[English] 日本語
Yorodumi
- PDB-5dcn: Crystal structure of LC3 in complex with TECPR2 LIR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dcn
TitleCrystal structure of LC3 in complex with TECPR2 LIR
ComponentsMicrotubule-associated proteins 1A/1B light chain 3B
KeywordsCELL CYCLE / LC3 / Autophagy
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / ceramide binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme / autophagosome membrane ...SARS-CoV-2 modulates autophagy / ceramide binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme / autophagosome membrane / organelle membrane / autophagosome maturation / mitophagy / autophagosome assembly / autophagosome / endomembrane system / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / mitochondrial membrane / macroautophagy / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / mitochondrion / cytosol
Similarity search - Function
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
Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsStadel, D. / Huber, J. / Dotsch, V. / Rogov, V.V. / Behrends, C. / Akutsu, M.
CitationJournal: Mol.Cell / Year: 2015
Title: TECPR2 Cooperates with LC3C to Regulate COPII-Dependent ER Export.
Authors: Stadel, D. / Millarte, V. / Tillmann, K.D. / Huber, J. / Tamin-Yecheskel, B.C. / Akutsu, M. / Demishtein, A. / Ben-Zeev, B. / Anikster, Y. / Perez, F. / Dotsch, V. / Elazar, Z. / Rogov, V.V. ...Authors: Stadel, D. / Millarte, V. / Tillmann, K.D. / Huber, J. / Tamin-Yecheskel, B.C. / Akutsu, M. / Demishtein, A. / Ben-Zeev, B. / Anikster, Y. / Perez, F. / Dotsch, V. / Elazar, Z. / Rogov, V.V. / Farhan, H. / Behrends, C.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2325
Polymers14,8481
Non-polymers3844
Water1,04558
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-42 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.705, 60.705, 99.946
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 14847.955 Da / Num. of mol.: 1 / Fragment: UNP residues 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.58 Å3/Da / Density % sol: 65.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.8M Lithium sulphate, 0.01M Magnesium chloride, 0.05M MES monohydrate, pH5.6

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2→19.87 Å / Num. obs: 14950 / % possible obs: 99.8 % / Redundancy: 19.4 % / Net I/σ(I): 24.2

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MOLREPphasing
RefinementResolution: 2→19.489 Å / FOM work R set: 0.7508 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1498 10.08 %
Rwork0.2091 13358 -
obs0.2131 14856 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.37 Å2 / Biso mean: 47.53 Å2 / Biso min: 22.29 Å2
Refinement stepCycle: final / Resolution: 2→19.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 20 58 1120
Biso mean--84.05 50.96 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031103
X-RAY DIFFRACTIONf_angle_d0.6481491
X-RAY DIFFRACTIONf_chiral_restr0.048160
X-RAY DIFFRACTIONf_plane_restr0.002191
X-RAY DIFFRACTIONf_dihedral_angle_d15.897426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.06450.33941390.27411177131699
2.0645-2.13820.32691250.25761190131599
2.1382-2.22370.29191390.23031195133499
2.2237-2.32480.30961330.2391186131999
2.3248-2.44710.26141260.223812021328100
2.4471-2.60010.28211330.22621206133999
2.6001-2.80030.27311470.22611951342100
2.8003-3.08120.28031450.217412091354100
3.0812-3.52470.28811170.207512521369100
3.5247-4.43210.19461490.181212291378100
4.4321-19.48970.21991450.20313171462100
Refinement TLS params.Method: refined / Origin x: -30.1801 Å / Origin y: 21.7686 Å / Origin z: 14.54 Å
111213212223313233
T0.2892 Å20.068 Å2-0.0053 Å2-0.2533 Å2-0.0247 Å2--0.1519 Å2
L4.6003 °21.0935 °2-0.5471 °2-1.4424 °2-0.0551 °2--1.5083 °2
S-0.0656 Å °-0.0281 Å °0.0154 Å °0.0516 Å °-0.0245 Å °-0.0155 Å °0.0114 Å °0.004 Å °0.0842 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-6 - 119
2X-RAY DIFFRACTION1allB1 - 4
3X-RAY DIFFRACTION1allS1 - 58

+
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