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- PDB-3vvw: NDP52 in complex with LC3C -

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Basic information

Entry
Database: PDB / ID: 3vvw
TitleNDP52 in complex with LC3C
Components
  • Calcium-binding and coiled-coil domain-containing protein 2
  • Microtubule-associated proteins 1A/1B light chain 3C
KeywordsPROTEIN TRANSPORT / autophagy adaptor protein
Function / homology
Function and homology information


protein exit from endoplasmic reticulum / aggrephagy / xenophagy / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of autophagosome maturation / Macroautophagy / response to type II interferon / organelle membrane / autophagosome membrane ...protein exit from endoplasmic reticulum / aggrephagy / xenophagy / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of autophagosome maturation / Macroautophagy / response to type II interferon / organelle membrane / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / endomembrane system / viral process / cellular response to starvation / macroautophagy / PML body / cytoplasmic ribonucleoprotein granule / cytoplasmic vesicle / microtubule / cytoskeleton / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / perinuclear region of cytoplasm / protein homodimerization activity / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Microtubule-associated protein 1A/1B light chain 3C / Immunoglobulin-like - #2840 / SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) ...Microtubule-associated protein 1A/1B light chain 3C / Immunoglobulin-like - #2840 / SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / 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 / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Calcium-binding and coiled-coil domain-containing protein 2 / Microtubule-associated proteins 1A/1B light chain 3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAkutsu, M. / Muhlinen, N.V. / Randow, F. / Komander, D.
CitationJournal: Mol.Cell / Year: 2012
Title: LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy
Authors: Muhlinen, N.V. / Akutsu, M. / Ravenhill, B.J. / Foeglein, A. / Bloor, S. / Rutherford, T.J. / Freund, S.M. / Komander, D. / Randow, F.
History
DepositionJul 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium-binding and coiled-coil domain-containing protein 2
B: Microtubule-associated proteins 1A/1B light chain 3C


Theoretical massNumber of molelcules
Total (without water)29,4112
Polymers29,4112
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-4 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.720, 37.420, 40.280
Angle α, β, γ (deg.)90.000, 94.660, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-201-

HOH

21B-212-

HOH

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Components

#1: Protein Calcium-binding and coiled-coil domain-containing protein 2 / Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 ...Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 / Nuclear dot protein 52


Mass: 14598.341 Da / Num. of mol.: 1 / Fragment: UNP residues 21-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCOCO2, NDP52 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13137
#2: 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: 14812.286 Da / Num. of mol.: 1 / Fragment: UNP residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXW4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 16% PEG6000, 0.01M sodium citrate , pH 7.0, Vapor Diffusion, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.77 Å / Num. all: 10306 / Num. obs: 10306 / % possible obs: 99.8 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 3.2 / Biso Wilson estimate: 31.68 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.5-2.644.10.4463.214721100
7.91-48.773.60.0617.6350198.8

