[English] 日本語
Yorodumi
- PDB-5v4k: Crystal structure of NEDD4 LIR-fused human LC3B_2-119 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v4k
TitleCrystal structure of NEDD4 LIR-fused human LC3B_2-119
ComponentsMicrotubule-associated proteins 1A/1B light chain 3B,Microtubule-associated proteins 1A/1B light chain 3B,Microtubule-associated proteins 1A/1B light chain 3B
KeywordsSIGNALING PROTEIN / Autophagy / Ubiquitin E3 ligase / HECT / LIR / LC3
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 / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsQiu, Y. / Zheng, Y. / Schulman, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Protein Sci. / Year: 2017
Title: Insights into links between autophagy and the ubiquitin system from the structure of LC3B bound to the LIR motif from the E3 ligase NEDD4.
Authors: Qiu, Y. / Zheng, Y. / Wu, K.P. / Schulman, B.A.
History
DepositionMar 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.2Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,3096
Polymers30,9332
Non-polymers3764
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.570, 69.570, 119.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B,Microtubule-associated proteins 1A/1B light chain 3B,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: 15466.554 Da / Num. of mol.: 2
Fragment: UNP residues 2-119,UNP residues 2-119,UNP residues 2-119,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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Sodium Acetate pH 5.0, 1.2M Ammonium Sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→45.5 Å / Num. obs: 17887 / % possible obs: 100 % / Redundancy: 7.6 % / Net I/σ(I): 18.4

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→45.496 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 907 5.09 %
Rwork0.182 --
obs0.1845 17829 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.099→45.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 22 135 2153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072060
X-RAY DIFFRACTIONf_angle_d0.7492789
X-RAY DIFFRACTIONf_dihedral_angle_d16.6471259
X-RAY DIFFRACTIONf_chiral_restr0.051315
X-RAY DIFFRACTIONf_plane_restr0.005358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.099-2.23050.31441290.21772774X-RAY DIFFRACTION100
2.2305-2.40270.25841390.19522768X-RAY DIFFRACTION100
2.4027-2.64440.25381570.19372766X-RAY DIFFRACTION100
2.6444-3.0270.25671680.19662781X-RAY DIFFRACTION100
3.027-3.81340.22341530.17772834X-RAY DIFFRACTION100
3.8134-45.5070.19571610.16312999X-RAY DIFFRACTION100
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)
11.7404-1.3533-0.71746.26514.00224.12710.17340.1962-0.0475-0.4318-0.4212-0.4213-0.07380.17870.0530.24230.15990.0420.40380.08420.3091-17.6893-4.6016-7.1562
22.07080.1596-0.89932.3354-0.75636.0084-0.20940.00490.0615-0.25990.0685-0.02950.06130.28940.12110.1256-0.0334-0.01960.13710.03790.1865-24.75528.8277-15.9553
34.39460.0867-0.75627.4846-1.31475.27440.33730.01-0.9555-0.2763-0.0011-0.4130.88340.4155-0.12150.41310.3467-0.09240.40940.22780.7857-48.4781-44.2499-6.9368
41.37840.6489-1.32290.2706-0.64241.6587-0.0737-0.4495-0.5155-0.2602-0.20610.2638-0.47210.19860.19190.5446-0.05730.07430.26210.06470.4695-43.1827-21.8038-17.9496
58.2778-7.1912.66778.9173-3.40873.545-0.00080.5617-0.5483-0.7035-0.1480.57110.7999-0.01560.10060.4224-0.0633-0.00480.2333-0.10380.2657-45.6535-10.4273-32.0947
62.3718-1.45141.15853.4015-2.65354.64470.09920.0487-0.53380.3866-0.09580.3780.4955-0.5882-0.13490.305-0.15060.02850.2144-0.04370.2434-49.686-5.0621-21.8789
73.3257-0.9893-3.50052.99892.22254.2115-0.4035-0.8489-0.38620.48590.52750.17750.89620.1818-0.10540.8304-0.15920.10930.41540.19340.3912-48.2981-11.9647-6.7603
80.66450.00671.94042.3058-0.53415.9677-0.1037-0.28830.03640.1729-0.07470.11890.0634-1.48560.13920.1855-0.10710.03530.3703-0.09390.249-53.4420.1518-14.5793
92.0592-1.73350.68782.330.38182.4944-0.0781-0.48970.3128-0.00060.01050.06370.3209-0.17630.01290.2657-0.1012-0.00640.2849-0.06560.2282-46.0340.5292-8.1379
101.6241-0.6837-0.62671.6381-2.02524.41950.0289-0.42690.0870.2979-0.16720.0161-0.00350.32510.13170.2604-0.06880.01560.1959-0.03050.176-42.0333-2.6734-18.4676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 264 through 1026 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1027 through 1118 )
3X-RAY DIFFRACTION3chain 'B' and (resid 264 through 268 )
4X-RAY DIFFRACTION4chain 'B' and (resid 269 through 1012 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1013 through 1026 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1027 through 1037 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1038 through 1050 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1051 through 1071 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1072 through 1094 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1095 through 1117 )

+
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