[English] 日本語
Yorodumi
- PDB-6yop: Structure of SAMM50 LIR bound to GABARAP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yop
TitleStructure of SAMM50 LIR bound to GABARAP
ComponentsSorting and assembly machinery component 50 homolog,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / LIR / SAMM50 / ATG8
Function / homology
Function and homology information


MIB complex / SAM complex / inner mitochondrial membrane organization / Cristae formation / mitochondrial respiratory chain complex assembly / positive regulation of protein K48-linked ubiquitination / cristae formation / regulation of Rac protein signal transduction / GABA receptor binding / Mitochondrial protein import ...MIB complex / SAM complex / inner mitochondrial membrane organization / Cristae formation / mitochondrial respiratory chain complex assembly / positive regulation of protein K48-linked ubiquitination / cristae formation / regulation of Rac protein signal transduction / GABA receptor binding / Mitochondrial protein import / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / autophagy of mitochondrion / protein insertion into mitochondrial outer membrane / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / RAC2 GTPase cycle / smooth endoplasmic reticulum / protein targeting / sperm midpiece / autophagosome / microtubule cytoskeleton organization / protein transport / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / mitochondrial outer membrane / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / synapse / mitochondrion / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Sorting and assembly machinery component 50 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMouilleron, S. / Wenxin, Z. / Johansen, T. / Tooze, S. / Abudu, Y.P. / Lamark, T.
CitationJournal: To Be Published
Title: Structure of SAMM50 LIR bound to GABARAP
Authors: Mouilleron, S. / Wenxin, Z. / Johansen, T. / Tooze, S. / Abudu, Y.P. / Lamark, T.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sorting and assembly machinery component 50 homolog,Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)15,9451
Polymers15,9451
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.323, 101.323, 101.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

-
Components

#1: Protein Sorting and assembly machinery component 50 homolog,Gamma-aminobutyric acid receptor-associated protein / Transformation-related gene 3 protein / TRG-3 / GABA(A) receptor-associated protein / MM46


Mass: 15945.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SAMM50, SAM50, CGI-51, TRG3, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y512, UniProt: O95166
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% v/v isopropanol, 0.1 M Na Acetate pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.1→50.66 Å / Num. obs: 5665274 / % possible obs: 99.9 % / Redundancy: 81.1 % / Biso Wilson estimate: 15.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.01 / Net I/σ(I): 27.3
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 81.8 % / Rmerge(I) obs: 2.64 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 567531 / CC1/2: 0.76 / Rpim(I) all: 0.29 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 1.1→50.66 Å / SU ML: 0.1054 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.3818
RfactorNum. reflection% reflection
Rfree0.1588 3458 4.95 %
Rwork0.1381 --
obs0.1392 69849 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.96 Å2
Refinement stepCycle: LAST / Resolution: 1.1→50.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 0 177 1272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02271258
X-RAY DIFFRACTIONf_angle_d1.68311725
X-RAY DIFFRACTIONf_chiral_restr0.4302181
X-RAY DIFFRACTIONf_plane_restr0.0134230
X-RAY DIFFRACTIONf_dihedral_angle_d29.2445514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.271440.25692640X-RAY DIFFRACTION100
1.12-1.130.24421210.24072625X-RAY DIFFRACTION100
1.13-1.150.2421230.21712649X-RAY DIFFRACTION100
1.15-1.170.2331580.20542650X-RAY DIFFRACTION99.96
1.17-1.180.21071500.19362600X-RAY DIFFRACTION100
1.19-1.210.21551250.18172667X-RAY DIFFRACTION99.96
1.21-1.230.20631820.17092588X-RAY DIFFRACTION100
1.23-1.250.20521440.16752644X-RAY DIFFRACTION100
1.25-1.280.16421180.16342648X-RAY DIFFRACTION100
1.28-1.30.17381360.15082646X-RAY DIFFRACTION100
1.3-1.330.18841240.14472665X-RAY DIFFRACTION100
1.33-1.370.14861520.13712592X-RAY DIFFRACTION99.96
1.37-1.40.17611290.13292692X-RAY DIFFRACTION100
1.41-1.450.15761070.11942685X-RAY DIFFRACTION100
1.45-1.490.15261150.11872679X-RAY DIFFRACTION100
1.49-1.550.14561560.11182611X-RAY DIFFRACTION100
1.55-1.610.14021420.11012661X-RAY DIFFRACTION100
1.61-1.680.1431460.10942631X-RAY DIFFRACTION100
1.68-1.770.14771660.11222645X-RAY DIFFRACTION100
1.77-1.880.13741360.10952660X-RAY DIFFRACTION100
1.88-2.030.12351460.10462678X-RAY DIFFRACTION100
2.03-2.230.12181400.10632666X-RAY DIFFRACTION100
2.23-2.550.13691350.12272678X-RAY DIFFRACTION100
2.55-3.210.16351410.14952706X-RAY DIFFRACTION100
3.22-50.660.18261220.1622785X-RAY DIFFRACTION98.91

+
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