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- PDB-3vtw: Crystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119 -

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Basic information

Entry
Database: PDB / ID: 3vtw
TitleCrystal structure of T7-tagged Optineurin LIR-fused human LC3B_2-119
ComponentsOptineurin, microtubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / ubiquitin-like fold / Autophagy
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Golgi ribbon formation / ceramide binding / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / phosphatidylethanolamine binding ...SARS-CoV-2 modulates autophagy / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / Golgi ribbon formation / ceramide binding / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / phosphatidylethanolamine binding / cellular response to nitrogen starvation / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / Macroautophagy / Receptor Mediated Mitophagy / Golgi organization / axoneme / autophagosome maturation / autophagosome membrane / organelle membrane / mitophagy / autophagosome assembly / polyubiquitin modification-dependent protein binding / autophagosome / endomembrane system / cellular response to unfolded protein / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / TNFR1-induced NF-kappa-B signaling pathway / mitochondrial membrane / Regulation of TNFR1 signaling / macroautophagy / trans-Golgi network / autophagy / recycling endosome membrane / KEAP1-NFE2L2 pathway / Regulation of PLK1 Activity at G2/M Transition / protein-macromolecule adaptor activity / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / defense response to Gram-negative bacterium / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / 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
Optineurin / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsSuzuki, H. / Kawasaki, M. / Kato, R. / Wakatsuki, S.
CitationJournal: Biochem.J. / Year: 2013
Title: Structural basis for phosphorylation-triggered autophagic clearance of Salmonella
Authors: Rogov, V.V. / Suzuki, H. / Fiskin, E. / Wild, P. / Kniss, A. / Rozenknop, A. / Kato, R. / Kawasaki, M. / McEwan, D.G. / Lohr, F. / Guntert, P. / Dikic, I. / Wakatsuki, S. / Dotsch, V.
History
DepositionJun 8, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,9107
Polymers51,5263
Non-polymers3844
Water1,53185
1
A: Optineurin, microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2712
Polymers17,1751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Optineurin, microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3683
Polymers17,1751
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Optineurin, microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2712
Polymers17,1751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.170, 64.120, 149.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Optineurin, 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: 17175.408 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 170-181, RESIDUES 2-119 / Mutation: S170E, S171E, S173E, S174E, S177E
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Optineurin LIR (RESIDUES 170-181) and Microtubule-associated proteins 1A/1B light chain 3B (RESIDUES 2-119)
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96CV9, 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.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.0M Ammonium sulfate, 0.05M Tri-sodium citrate, 0.1M Potassium sodium tartrate, 5% Glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 5, 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: 2.52→49.92 Å / Num. obs: 20055 / % possible obs: 97.5 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 12.9
Reflection shellResolution: 2.52→2.66 Å / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 3 / Num. unique all: 2828 / % possible all: 95.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VTU

3vtu


Resolution: 2.52→49.92 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.877 / SU B: 21.796 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27953 1025 5.1 %RANDOM
Rwork0.21127 ---
obs0.21479 18984 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---2.71 Å20 Å2
3---3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.52→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 20 85 3207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223178
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9744281
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1865372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43523.889162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.75315606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8441527
X-RAY DIFFRACTIONr_chiral_restr0.1290.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212373
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9651.51875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84323072
X-RAY DIFFRACTIONr_scbond_it2.62931303
X-RAY DIFFRACTIONr_scangle_it4.514.51209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 70 -
Rwork0.308 1354 -
obs--95.12 %
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)
11.2401-0.5873-0.49090.8822-0.22890.6279-0.0573-0.0834-0.04810.01390.07220.0168-0.0602-0.0093-0.0150.11630.0067-0.00560.11990.03010.12474.5019-21.5189-0.6851
21.4950.8741-0.60361.1539-0.11370.3387-0.00460.0245-0.03170.0082-0.03260.0381-0.0007-0.00340.03720.07050.0088-0.00240.10870.01770.15051.1363-49.8691-3.7683
30.10010.4105-0.29572.729-1.07931.4125-0.08890.0141-0.0128-0.04510.0848-0.14470.0526-0.04750.00420.21120.0294-0.00950.1080.00320.01643.7328-15.0338-35.5883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 134
2X-RAY DIFFRACTION2B10 - 134
3X-RAY DIFFRACTION3C10 - 134

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