[English] 日本語
Yorodumi
- PDB-7fb5: Crystal structure of FAM134B/GABARAP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fb5
TitleCrystal structure of FAM134B/GABARAP complex
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • Reticulophagy regulator 1
KeywordsPROTEIN BINDING / MEMBRANE PROTEIN / ENDOPLASMIC RETICULUM / AUTOPHAGY
Function / homology
Function and homology information


endoplasmic reticulum-autophagosome adaptor activity / TBC/RABGAPs / Macroautophagy / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / cis-Golgi network / endoplasmic reticulum organization ...endoplasmic reticulum-autophagosome adaptor activity / TBC/RABGAPs / Macroautophagy / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / cis-Golgi network / endoplasmic reticulum organization / reticulophagy / microtubule associated complex / beta-tubulin binding / axoneme / autophagosome membrane / mitophagy / autophagosome assembly / white fat cell differentiation / extrinsic apoptotic signaling pathway via death domain receptors / collagen catabolic process / smooth endoplasmic reticulum / autophagosome / sensory perception of pain / sperm midpiece / macroautophagy / microtubule cytoskeleton organization / : / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein transport / cell body / cytoplasmic vesicle / microtubule binding / microtubule / negative regulation of neuron apoptotic process / lysosome / nuclear body / Golgi membrane / ubiquitin protein ligase binding / endoplasmic reticulum membrane / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / plasma membrane / cytosol
Similarity search - Function
Reticulophagy receptor 1 / Reticulophagy receptor 1/3 / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Reticulophagy regulator 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsZhao, J. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21907033 China
CitationJournal: Febs Open Bio / Year: 2022
Title: The crystal structure of the FAM134B-GABARAP complex provides mechanistic insights into the selective binding of FAM134 to the GABARAP subfamily.
Authors: Zhao, J. / Li, Z. / Li, J.
History
DepositionJul 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Gamma-aminobutyric acid receptor-associated protein
B: Reticulophagy regulator 1


Theoretical massNumber of molelcules
Total (without water)16,9092
Polymers16,9092
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-6 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.250, 73.250, 80.852
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein / GABARAP / GABA(A) receptor-associated protein


Mass: 13942.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gabarap / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DCD6
#2: Protein/peptide Reticulophagy regulator 1 / Reticulophagy receptor 1


Mass: 2967.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H6L5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: containing 0.1 M bis-tris propane pH 8.0, 2.2 M DL-Malic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 6205 / % possible obs: 99.9 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.028 / Rrim(I) all: 0.113 / Χ2: 0.402 / Net I/σ(I): 3.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.915.91.1743100.970.3011.2130.4299.7
2.9-2.9516.91.1282980.940.2781.1630.418100
2.95-3.0116.70.9252990.970.2290.9530.409100
3.01-3.0716.70.6913020.9730.1720.7120.416100
3.07-3.1416.40.5223030.9850.130.5390.408100
3.14-3.2116.50.463160.9870.1150.4750.415100
3.21-3.2916.10.3212970.9950.0810.3310.417100
3.29-3.38160.262970.9960.0660.2690.424100
3.38-3.4816.20.2433070.9950.0620.250.451100
3.48-3.5915.60.1813010.9970.0470.1870.419100
3.59-3.7215.50.1483130.9980.0390.1530.425100
3.72-3.8714.30.1093160.9990.030.1130.429100
3.87-4.0414.40.0953070.9980.0260.0990.421100
4.04-4.2614.60.0853020.9990.0230.0880.42100
4.26-4.5216.10.0683140.9990.0170.070.407100
4.52-4.8716.10.063130.9990.0150.0620.398100
4.87-5.3615.90.0633160.9990.0160.0650.369100
5.36-6.1415.20.0633180.9990.0160.0650.359100
6.14-7.7313.60.0533210.9990.0150.0550.308100
7.73-5013.70.03635510.0090.0370.2998.3

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXv1.18.2refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YIR

5yir


Resolution: 2.84→24.95 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 365 5.9 %
Rwork0.186 5818 -
obs0.1892 6183 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.34 Å2 / Biso mean: 71.0947 Å2 / Biso min: 43.88 Å2
Refinement stepCycle: final / Resolution: 2.84→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1142 0 0 0 1142
Num. residues----138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.84-3.250.37041320.30671872
3.26-4.090.26811030.20561942
4.1-24.950.20361300.15132004

+
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