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- PDB-2f6m: Structure of a Vps23-C:Vps28-N subcomplex -

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Basic information

Entry
Database: PDB / ID: 2f6m
TitleStructure of a Vps23-C:Vps28-N subcomplex
Components
  • Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
  • Vacuolar protein sorting-associated protein VPS28
KeywordsTRANSPORT PROTEIN / endosomes / trafficking complex / Vps23 / Vps28 / Vacuole 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / ATP export / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to membrane / reticulophagy ...negative regulation of protein polyubiquitination / ESCRT I complex / Endosomal Sorting Complex Required For Transport (ESCRT) / ATP export / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to membrane / reticulophagy / ubiquitin binding / protein modification process / cytoplasmic side of plasma membrane / late endosome membrane / endosome / protein-containing complex binding / cytosol
Similarity search - Function
Vps28 N-terminal domain / Helix Hairpins - #820 / 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. ...Vps28 N-terminal domain / Helix Hairpins - #820 / 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 / de novo design (two linked rop proteins) / Helix Hairpins / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DECYLAMINE-N,N-DIMETHYL-N-OXIDE / Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease / Vacuolar protein sorting-associated protein 28
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 29, 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: Advisory / 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 1.4Feb 14, 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 VPS28
C: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
D: Vacuolar protein sorting-associated protein VPS28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,80413
Polymers40,1694
Non-polymers1,6359
Water72140
1
A: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
B: Vacuolar protein sorting-associated protein VPS28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1168
Polymers20,0852
Non-polymers1,0316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-22 kcal/mol
Surface area11970 Å2
MethodPISA
2
C: Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
D: Vacuolar protein sorting-associated protein VPS28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6895
Polymers20,0852
Non-polymers6043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-10 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.239, 119.252, 125.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Detailsthe asymmetric unit contains two units. complex 1 = chains A,B and complex 2 = chains C,D

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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


Mass: 12533.921 Da / Num. of mol.: 2 / Fragment: Vps28N-terminal domain (13-118) / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H27NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR ...Details: 5mg/ml protein solution containing 40 mM TRIS pH 7.4, 120 mM NaCl, and 20 mM DDAO was mixed with equal volume of crystallant containing 13% PEG 3350, 200 mM MgCl2 and 20% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9190, 0.9800
SYNCHROTRONAPS 22-ID20.9795
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 11, 2005
MARRESEARCH2CCDJul 29, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9191
20.981
30.97951
ReflectionResolution: 2.1→20 Å / Num. all: 26400 / Num. obs: 25067 / % possible obs: 97.9 % / Redundancy: 6.1 % / Rsym value: 0.075 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 2309 / Rsym value: 0.285 / % possible all: 87.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→19.51 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.451 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26096 1332 5 %RANDOM
Rwork0.24065 ---
obs0.24168 25067 100 %-
all-26400 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.108 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2--0.44 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2760 0 113 40 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222909
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.9853918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9075333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97825.034145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43615518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.561516
X-RAY DIFFRACTIONr_chiral_restr0.0590.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022094
X-RAY DIFFRACTIONr_nbd_refined0.1930.21267
X-RAY DIFFRACTIONr_nbtor_refined0.2920.22031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.28
X-RAY DIFFRACTIONr_mcbond_it0.4081.51741
X-RAY DIFFRACTIONr_mcangle_it0.67522746
X-RAY DIFFRACTIONr_scbond_it1.10631296
X-RAY DIFFRACTIONr_scangle_it1.7974.51172
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 74 -
Rwork0.234 1477 -
obs-1477 100 %
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)
13.5788-4.42250.76389.3596-2.27092.52660.030.04790.05810.1603-0.0633-0.1378-0.12570.18540.0333-0.3321-0.0605-0.0205-0.228-0.0274-0.236418.226110.624752.0683
215.5515-4.8693-16.21474.21622.779118.86790.5479-0.54221.1625-0.5560.44010.1423-1.10250.5872-0.9880.03610.0623-0.0047-0.1666-0.04390.0139.902628.066845.8802
35.9737-6.00367.123511.2751-9.086715.820.22460.2059-0.0657-0.5289-0.2055-0.48120.13160.7685-0.0191-0.277-0.01270.0834-0.0792-0.0261-0.144228.36089.330244.5775
47.8127-5.4622.925519.7429-13.458319.7396-0.2548-0.0863-0.6231-0.3806-0.0512-1.04551.00061.20810.306-0.14210.23850.11080.2656-0.07590.115635.5161-1.04244.9846
55.58-2.6785-4.750914.80430.291438.01330.75750.88140.6946-2.4435-0.513-2.4965-1.88583.1111-0.24450.4542-0.25510.32590.60680.04430.386131.309220.67539.92
615.3539-14.9692-6.166220.09546.61119.49660.0422-0.15920.59670.193-0.0571-1.0683-0.5181.03530.0149-0.2086-0.1397-0.04310.1861-0.02540.069235.207312.704852.0626
73.8355-3.15910.59156.4748-0.66742.77790.03590.11080.0375-0.23890.04840.14320.5459-0.0721-0.0844-0.1978-0.09-0.0539-0.242-0.0049-0.248811.3241-7.800553.5996
84.5956-2.21869.12823.2114-4.254118.14190.06710.1857-0.36680.27420.5798-0.37361.28810.4104-0.6470.60920.1833-0.0758-0.0418-0.0685-0.053121.3843-24.574648.8428
97.5717-9.8722-7.586718.20289.36648.98530.20330.2268-0.0856-0.6085-0.2430.70550.1123-0.40040.0397-0.1321-0.1605-0.1665-0.0483-0.0161-0.12412.5497-8.924345.1588
109.211-7.5952-1.45622.794111.533812.70860.64270.6852-0.1276-0.9094-0.86441.15320.0813-0.86870.2217-0.1938-0.0457-0.17660.15610.04620.0553-5.4450.44943.0393
1155.4095-9.575323.632176.4833-36.412368.7047-0.1656-1.6757-1.1076-4.10321.2941-0.16482.0932-1.2013-1.12850.5024-0.0581-0.01650.4203-0.16940.48841.3471-20.70735.0853
1227.5172-12.83215.963215.3691-0.296910.95560.22210.2593-1.1648-0.4079-0.32822.45160.5634-1.79880.10610.2816-0.3459-0.01060.3771-0.02030.3396-4.5296-14.708949.657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA321 - 3851 - 65
2X-RAY DIFFRACTION2BB12 - 303 - 21
3X-RAY DIFFRACTION3BB31 - 5822 - 49
4X-RAY DIFFRACTION4BB59 - 8250 - 73
5X-RAY DIFFRACTION5BB83 - 10074 - 91
6X-RAY DIFFRACTION6BB101 - 11892 - 109
7X-RAY DIFFRACTION7CC321 - 3831 - 63
8X-RAY DIFFRACTION8DD16 - 307 - 21
9X-RAY DIFFRACTION9DD31 - 5822 - 49
10X-RAY DIFFRACTION10DD59 - 8250 - 73
11X-RAY DIFFRACTION11DD83 - 9374 - 84
12X-RAY DIFFRACTION12DD94 - 11785 - 108

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