 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: Q99176
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100mM trisodium citrate (pH 5.6), 900mM lithium sulfate, 500mM ammonium sulfate, 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: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 17885 / Num. obs: 17872 / % possible obs: 95.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 62.9 Å2 / Rsym value: 0.088 / Net I/σ(I): 15.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 17885 / Rsym value: 0.449 / % possible all: 76.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Vps23C/Vps28N complex structure, PDB Code 2F6M

2f6m


Resolution: 2.8→19.93 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2114242.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 905 5.1 %RANDOM
Rwork0.203 ---
all-17885 --
obs-17872 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9325 Å2 / ksol: 0.35178 e/Å3
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1--10.54 Å20 Å20 Å2
2--11.51 Å20 Å2
3----0.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 10 23 3978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d16.8
X-RAY DIFFRACTIONc_improper_angle_d0.67
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 115 4.7 %
Rwork0.291 2355 -
obs-2355 80.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4_xplor.paramso4_xplor.top

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