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- PDB-4waa: Crystal structure of Nix LIR-fused human LC3B_2-119 -

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Basic information

Entry
Database: PDB / ID: 4waa
TitleCrystal structure of Nix LIR-fused human LC3B_2-119
ComponentsMicrotubule-associated proteins 1A/1B light chain 3B
KeywordsSTRUCTURAL PROTEIN / Autophagy / selective autophagy / degradation / Nix / LC3 / recycling / LIR
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 / organelle 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 / organelle membrane / autophagosome membrane / mitophagy / autophagosome maturation / 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: 2.35 Å
AuthorsSuzuki, H. / Ravichandran, A.C. / Dobson, R.C.J. / Novak, I. / Wakatsuki, S.
CitationJournal: Sci Rep / Year: 2017
Title: Phosphorylation of the mitochondrial autophagy receptor Nix enhances its interaction with LC3 proteins.
Authors: Rogov, V.V. / Suzuki, H. / Marinkovic, M. / Lang, V. / Kato, R. / Kawasaki, M. / Buljubasic, M. / Sprung, M. / Rogova, N. / Wakatsuki, S. / Hamacher-Brady, A. / Dotsch, V. / Dikic, I. / Brady, N.R. / Novak, I.
History
DepositionAug 29, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,1722
Polymers31,1722
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-4 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.385, 67.385, 116.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 15585.760 Da / Num. of mol.: 2 / Fragment: UNP residues 2-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 20% PEG3350, 8% Tacsimate pH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→38.99 Å / Num. obs: 11860 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 15.7
Reflection shellResolution: 2.35→2.48 Å / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VTU

3vtu


Resolution: 2.35→44.15 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.876 / SU B: 16.824 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27283 560 4.7 %RANDOM
Rwork0.19974 ---
obs0.20311 11252 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.627 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.35→44.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 0 112 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192122
X-RAY DIFFRACTIONr_bond_other_d0.0010.022068
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9672861
X-RAY DIFFRACTIONr_angle_other_deg0.834767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18724.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21915409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7781518
X-RAY DIFFRACTIONr_chiral_restr0.0830.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212347
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02483
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 43 -
Rwork0.223 824 -
obs--100 %
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)
10.06410.06120.13310.5148-0.16730.509-0.01770.0051-0.02380.00920.08880.005-0.0002-0.0654-0.07110.0609-0.01410.00460.0981-0.00040.0109-12.149128.7132-12.0191
20.60070.3593-0.08850.216-0.06320.21430.0220.0047-0.06870.020.0083-0.0391-0.0415-0.0024-0.03030.07490.02580.00320.08240.00040.01596.288220.628815.6618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 134
2X-RAY DIFFRACTION2B10 - 134

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