[English] 日本語
Yorodumi
- PDB-1w7p: The crystal structure of endosomal complex ESCRT-II (VPS22/VPS25/... -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / ATP export / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / ubiquitin binding ...ESCRT II complex / 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 / ATP export / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylinositol-3-phosphate binding / ubiquitin binding / macroautophagy / late endosome membrane / lipid binding / structural molecule activity / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more