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- PDB-1w7p: The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/... -

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Basic information

Entry
Database: PDB / ID: 1w7p
TitleThe crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/VPS36)
Components
  • VPS22, YPL002C
  • VPS25, YJR102C
  • VPS36P, YLR417W
KeywordsPROTEIN TRANSPORT / ESCRT-II COMPLEX / ENDOSOMAL PROTEIN SORTING
Function / homology
Function and homology information


ESCRT II complex / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / ATP export / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / cytoplasm to vacuole targeting by the Cvt pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding ...ESCRT II complex / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / ATP export / protein retention in Golgi apparatus / Endosomal Sorting Complex Required For Transport (ESCRT) / cytoplasm to vacuole targeting by the Cvt pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / localization / ubiquitin binding / macroautophagy / late endosome membrane / lipid binding / structural molecule activity / protein homodimerization activity / metal ion binding / cytosol
Similarity search - Function
Helix Hairpins - #180 / ESCRT-2 complex, Snf8 / Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain / Vacuolar protein sorting 36 NZF-N zinc-finger domain / "Winged helix" DNA-binding domain. Chain C. Domain 1 / ESCRT-II complex, Vps25 subunit, N-terminal winged helix / ESCRT-II complex, Vps25 subunit / ESCRT-II complex subunit / Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 ...Helix Hairpins - #180 / ESCRT-2 complex, Snf8 / Vacuolar protein-sorting-associated protein 36, NZF-N zinc-finger domain / Vacuolar protein sorting 36 NZF-N zinc-finger domain / "Winged helix" DNA-binding domain. Chain C. Domain 1 / ESCRT-II complex, Vps25 subunit, N-terminal winged helix / ESCRT-II complex, Vps25 subunit / ESCRT-II complex subunit / Vacuolar protein sorting protein 36, GLUE domain / Vacuolar protein sorting protein 36 / Snf8/Vps36 family / EAP30/Vps36 family / Vacuolar protein sorting protein 36 Vps36 / GLUE domain profile. / Zinc finger domain / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein-sorting-associated protein 25 / Vacuolar protein-sorting-associated protein 36 / Vacuolar-sorting protein SNF8
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.6 Å
AuthorsTeo, H. / Perisic, O. / Gonzalez, B. / Williams, R.L.
Citation
Journal: Dev.Cell / Year: 2004
Title: Escrt-II, an Endosome-Associated Complex Required for Protein Sorting: Crystal Structure and Interactions with Escrt-III and Membranes
Authors: Teo, H. / Perisic, O. / Gonzalez, B. / Williams, R.L.
#1: Journal: Nature / Year: 2004
Title: Structure of the Escrt-II Endosomal Trafficking Complex
Authors: Hierro, A. / Sun, J. / Rusnak, A.S. / Kim, J. / Prag, G. / Emr, S.D. / Hurley, J.H.
History
DepositionSep 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 29, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 25, 2015Group: Data collection / Database references / Source and taxonomy
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: cell / chem_comp_atom ...cell / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim / struct_ncs_oper
Item: _cell.Z_PDB / _database_2.pdbx_DOI ..._cell.Z_PDB / _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 / _struct_ncs_oper.code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VPS22, YPL002C
B: VPS25, YJR102C
C: VPS25, YJR102C
D: VPS36P, YLR417W


Theoretical massNumber of molelcules
Total (without water)138,2464
Polymers138,2464
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-56.3 kcal/mol
Surface area50380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.908, 149.908, 186.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22C

NCS domain segments:

Refine code: 6

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROSERSERBB6 - 476 - 47
211PROPROSERSERCC6 - 476 - 47
121GLUGLUTRPTRPBB79 - 12579 - 125
221GLUGLUTRPTRPCC79 - 12579 - 125
112LYSLYSTRPTRPBB126 - 138126 - 138
212LYSLYSTRPTRPCC126 - 138126 - 138
122LEULEUGLUGLUBB145 - 192145 - 192
222LEULEUGLUGLUCC145 - 192145 - 192

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.9228, -0.3852, 0.0096), (0.3775, -0.9087, -0.1784), (0.0774, -0.161, 0.9839)
Vector: 226.5329, 68.7742, 19.5745)

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Components

#1: Protein VPS22, YPL002C / SNF8P


Mass: 26988.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q12483
#2: Protein VPS25, YJR102C / VPT25


Mass: 23582.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P47142
#3: Protein VPS36P, YLR417W / GRD12 / VAC3 / VPL11


