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- PDB-2p22: Structure of the Yeast ESCRT-I Heterotetramer Core -

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Basic information

Entry
Database: PDB / ID: 2p22
TitleStructure of the Yeast ESCRT-I Heterotetramer Core
Components
  • Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
  • Protein SRN2
  • Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
  • Vacuolar protein sorting-associated protein 28Vacuole
KeywordsTRANSPORT PROTEIN / Endosome / Trafficking complex / Vps23 / Vps28 / Vps37 / Mvb12 / 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 / negative regulation of protein-containing complex assembly / 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1830 / Multivesicular body sorting factor 12 / ESCRT-I subunit Mvb12 / ESCRT-1 complex, Vps37, fungi / Vps28 N-terminal domain / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1830 / Multivesicular body sorting factor 12 / ESCRT-I subunit Mvb12 / ESCRT-1 complex, Vps37, fungi / Vps28 N-terminal domain / 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. / 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 / Ubiquitin-conjugating enzyme/RWD-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease / Multivesicular body sorting factor 12 / Vacuolar protein sorting-associated protein 28 / Protein SRN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR / Resolution: 2.7 Å
AuthorsKostelansky, M.S. / Hurley, J.H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Molecular architecture and functional model of the complete yeast ESCRT-I heterotetramer.
Authors: Kostelansky, M.S. / Schluter, C. / Tam, Y.Y. / Lee, S. / Ghirlando, R. / Beach, B. / Conibear, E. / Hurley, J.H.
History
DepositionMar 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2015Group: Data collection
Revision 1.4Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.5Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6Apr 15, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs ..._reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _struct_ref_seq_dif.details
Revision 1.7Oct 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 1.8Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3028
Polymers65,9184
Non-polymers3844
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19180 Å2
ΔGint-208 kcal/mol
Surface area31050 Å2
MethodPISA
2
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,21032
Polymers263,67316
Non-polymers1,53716
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_544x,-y-1,-z-11
Buried area97340 Å2
ΔGint-1011 kcal/mol
Surface area103560 Å2
MethodPISA
3
C: Protein SRN2
hetero molecules

C: Protein SRN2
hetero molecules

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,60516
Polymers131,8368
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_544x,-y-1,-z-11
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area20860 Å2
ΔGint-254 kcal/mol
Surface area79590 Å2
MethodPISA
4
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,60516
Polymers131,8368
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area45080 Å2
ΔGint-469 kcal/mol
Surface area55370 Å2
MethodPISA
5
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,60516
Polymers131,8368
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_544x,-y-1,-z-11
Buried area39580 Å2
ΔGint-422 kcal/mol
Surface area60870 Å2
MethodPISA
6
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules

A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein 28
C: Protein SRN2
D: Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,60516
Polymers131,8368
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-11
Buried area40740 Å2
ΔGint-447 kcal/mol
Surface area59710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.054, 83.766, 269.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease / Vacuolar protein sorting-associated protein 23


Mass: 19903.428 Da / Num. of mol.: 1 / Fragment: Vps23 (215-385)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS23 / Plasmid: pst39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 RIL / References: UniProt: P25604
#2: Protein Vacuolar protein sorting-associated protein 28 / Vacuole


Mass: 13755.307 Da / Num. of mol.: 1 / Fragment: Vps28N-Terminal Domain (1-118) / Mutation: C101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPT28 / Plasmid: pst39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 RIL / References: UniProt: Q02767
#3: Protein Protein SRN2 / Vacuolar protein sorting-associated protein 37


Mass: 22598.469 Da / Num. of mol.: 1 / Fragment: Vps37 (22-213) / Mutation: C123A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VPS37 / Plasmid: pst39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 RIL / References: UniProt: Q99176
#4: Protein Hypothetical 12.0 kDa protein in ADE3-SER2 intergenic region


Mass: 9661.012 Da / Num. of mol.: 1 / Fragment: Mvb12 (4-81)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: Mvb12 / Plasmid: pst39 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 RIL / References: UniProt: P42939

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Non-polymers , 2 types, 26 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR ...Details: Crystals were grown by mixing 2 microL of 4 mg/mL protein in 50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM DTT with an equal volume of 100 mM citric acid (pH 4.0), 800 mM ammonium sulfate., VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.9795
SYNCHROTRONAPS 22-ID20.9795
SYNCHROTRONAPS 22-BM31.0332
SYNCHROTRONAPS 22-BM41.0688
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDJul 28, 2006
MARMOSAIC 300 mm CCD2CCDJul 28, 2006
MARMOSAIC 225 mm CCD3CCDAug 22, 2006
MARMOSAIC 225 mm CCD4CCDAug 22, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
3SINGLE WAVELENGTHMx-ray1
4SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.03321
31.06881
ReflectionResolution: 2.7→20 Å / Num. obs: 19506 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 66.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 29.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.75 / Num. unique obs: 1297 / Rsym value: 0.385 / % possible all: 61.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD, MIR / Resolution: 2.7→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2769929.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.315 988 5.1 %RANDOM
Rwork0.233 ---
obs0.233 19504 90.8 %-
all-0 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9151 Å2 / ksol: 0.288583 e/Å3
Displacement parametersBiso mean: 95.9 Å2
Baniso -1Baniso -2Baniso -3
1-43.12 Å20 Å20 Å2
2---12.13 Å20 Å2
3----30.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4337 0 20 22 4379
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it5.771.5
X-RAY DIFFRACTIONc_mcangle_it8.92
X-RAY DIFFRACTIONc_scbond_it9.492
X-RAY DIFFRACTIONc_scangle_it12.512.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.047 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.478 104 4.7 %
Rwork0.4 2109 -
obs-2213 62.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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