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- PDB-8q53: Crystal structure of truncated human Microtubule-associated prote... -

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Basic information

Entry
Database: PDB / ID: 8q53
TitleCrystal structure of truncated human Microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B) in apo form
ComponentsMicrotubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / autophagy / SGC / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autophagosome membrane ...SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / mitophagy / endomembrane system / autophagosome / Pexophagy / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / mitochondrial membrane / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / microtubule binding / cytoplasmic vesicle / microtubule / ubiquitin protein ligase binding / mitochondrion / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Microtubule-associated protein 1 light chain 3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKumar, A. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)875510European Union
CitationJournal: To Be Published
Title: Crystal structure of truncated human Microtubule-associated proteins 1A/1B light chain 3B in apo form
Authors: Kumar, A. / Knapp, S.
History
DepositionAug 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,39111
Polymers14,7971
Non-polymers59410
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint12 kcal/mol
Surface area7280 Å2
Unit cell
Length a, b, c (Å)60.255, 60.255, 34.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B


Mass: 14797.105 Da / Num. of mol.: 1 / Mutation: Truncation after Gly120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9GZQ8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7 / Details: 36% PEG 8000, 0.1M acetate pH 4.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.36→42.61 Å / Num. obs: 26382 / % possible obs: 97.08 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04224 / Rpim(I) all: 0.01733 / Rrim(I) all: 0.04575 / Net I/σ(I): 21.11
Reflection shellResolution: 1.36→1.409 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.7331 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2575 / CC1/2: 0.825 / Rpim(I) all: 0.3021 / Rrim(I) all: 0.794 / % possible all: 96.12

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
PHENIXphasing
PHENIX1.20.1-4487refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→42.61 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 3668 7.25 %
Rwork0.1904 --
obs0.1918 26378 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→42.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 37 95 1086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071056
X-RAY DIFFRACTIONf_angle_d0.9781414
X-RAY DIFFRACTIONf_dihedral_angle_d7.777152
X-RAY DIFFRACTIONf_chiral_restr0.084156
X-RAY DIFFRACTIONf_plane_restr0.013182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.32921300.3171789X-RAY DIFFRACTION92
1.38-1.390.35791560.30211764X-RAY DIFFRACTION94
1.39-1.410.30061360.2751732X-RAY DIFFRACTION94
1.41-1.440.27621250.26591811X-RAY DIFFRACTION94
1.44-1.460.29841210.24861678X-RAY DIFFRACTION87
1.46-1.480.2681360.24171763X-RAY DIFFRACTION95
1.48-1.510.2491430.24291798X-RAY DIFFRACTION94
1.51-1.540.28091300.24791802X-RAY DIFFRACTION96
1.54-1.560.29741470.22841831X-RAY DIFFRACTION95
1.56-1.60.23441380.22021774X-RAY DIFFRACTION94
1.6-1.630.28761470.22891810X-RAY DIFFRACTION97
1.63-1.670.24451390.21311824X-RAY DIFFRACTION95
1.67-1.710.19791420.19991797X-RAY DIFFRACTION97
1.71-1.760.18741410.20061807X-RAY DIFFRACTION96
1.76-1.810.19941440.20891846X-RAY DIFFRACTION97
1.81-1.870.22311480.21731793X-RAY DIFFRACTION97
1.87-1.930.18831480.20171866X-RAY DIFFRACTION95
1.93-2.010.23911350.18211663X-RAY DIFFRACTION90
2.01-2.10.22241470.19211822X-RAY DIFFRACTION97
2.1-2.210.19971410.19331852X-RAY DIFFRACTION97
2.21-2.350.22411410.18551854X-RAY DIFFRACTION98
2.35-2.530.21121510.18241856X-RAY DIFFRACTION98
2.53-2.790.2161430.19071887X-RAY DIFFRACTION99
2.79-3.190.16011460.18751864X-RAY DIFFRACTION99
3.19-4.020.18591410.16961748X-RAY DIFFRACTION93
4.02-42.610.20121520.15911876X-RAY DIFFRACTION99

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