Mass: 64092.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q06696
Sequence detailsTHE SAMPLE USED FOR CRYSTALLIZATION INCLUDED THE FULL LENGTH PROTEIN BUT IT APPEARS THAT CHAIN D ...THE SAMPLE USED FOR CRYSTALLIZATION INCLUDED THE FULL LENGTH PROTEIN BUT IT APPEARS THAT CHAIN D WAS PROTEOLYTICALLY CLEAVED DURING CRYSTALLIZATION SOLUTION AND IS ONLY VISIBLE IN ELECTRON DENSITY MAPS FROM RESIDUE D396 ONWARDS

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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: 6.09 Å3/Da / Density % sol: 79.64 %
Crystal growpH: 8.5
Details: 3.1% PEG35000, 0.1 M TRIS ACETATE PH 8.5, 1.36 M SODIUM FORMIATE, 19% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.055
DetectorType: MARRESEARCH / Detector: CCD / Date: May 31, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.055 Å / Relative weight: 1
ReflectionResolution: 3.6→92.06 Å / Num. obs: 24861 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.7
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.4 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
autoSHARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD / Resolution: 3.6→92.06 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.884 / SU B: 44.696 / SU ML: 0.616 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.615 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33 1216 4.9 %RANDOM
Rwork0.292 ---
obs0.294 23786 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å20 Å2
2---2.14 Å20 Å2
3---4.28 Å2
Refinement stepCycle: LAST / Resolution: 3.6→92.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6134 0 0 0 6134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226258
X-RAY DIFFRACTIONr_bond_other_d0.0030.025651
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9548454
X-RAY DIFFRACTIONr_angle_other_deg1.004313205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2715742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026784
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021249
X-RAY DIFFRACTIONr_nbd_refined0.2640.21803
X-RAY DIFFRACTIONr_nbd_other0.2450.27400
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.24005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3410.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1811.53729
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.35726067
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.55532529
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9244.52387
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 / Auth asym-ID: B / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11435loose positional0.615
2978loose positional1.055
11435loose thermal0.6410
2978loose thermal0.2310
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.467 83
Rwork0.489 1629
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)
12.2109-1.409-4.413912.2818.35185.27020.1069-0.07480.50910.7075-0.34411.0691-0.4991-1.69980.23721.44340.7477-0.2532.3604-0.15831.57269.504966.873158.7599
29.58950.83473.4644.06884.04429.45940.06611.3938-0.7395-1.5359-0.79860.49260.8998-0.68050.73252.0551-0.39580.12340.9265-0.39161.250588.658537.3105115.7012
36.9679-5.1942-3.8637-0.779-3.80978.2738-0.8201-0.1423-1.3271-0.22420.66450.4587-0.0698-1.82180.15562.4315-0.703-0.22551.4061-0.76332.587167.529221.9275113.8356
417.6583-2.1202-1.30686.16771.107112.2308-0.6435-0.5549-1.0020.07290.02330.29850.8265-0.74660.62020.68-0.17470.28660.72740.10940.747486.701839.7446159.625
57.91224.1496-2.959611.5851-2.805712.67220.1136-0.0080.2703-1.7373-0.2829-0.698-0.82870.83850.16931.4228-0.15930.37240.3510.08310.6438104.156757.4548126.9101
610.5441-0.9621-6.272710.2595-1.937614.4466-0.6778-0.2917-1.5599-0.279-0.0512-0.78720.82350.2510.7290.90730.10370.52470.53110.16361.3215107.372335.7516144.8605
713.01090.9882-0.97884.92371.58526.30740.14530.8204-0.0148-0.5297-0.0902-1.47-0.95291.8236-0.0551.0479-0.37431.15461.79110.48751.7607131.381547.6863134.1777
81.3736-5.93814.39112.63160.05837.46590.31360.00190.14091.13930.2747-0.5320.40880.5705-0.58821.5035-0.72830.75422.76760.35212.6653156.858154.0194133.4906
916.29470.552-9.37398.402-3.317613.5011-0.38870.1141-0.2649-0.98720.14770.5968-0.4591-1.08080.2410.9977-0.0301-0.02990.4357-0.09860.494986.946553.612141.2572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 90
2X-RAY DIFFRACTION2B1 - 125
3X-RAY DIFFRACTION3B126 - 201
4X-RAY DIFFRACTION4D396 - 493
5X-RAY DIFFRACTION5A165 - 232
6X-RAY DIFFRACTION6D494 - 566
7X-RAY DIFFRACTION7C1 - 125
8X-RAY DIFFRACTION8C126 - 201
9X-RAY DIFFRACTION9A91 - 164

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