[English] 日本語
Yorodumi
- PDB-8e22: VPS37A_21-148 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8.0E+22
TitleVPS37A_21-148
ComponentsVacuolar protein sorting-associated protein 37A
KeywordsSTRUCTURAL PROTEIN / ESCRT / Autophagy
Function / homology
Function and homology information


ESCRT I complex / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / protein targeting to membrane / viral budding via host ESCRT complex / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) ...ESCRT I complex / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / protein targeting to vacuole / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / multivesicular body assembly / protein targeting to membrane / viral budding via host ESCRT complex / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / HCMV Late Events / macroautophagy / Late endosomal microautophagy / Budding and maturation of HIV virion / late endosome membrane / endosome membrane / intracellular membrane-bounded organelle / centrosome / nucleoplasm / cytosol
Similarity search - Function
Modifier of rudimentary, Modr / Modifier of rudimentary (Mod(r)) protein / VPS37 C-terminal domain profile. / ESCRT assembly domain / Helix hairpin bin domain superfamily / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 37A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsTian, F. / Ye, Y.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127730 United States
CitationJournal: Commun Biol / Year: 2024
Title: Identification of membrane curvature sensing motifs essential for VPS37A phagophore recruitment and autophagosome closure.
Authors: Ye, Y. / Liang, X. / Wang, G. / Bewley, M.C. / Hamamoto, K. / Liu, X. / Flanagan, J.M. / Wang, H.G. / Takahashi, Y. / Tian, F.
History
DepositionAug 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Database references / Category: citation / database_2
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Vacuolar protein sorting-associated protein 37A


Theoretical massNumber of molelcules
Total (without water)14,5721
Polymers14,5721
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1medoid

-
Components

#1: Protein Vacuolar protein sorting-associated protein 37A / hVps37A / ESCRT-I complex subunit VPS37A / Hepatocellular carcinoma-related protein 1


Mass: 14571.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS37A, HCRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NEZ2

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D TROSY
121isotropic23D 1H-13C NOESY
131isotropic23D 1H-15N NOESY
141anisotropic12D IPAP-HSQC
151isotropic13D HNCA
171isotropic13D HNCO
161isotropic13D HN(CA)CO
181isotropic13D (H)CCH-TOCSY
191isotropic12D 1H-13C HSQC
1111isotropic12D 1H-13C HSQC aromatic
1101isotropic13D 1H-13C NOESY aromatic

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] VPS37A_21-148, 50 mM HEPES, 250 mM NaCl, 6.5 mg/mL phage Pf1, 95% H2O/5% D2Osample_195% H2O/5% D2O
solution225 mM HEPES, 150 mM NaCl, 12 % w/v bicelles (DMPC:DMPG:DHPC = 4:1:10, molar ratio, q=0.5)30, 0.5 mM [U-13C; U-15N] VPS37A_21-148, 95% H2O/5% D2Osample_295% H2O/5% D2O
solution3150 mM NaCl, 20 mM PBS, 0.02 % NaN3, 0.5 mM [U-13C; U-15N] VPS37A_21-148, 95% H2O/5% D2Osample_395% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMVPS37A_21-148[U-13C; U-15N]1
50 mMHEPESnatural abundance1
250 mMNaClnatural abundance1
6.5 mg/mLphage Pf1natural abundance1
25 mMHEPESnatural abundance2
150 mMNaClnatural abundance2
12 % w/vbicelles (DMPC:DMPG:DHPC = 4:1:10, molar ratio, q=0.5)30natural abundance2
0.5 mMVPS37A_21-148[U-13C; U-15N]2
150 mMNaClnatural abundance3
20 mMPBSnatural abundance3
0.02 %NaN3natural abundance3
0.5 mMVPS37A_21-148[U-13C; U-15N]3
Sample conditionsIonic strength: 150 mM / Ionic strength err: 1 / Label: condition_2 / pH: 6.5 / PH err: 0.05 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIBrukerAVANCE II6001Bruker 600MHz with Cryoprobe
Bruker AVANCE III HDBrukerAVANCE III HD8502Bruker 850 MHz with Cryoprobe

-
Processing

NMR software
NameDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANACYANA by Guntert, P.structure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1 / Details: 2385 NOEs, 74 RDCs, 193 torsion angles
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
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://pdbjlvh1.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