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Processing

Software
NameVersionClassificationNB
PHENIXdev_723refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.147 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7883 / SU ML: 0.73 / σ(F): 1.35 / σ(I): 3.2 / Phase error: 27.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.252 487 4.73 %RANDOM
Rwork0.2101 ---
obs0.2121 10302 99.7 %-
all-10302 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.695 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 86.52 Å2 / Biso mean: 35.3352 Å2 / Biso min: 5.31 Å2
Baniso -1Baniso -2Baniso -3
1--6.4455 Å20 Å24.6395 Å2
2--11.0554 Å20 Å2
3----4.6099 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 0 41 1902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081911
X-RAY DIFFRACTIONf_angle_d1.0462588
X-RAY DIFFRACTIONf_chiral_restr0.08278
X-RAY DIFFRACTIONf_plane_restr0.006328
X-RAY DIFFRACTIONf_dihedral_angle_d16.422704
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.86180.34841640.270132203384100
2.8618-3.60520.27111540.211832513405100
3.6052-40.1520.21071690.18873344351399
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)
15.538-2.1307-3.59956.6519-2.61736.3141-0.06960.86280.3244-0.57030.220.58130.2403-0.3937-0.14220.3234-0.0225-0.07430.13840.05150.18942.25223.956524.054
20.42940.3507-0.91251.6165-0.23613.737-0.18570.0761-0.0447-0.2107-0.0453-0.3846-0.00960.77830.27540.2552-0.10920.05810.47820.18080.385360.19084.651423.4644
31.3150.3257-0.03510.50280.03591.1315-0.18410.27090.3617-0.1813-0.1377-0.3468-0.20280.11730.26150.28110.04840.02410.12310.07570.178148.21237.806728.3484
47.21160.98331.16913.93083.65255.19130.05140.60760.4372-0.2192-0.10240.4597-0.3736-0.1180.13390.0422-0.0166-0.03460.11160.02340.199136.24074.102633.2892
52.83451.3-0.55222.94382.53553.9643-0.05240.4259-0.5329-0.4777-0.0205-0.35850.38130.0231-0.16590.2980.01440.0560.1108-0.0530.118250.0628-7.914728.6537
61.46551.00380.30823.3072-0.49420.6302-0.07060.1104-0.1737-0.1859-0.057-0.27370.28490.0425-0.03920.23080.01470.07650.04970.01440.152251.1327-5.838135.4286
72.3420.4894-1.3890.38850.38583.0160.00890.22390.4493-0.2556-0.00960.1836-0.4509-0.283-0.34680.25060.0584-0.0960.08680.03420.170942.968910.977636.8899
83.2759-3.02362.6463.4132-1.76574.2016-0.1106-0.17870.7370.0288-0.0944-0.3886-0.35080.40020.17380.1759-0.03750.04530.1716-0.03950.204356.59164.694734.5693
93.1919-3.2771-3.10956.22242.8733.0649-0.1930.1613-0.5210.17490.5396-0.61040.65340.9511-0.25840.30860.12430.12750.3874-0.06470.297162.18-6.177925.0878
100.3969-0.090.75452.28720.00631.44850.02870.0755-0.00140.0070.06940.08590.2293-0.0584-0.01060.24590.00810.02040.04410.00720.040844.813-3.559830.4045
112.3704-1.8717-0.87413.76213.69934.28640.31490.15660.11270.02370.17280.2435-0.4748-0.58-0.39120.23090.12460.08270.55120.00280.298175.73966.677211.936
120.7468-1.69510.6993.8722-1.33043.2390.0759-0.8915-0.75980.8747-0.1529-0.74310.68240.48470.08780.66980.0267-0.19560.72830.36480.706279.369-10.79212.4444
132.19090.88330.430.53740.03790.28770.0453-0.5735-0.13350.0847-0.143-0.02440.1745-0.13750.00970.06-0.06090.01860.36820.09550.217273.7684-2.09896.843
144.4375-0.66490.00841.85440.33541.535-0.0278-0.34180.30930.16830.0315-0.1516-0.0059-0.03120.00410.0791-0.0174-0.00760.31730.03140.141888.92065.36329.0102
152.6513-0.76040.65720.8008-0.80712.8219-0.15840.1648-0.0174-0.11520.12870.050.20460.06330.03990.1268-0.0333-0.02190.31830.03490.244186.7317-1.80220.0702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 21:26)A21 - 26
2X-RAY DIFFRACTION2chain A and (resseq 27:37)A27 - 37
3X-RAY DIFFRACTION3chain A and (resseq 38:44)A38 - 44
4X-RAY DIFFRACTION4chain A and (resseq 45:54)A45 - 54
5X-RAY DIFFRACTION5chain A and (resseq 55:65)A55 - 65
6X-RAY DIFFRACTION6chain A and (resseq 66:74)A66 - 74
7X-RAY DIFFRACTION7chain A and (resseq 75:88)A75 - 88
8X-RAY DIFFRACTION8chain A and (resseq 89:97)A89 - 97
9X-RAY DIFFRACTION9chain A and (resseq 98:104)A98 - 104
10X-RAY DIFFRACTION10chain A and (resseq 105:115)A105 - 115
11X-RAY DIFFRACTION11chain A and (resseq 130:137)A130 - 137
12X-RAY DIFFRACTION12chain B and (resseq 13:18)B13 - 18
13X-RAY DIFFRACTION13chain B and (resseq 19:43)B19 - 43
14X-RAY DIFFRACTION14chain B and (resseq 44:91)B44 - 91
15X-RAY DIFFRACTION15chain B and (resseq 92:126)B92 - 126

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