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- PDB-3wam: Crystal structure of human LC3C_8-125 -

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Basic information

Entry
Database: PDB / ID: 3wam
TitleCrystal structure of human LC3C_8-125
ComponentsMicrotubule-associated proteins 1A/1B light chain 3C
KeywordsPROTEIN TRANSPORT / UBIQUITIN-LIKE FOLD / AUTOPHAGY
Function / homology
Function and homology information


protein exit from endoplasmic reticulum / aggrephagy / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Macroautophagy / autophagosome membrane / organelle membrane / autophagosome maturation / autophagosome assembly / autophagosome ...protein exit from endoplasmic reticulum / aggrephagy / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Macroautophagy / autophagosome membrane / organelle membrane / autophagosome maturation / autophagosome assembly / autophagosome / endomembrane system / cellular response to starvation / macroautophagy / cytoplasmic ribonucleoprotein granule / cytoplasmic vesicle / microtubule / ubiquitin protein ligase binding / cytosol
Similarity search - Function
Microtubule-associated protein 1A/1B light chain 3C / 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
CITRIC ACID / Microtubule-associated proteins 1A/1B light chain 3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSuzuki, H. / Tabata, K. / Morita, E. / Kawasaki, M. / Kato, R. / Dobson, R.C.J. / Yoshimori, T. / Wakatsuki, S.
CitationJournal: Structure / Year: 2014
Title: Structural basis of the autophagy-related LC3/Atg13 LIR complex: recognition and interaction mechanism.
Authors: Suzuki, H. / Tabata, K. / Morita, E. / Kawasaki, M. / Kato, R. / Dobson, R.C. / Yoshimori, T. / Wakatsuki, S.
History
DepositionMay 6, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,1442
Polymers13,9521
Non-polymers1921
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Microtubule-associated proteins 1A/1B light chain 3C
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)28,2894
Polymers27,9042
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area1430 Å2
ΔGint-10 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.720, 71.720, 55.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 13952.190 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 8-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3C / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BXW4
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.5M di-Ammonium hydrogen citrate, 10% PEG 3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→27.83 Å / Num. obs: 16985 / % possible obs: 99.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.2
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2430 / % possible all: 100

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Processing

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

3vtu


Resolution: 1.75→27.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.111 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21129 860 5.1 %RANDOM
Rwork0.17161 ---
obs0.17358 16082 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 13 114 1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.022982
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4461.9951325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90922.44445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25415182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6061510
X-RAY DIFFRACTIONr_chiral_restr0.1880.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021734
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_it1.711.5579
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8282947
X-RAY DIFFRACTIONr_scbond_it4.5453403
X-RAY DIFFRACTIONr_scangle_it7.2324.5378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 60 -
Rwork0.244 1168 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: -30.8184 Å / Origin y: 6.6729 Å / Origin z: 5.7213 Å
111213212223313233
T0.078 Å2-0.0046 Å20.0184 Å2-0.0216 Å20.0075 Å2--0.0285 Å2
L0.1829 °20.0743 °20.0518 °2-1.0727 °2-0.4205 °2--0.5402 °2
S-0.0334 Å °0.0201 Å °0.0492 Å °-0.0584 Å °-0.0316 Å °-0.0489 Å °0.1238 Å °0.0088 Å °0.0651 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 115
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 414

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