[English] 日本語
Yorodumi
- PDB-2xze: Structural basis for AMSH-ESCRT-III CHMP3 interaction -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xze
TitleStructural basis for AMSH-ESCRT-III CHMP3 interaction
Components
  • CHARGED MULTIVESICULAR BODY PROTEIN 3
  • STAM-BINDING PROTEIN
KeywordsHYDROLASE/PROTEIN TRANSPORT / HYDROLASE-PROTEIN TRANSPORT COMPLEX
Function / homology
Function and homology information


regulation of endosome size / negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / suppression of viral release by host / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule ...regulation of endosome size / negative regulation of hippocampal neuron apoptotic process / hippocampal neuron apoptotic process / suppression of viral release by host / multivesicular body-lysosome fusion / amphisome membrane / vesicle fusion with vacuole / late endosome to lysosome transport / ESCRT III complex / kinetochore microtubule / endosome transport via multivesicular body sorting pathway / regulation of centrosome duplication / nuclear membrane reassembly / multivesicular body sorting pathway / Sealing of the nuclear envelope (NE) by ESCRT-III / deubiquitinase activity / midbody abscission / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / membrane fission / plasma membrane repair / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / phosphatidylcholine binding / multivesicular body membrane / multivesicular body assembly / negative regulation of Ras protein signal transduction / regulation of mitotic spindle assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / regulation of early endosome to late endosome transport / molecular function inhibitor activity / K63-linked deubiquitinase activity / mitotic metaphase chromosome alignment / Macroautophagy / ubiquitin-specific protease binding / nucleus organization / viral budding via host ESCRT complex / positive regulation of cytokinesis / cleavage furrow / mitotic cytokinesis / viral release from host cell / autophagosome membrane / protein polymerization / autophagosome maturation / protein deubiquitination / cell surface receptor signaling pathway via JAK-STAT / Pyroptosis / nuclear pore / phosphatidylinositol-4,5-bisphosphate binding / multivesicular body / Endosomal Sorting Complex Required For Transport (ESCRT) / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / viral budding from plasma membrane / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / kinetochore / autophagy / Metalloprotease DUBs / late endosome / protein transport / Translation of Replicase and Assembly of the Replication Transcription Complex / midbody / cytoplasmic vesicle / early endosome / endosome / protein domain specific binding / lysosomal membrane / apoptotic process / positive regulation of cell population proliferation / proteolysis / extracellular exosome / nucleoplasm / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Snf7 family / Snf7 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Snf7 family / Snf7 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
STAM-binding protein / Charged multivesicular body protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsSolomons, J. / Sabin, C. / Weissenhorn, W.
Citation
Journal: Structure / Year: 2011
Title: Structural Basis for Escrt-III Chmp3 Recruitment of Amsh.
Authors: Solomons, J. / Sabin, C. / Poudevigne, E. / Usami, Y. / Hulsik, D.L. / Macheboeuf, P. / Hartlieb, B. / Gottlinger, H. / Weissenhorn, W.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Structural Basis for Autoinhibition of Escrt-III Chmp3.
Authors: Lata, S. / Roessle, M. / Solomons, J. / Jamin, M. / Gottlinger, H.G. / Svergun, D.I. / Weissenhorn, W.
History
DepositionNov 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STAM-BINDING PROTEIN
B: STAM-BINDING PROTEIN
Q: CHARGED MULTIVESICULAR BODY PROTEIN 3
R: CHARGED MULTIVESICULAR BODY PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)42,9894
Polymers42,9894
Non-polymers00
Water6,954386
1
B: STAM-BINDING PROTEIN
R: CHARGED MULTIVESICULAR BODY PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)21,4942
Polymers21,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-7.2 kcal/mol
Surface area9710 Å2
MethodPISA
2
A: STAM-BINDING PROTEIN
Q: CHARGED MULTIVESICULAR BODY PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)21,4942
Polymers21,4942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-4.7 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.970, 45.970, 206.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein STAM-BINDING PROTEIN / ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM / ENDOSOME-ASSOCIATED UBIQUITIN ISOPEPTIDASE


Mass: 17162.611 Da / Num. of mol.: 2 / Fragment: MIT DOMAIN, RESIDUES 1-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O95630, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein/peptide CHARGED MULTIVESICULAR BODY PROTEIN 3 / CHROMATIN-MODIFYING PROTEIN 3 / NEUROENDOCRINE DIFFERENTIATION FACTOR / VACUOLAR PROTEIN SORTING- ...CHROMATIN-MODIFYING PROTEIN 3 / NEUROENDOCRINE DIFFERENTIATION FACTOR / VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 24 / HVPS24 / CHMP3


Mass: 4331.674 Da / Num. of mol.: 2 / Fragment: C-TERM FRAGMENT, RESIDUES 183-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9Y3E7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 6
Details: 3.3 MG/ML OF AMSH PROTEIN IN 10 MM HEPES PH 8.0, 100 MM NACL WAS MIXED WITH AN EQUAL VOLUME WELL CONDITION: 2.2 M SODIUM MALONATE,WITH 30 % GLYCEROL AS CRYO-PROTECTANT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9760, 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009 / Details: TORODIAL FOCUSING MIRROR
RadiationMonochromator: U35 UNDULATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
20.97951
ReflectionResolution: 1.75→44.85 Å / Num. obs: 141404 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.1
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.75→51.71 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.52 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22694 2164 5 %RANDOM
Rwork0.19163 ---
obs0.19333 40725 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.212 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 386 3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.9953686
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6995329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.88424.366142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39415556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9981525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022069
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21376
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21901
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2320
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1361.51712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81722660
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.06431164
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.9614.51024
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
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 171 -
Rwork0.305 3014 -
obs--99.97 %

+
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