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- PDB-2caz: ESCRT-I core -

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Basic information

Entry
Database: PDB / ID: 2caz
TitleESCRT-I core
Components
  • PROTEIN SRN2
  • SUPPRESSOR PROTEIN STP22 OF TEMPERATURE-SENSITIVE ALPHA-FACTOR RECEPTOR AND ARGININE PERMEASE
  • VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS28
KeywordsPROTEIN TRANSPORT / ESCRT / MVB / MULTIVESICULAR BODIES / ENDOSOME / LYSOSOME / PH DOMAIN / PROTEIN SORTING / VESICLE TRAFFICKING / UBIQUITIN / PHOSPHOINOSITIDE / PTDINS3P / VPS23 / VPS28 / VPS37 / VPS36 / COILED COIL / UBL CONJUGATION PATHWAY
Function / homology
Function and homology information


negative regulation of protein polyubiquitination / ESCRT I complex / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / endosome transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / ATP export / 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 / ubiquitin binding / protein modification process / cytoplasmic side of plasma membrane / 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) / Helix Hairpins / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / 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 / MAD / Resolution: 3.6 Å
AuthorsGill, D.J. / Teo, H. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Vallis, Y. / Emr, S.D. / Williams, R.L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Escrt-I Core and Escrt-II Glue Domain Structures Reveal Role for Glue in Linking to Escrt-I and Membranes.
Authors: Teo, H. / Gill, D.J. / Sun, J. / Perisic, O. / Veprintsev, D.B. / Wallis, Y. / Emr, S.D. / Williams, R.L.
History
DepositionDec 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 1.5May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)74,6616
Polymers74,6616
Non-polymers00
Water00
1
A: SUPPRESSOR PROTEIN STP22 OF TEMPERATURE-SENSITIVE ALPHA-FACTOR RECEPTOR AND ARGININE PERMEASE
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS28
C: PROTEIN SRN2


Theoretical massNumber of molelcules
Total (without water)37,3313
Polymers37,3313
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
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)37,3313
Polymers37,3313
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)167.914, 167.914, 50.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNARGARG1AA330 - 35127 - 48
211ASNASNARGARG1DD330 - 35127 - 48
121LEULEUILEILE1AA356 - 38053 - 77
221LEULEUILEILE1DD356 - 38053 - 77
112LYSLYSGLNGLN1BB32 - 9540 - 103
212LYSLYSGLNGLN1EE32 - 9540 - 103
122SERSERARGARG6BB96 - 114104 - 122
222SERSERARGARG6EE96 - 114104 - 122
113GLUGLUARGARG1CC155 - 17327 - 45
213GLUGLUARGARG1FF155 - 17327 - 45
123SERSERLYSLYS1CC177 - 20149 - 73
223SERSERLYSLYS1FF177 - 20149 - 73

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.86222, 0.50648, -0.00773), (-0.50631, 0.86218, 0.01718), (0.01536, -0.0109, 0.99982)-0.21481, -0.39757, -3.46403
2given(0.86796, 0.49642, -0.01495), (-0.49624, 0.86807, 0.01413), (0.01999, -0.00485, 0.99979)0.29356, 0.01556, -3.25638
3given(0.86503, 0.50136, -0.01893), (-0.50047, 0.86493, 0.03781), (0.03533, -0.02323, 0.99911)0.14139, 0.20282, -2.28402

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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: 9353.570 Da / Num. of mol.: 2 / Fragment: RESIDUES 305-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: POPCH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RILX / References: UniProt: P25604
#2: Protein VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS28


Mass: 17763.697 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: POPCH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RILX / References: UniProt: Q02767
#3: Protein PROTEIN SRN2 / VPS37


Mass: 10213.293 Da / Num. of mol.: 2 / Fragment: RESIDUES 130-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: POPCH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RILX / References: UniProt: Q99176
Compound detailsTHE ESCRT-I COMPLEX RECOGNIZES UBIQUITINATED MULTIVESICULAR BODY (MVB) CARGO. REQUIRED FOR NORMAL ...THE ESCRT-I COMPLEX RECOGNIZES UBIQUITINATED MULTIVESICULAR BODY (MVB) CARGO. REQUIRED FOR NORMAL ENDOCYTIC AND BIOSYNTHETIC TRAFFIC TO THE YEAST VACUOLE
Sequence detailsRESIDUES 305-385 RESIDUES 1-147 WITH N-TERMINAL MAHHHHHH AFFINITY TAG RESIDUES 130-213

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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: 2.8 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / pH: 7
Details: 8-10% PEG 8000, 8-9% ETHYLENE GLYCOL, 0.1 M HEPES (PH 7.0- 8.0), 17 DEG C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: May 6, 2005 / Details: TORROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.6→43 Å / Num. obs: 9610 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.21
Reflection shellResolution: 3.6→3.8 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 3.6→145.86 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.859 / SU B: 130.104 / SU ML: 0.822 / Cross valid method: THROUGHOUT / ESU R Free: 0.819
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.357 465 4.8 %RANDOM
Rwork0.328 ---
obs0.329 9187 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 1.8 Å / VDW probe radii: 1.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.51 Å2-1.75 Å20 Å2
2---3.51 Å20 Å2
3---5.26 Å2
Refinement stepCycle: LAST / Resolution: 3.6→145.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 0 0 3602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223651
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9674928
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8895430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.07624.973187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.61715711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5971524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022693
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2820.22143
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22613
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A399tight positional0.040.05
2B536tight positional0.030.05
3C376tight positional0.030.05
2B145loose positional1.175
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 45 -
Rwork0.397 648 -
obs--100 %

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