[English] 日本語
Yorodumi
- PDB-8edv: Mitoguardin homolog (MIGA) delta TM residues 106-496 from Caenorh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8edv
TitleMitoguardin homolog (MIGA) delta TM residues 106-496 from Caenorhabditis elegans bound to modelled lipid phosphatidylethanolamine
ComponentsMItoGuArdin homolog
KeywordsLIPID TRANSPORT / mitochondria / lipid droplets
Function / homologyMitoguardin / Mitoguardin / mitochondrial fusion / mitochondrion / membrane / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / MItoGuArdin homolog
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsHong, Z. / Adlakha, J. / Reinisch, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM131715 United States
CitationJournal: J.Cell Biol. / Year: 2022
Title: Mitoguardin-2-mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation.
Authors: Hong, Z. / Adlakha, J. / Wan, N. / Guinn, E. / Giska, F. / Gupta, K. / Melia, T.J. / Reinisch, K.M.
History
DepositionSep 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MItoGuArdin homolog
B: MItoGuArdin homolog
C: MItoGuArdin homolog
D: MItoGuArdin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,4248
Polymers180,6574
Non-polymers2,7684
Water00
1
A: MItoGuArdin homolog
B: MItoGuArdin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7124
Polymers90,3282
Non-polymers1,3842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-68 kcal/mol
Surface area32720 Å2
MethodPISA
2
C: MItoGuArdin homolog
D: MItoGuArdin homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7124
Polymers90,3282
Non-polymers1,3842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-70 kcal/mol
Surface area33120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.278, 91.278, 366.745
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 135 or resid 138 through 143...
21(chain B and (resid 135 or resid 138 through 391 or resid 401))
31(chain C and (resid 135 or resid 138 through 143...
41(chain D and (resid 135 or resid 138 through 143...
12(chain E and resid 1 through 63)
22(chain F and resid 1 through 63)
32chain G
42(chain H and resid 1 through 63)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 135 or resid 138 through 143...A135
121(chain A and (resid 135 or resid 138 through 143...A138 - 143
131(chain A and (resid 135 or resid 138 through 143...A145 - 148
141(chain A and (resid 135 or resid 138 through 143...A151 - 359
151(chain A and (resid 135 or resid 138 through 143...A364 - 391
161(chain A and (resid 135 or resid 138 through 143...A401
211(chain B and (resid 135 or resid 138 through 391 or resid 401))B135
221(chain B and (resid 135 or resid 138 through 391 or resid 401))B138 - 391
231(chain B and (resid 135 or resid 138 through 391 or resid 401))B401
311(chain C and (resid 135 or resid 138 through 143...C135
321(chain C and (resid 135 or resid 138 through 143...C138 - 143
331(chain C and (resid 135 or resid 138 through 143...C145 - 148
341(chain C and (resid 135 or resid 138 through 143...C151 - 359
351(chain C and (resid 135 or resid 138 through 143...C364 - 391
361(chain C and (resid 135 or resid 138 through 143...C401
411(chain D and (resid 135 or resid 138 through 143...D135
421(chain D and (resid 135 or resid 138 through 143...D138 - 143
431(chain D and (resid 135 or resid 138 through 143...D145 - 148
441(chain D and (resid 135 or resid 138 through 143...D151 - 359
451(chain D and (resid 135 or resid 138 through 143...D364 - 391
461(chain D and (resid 135 or resid 138 through 143...D401
112(chain E and resid 1 through 63)E1 - 63
212(chain F and resid 1 through 63)F1 - 63
312chain GG0
412(chain H and resid 1 through 63)H1 - 63

NCS ensembles :
ID
1
2

-
Components

#1: Protein
MItoGuArdin homolog / Mitoguardin 2 (MIGA2)


Mass: 45164.164 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: miga-1, CELE_K01D12.6, K01D12.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21096
#2: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H74NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M sodium malonate pH 7.4, 22% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3.3→48.36 Å / Num. obs: 27736 / % possible obs: 99.9 % / Redundancy: 10.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.056 / Rrim(I) all: 0.179 / Net I/σ(I): 14
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.736 / Num. unique obs: 2670 / CC1/2: 0.835 / Rpim(I) all: 0.236 / Rrim(I) all: 0.774 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2 model

Resolution: 3.3→48.35 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 1330 4.81 %
Rwork0.2698 26328 -
obs0.2711 27658 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 386.88 Å2 / Biso mean: 129.7132 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.3→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10265 0 480 0 10745
Biso mean--154.89 --
Num. residues----1272
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3156X-RAY DIFFRACTION4.217TORSIONAL
12B3156X-RAY DIFFRACTION4.217TORSIONAL
13C3156X-RAY DIFFRACTION4.217TORSIONAL
14D3156X-RAY DIFFRACTION4.217TORSIONAL
21A756X-RAY DIFFRACTION4.217TORSIONAL
22B756X-RAY DIFFRACTION4.217TORSIONAL
23C756X-RAY DIFFRACTION4.217TORSIONAL
24D756X-RAY DIFFRACTION4.217TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.420.31061120.34112545265799
3.42-3.550.37481420.311325772719100
3.55-3.720.34971350.335625882723100
3.72-3.910.34761600.292725782738100
3.91-4.160.29811490.291626102759100
4.16-4.480.28441390.260625642703100
4.48-4.930.35271260.273726562782100
4.93-5.640.29271160.272926732789100
5.64-7.10.3131330.302126802813100
7.1-48.350.23511180.22552857297599
Refinement TLS params.Method: refined / Origin x: -45.7624 Å / Origin y: 42.9299 Å / Origin z: 30.3252 Å
111213212223313233
T0.7814 Å2-0.0084 Å20.0951 Å2-0.7818 Å20.0021 Å2--0.9468 Å2
L0.4596 °2-0.072 °2-0.2562 °2-0.45 °20.0565 °2--0.7833 °2
S-0.0188 Å °-0.0036 Å °0.0132 Å °-0.0041 Å °-0.0111 Å °0.0161 Å °-0.1574 Å °0.0272 Å °0.0392 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA109 - 495
2X-RAY DIFFRACTION1allA505
3X-RAY DIFFRACTION1allB109 - 495
4X-RAY DIFFRACTION1allB505
5X-RAY DIFFRACTION1allC110 - 495
6X-RAY DIFFRACTION1allC505
7X-RAY DIFFRACTION1allD109 - 495
8X-RAY DIFFRACTION1allD505

+
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