[English] 日本語
Yorodumi
- PDB-7brq: Crystal structure of human FAM134B LIR fused to human GABARAP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7brq
TitleCrystal structure of human FAM134B LIR fused to human GABARAP
ComponentsReticulophagy regulator 1,Gamma-aminobutyric acid receptor-associated protein
KeywordsMEMBRANE PROTEIN / autophagy / endoplasmic reticulum
Function / homology
Function and homology information


endoplasmic reticulum-autophagosome adaptor activity / 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 / TBC/RABGAPs / reticulophagy ...endoplasmic reticulum-autophagosome adaptor activity / 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 / TBC/RABGAPs / reticulophagy / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / white fat cell differentiation / extrinsic apoptotic signaling pathway via death domain receptors / collagen catabolic process / smooth endoplasmic reticulum / autophagosome / protein targeting / sensory perception of pain / sperm midpiece / microtubule cytoskeleton organization / : / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein transport / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / negative regulation of neuron apoptotic process / lysosome / nuclear body / Golgi membrane / synapse / ubiquitin protein ligase binding / endoplasmic reticulum membrane / nucleolus / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Reticulophagy regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.404 Å
AuthorsYamasaki, A. / Noda, N.N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K18339 Japan
Japan Society for the Promotion of Science (JSPS)19H05707 Japan
Japan Science and TechnologyJPMJCR13M7 Japan
CitationJournal: Nat Commun / Year: 2020
Title: Super-assembly of ER-phagy receptor Atg40 induces local ER remodeling at contacts with forming autophagosomal membranes.
Authors: Mochida, K. / Yamasaki, A. / Matoba, K. / Kirisako, H. / Noda, N.N. / Nakatogawa, H.
History
DepositionMar 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reticulophagy regulator 1,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2102
Polymers16,1181
Non-polymers921
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.892, 81.892, 33.324
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Reticulophagy regulator 1,Gamma-aminobutyric acid receptor-associated protein / FAM134B / Reticulophagy receptor 1 / GABA(A) receptor-associated protein / MM46


Mass: 16118.130 Da / Num. of mol.: 1 / Mutation: F3S,V4T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM134B, GABARAP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6L5, UniProt: O95166
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.91 M ammonium sulfate, 0.1 M sodium citrate pH 5.5, 0.18 M potassium sodium tartrate

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.404→40.95 Å / Num. obs: 24609 / % possible obs: 97.71 % / Redundancy: 9.7 % / Biso Wilson estimate: 20.05 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07419 / Rpim(I) all: 0.02491 / Rrim(I) all: 0.07837 / Net I/σ(I): 18.8
Reflection shellResolution: 1.404→1.454 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.6313 / Mean I/σ(I) obs: 2.68 / Num. unique obs: 2058 / CC1/2: 0.755 / CC star: 0.928 / Rpim(I) all: 0.2538 / Rrim(I) all: 0.6831 / % possible all: 82.68

-
Processing

Software
NameVersionClassification
PHENIXdev_2450refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXdev_2450phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 1.404→40.946 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.71
RfactorNum. reflection% reflection
Rfree0.2061 1231 5 %
Rwork0.1915 --
obs0.1922 24609 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.46 Å2 / Biso mean: 30.2026 Å2 / Biso min: 9.91 Å2
Refinement stepCycle: final / Resolution: 1.404→40.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 14 105 1205
Biso mean--49.7 38.64 -
Num. residues----132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061142
X-RAY DIFFRACTIONf_angle_d0.791544
X-RAY DIFFRACTIONf_chiral_restr0.075160
X-RAY DIFFRACTIONf_plane_restr0.006202
X-RAY DIFFRACTIONf_dihedral_angle_d14.919431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.404-1.460.37931160.344219583
1.46-1.52640.311330.2729253596
1.5264-1.60690.25951390.24022643100
1.6069-1.70760.24921390.2172629100
1.7076-1.83940.23781380.21012638100
1.8394-2.02450.19121390.19792641100
2.0245-2.31740.19671410.1912662100
2.3174-2.91960.22191410.19352679100
2.9196-40.9460.17931450.16862756100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.02232.7433-2.78592.1688-2.65515.55010.164-0.24410.0865-0.0002-0.2712-1.66090.03270.78760.15780.25680.030.05820.30070.07050.7448105.61657.48649.0353
24.34554.8951-3.75767.0734-4.45843.28040.3582-0.14770.1858-0.2785-0.7649-1.56250.0160.70380.54520.27440.06430.04020.31850.09730.5852100.299938.138712.4266
37.9423-4.6085-1.93355.8223.16323.04540.1324-0.3457-1.05980.80110.33180.0670.4490.2359-0.36050.3080.0538-0.10.23680.06280.502295.562120.442515.6407
44.1896-1.2024.75123.953-1.67035.41110.16920.6838-0.5561-0.3224-0.45090.04080.31230.15220.20560.24430.0666-0.04150.2943-0.12290.446591.841918.73232.4644
53.4991-0.9599-0.17222.19780.66741.7738-0.0133-0.1897-0.56470.1440.03220.23470.0492-0.0319-0.00760.1392-0.00080.00150.11770.02650.193582.497433.098414.5143
65.3811-6.28180.45777.886-0.03451.5090.6780.81890.127-0.5035-0.6799-0.1938-0.24220.11870.11140.25660.0368-0.00060.2574-0.00330.13489.046934.89762.4124
73.4115-1.0243-0.43056.69843.76385.83370.0835-0.0341-0.29410.05480.0709-0.23240.0460.1004-0.16930.10.0078-0.03060.13750.03290.153191.584831.646512.8583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 12 )A6 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 24 )A13 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 31 )A25 - 31
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 45 )A32 - 45
5X-RAY DIFFRACTION5chain 'A' and (resid 46 through 111 )A46 - 111
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 119 )A112 - 119
7X-RAY DIFFRACTION7chain 'A' and (resid 120 through 137 )A120 - 137

+
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