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- PDB-3r3q: Crystal structure of the yeast Vps23 UEV domain -

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Basic information

Entry
Database: PDB / ID: 3r3q
TitleCrystal structure of the yeast Vps23 UEV domain
ComponentsSuppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
KeywordsPROTEIN TRANSPORT / endosomal sorting / ESCRT-I
Function / homology
Function and homology information


negative regulation of protein polyubiquitination / ESCRT I complex / Endosomal Sorting Complex Required For Transport (ESCRT) / ATP export / 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 ...negative regulation of protein polyubiquitination / ESCRT I complex / Endosomal Sorting Complex Required For Transport (ESCRT) / ATP export / 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 / cytosol
Similarity search - Function
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 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...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 / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IMIDAZOLE / Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsRen, X. / Hurley, J.H.
CitationJournal: Embo J. / Year: 2011
Title: Structural basis for endosomal recruitment of ESCRT-I by ESCRT-0 in yeast.
Authors: Ren, X. / Hurley, J.H.
History
DepositionMar 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,35322
Polymers18,0101
Non-polymers1,34421
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.059, 47.139, 92.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Suppressor protein STP22 of temperature-sensitive alpha-factor receptor and arginine permease / ESCRT-I complex subunit VPS23 / Vacuolar protein sorting-associated protein 23


Mass: 18009.535 Da / Num. of mol.: 1 / Fragment: N-terminal UEV domain (UNP residues 1-160) / Mutation: C133A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: STP22, VPS23, YCL008C, YCL8C / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25604

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Non-polymers , 5 types, 143 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M zinc acetate, 0.1 M imidazole, 25% 1,2-propanediol, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2011 / 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: 1.45→50 Å / Num. all: 28882 / Num. obs: 27632 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13 % / Biso Wilson estimate: 10.11 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 22.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1389 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UZX

1uzx


Resolution: 1.45→33.618 Å / SU ML: 0.14 / σ(F): 0.14 / Phase error: 15.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1839 1399 5.06 %RANDOM
Rwork0.1642 ---
obs0.1652 27632 95.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.448 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6062 Å20 Å20 Å2
2--2.026 Å20 Å2
3---0.5802 Å2
Refinement stepCycle: LAST / Resolution: 1.45→33.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 61 122 1393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061332
X-RAY DIFFRACTIONf_angle_d1.0911815
X-RAY DIFFRACTIONf_dihedral_angle_d12.688464
X-RAY DIFFRACTIONf_chiral_restr0.071202
X-RAY DIFFRACTIONf_plane_restr0.007239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.50180.22581310.19892333X-RAY DIFFRACTION87
1.5018-1.5620.18831320.17882466X-RAY DIFFRACTION91
1.562-1.63310.18521270.15242550X-RAY DIFFRACTION94
1.6331-1.71920.16861310.14542530X-RAY DIFFRACTION94
1.7192-1.82690.14691370.13782606X-RAY DIFFRACTION96
1.8269-1.96790.16441300.1352668X-RAY DIFFRACTION97
1.9679-2.16590.15821330.14052689X-RAY DIFFRACTION98
2.1659-2.47920.19431400.15652740X-RAY DIFFRACTION99
2.4792-3.12320.18281670.16792749X-RAY DIFFRACTION100
3.1232-33.62680.19461710.18452902X-RAY DIFFRACTION100

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