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- PDB-5cx3: Crystal structure of FYCO1 LIR in complex with LC3A -

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Basic information

Entry
Database: PDB / ID: 5cx3
TitleCrystal structure of FYCO1 LIR in complex with LC3A
Components
  • FYVE and coiled-coil domain-containing protein 1
  • Microtubule-associated proteins 1A/1B light chain 3A
KeywordsPROTEIN BINDING / autophagy adaptor
Function / homology
Function and homology information


plus-end-directed vesicle transport along microtubule / cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / cellular response to nitrogen starvation / SMAD protein signal transduction / response to iron(II) ion / positive regulation of autophagosome maturation / autolysosome / Macroautophagy / Receptor Mediated Mitophagy ...plus-end-directed vesicle transport along microtubule / cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / cellular response to nitrogen starvation / SMAD protein signal transduction / response to iron(II) ion / positive regulation of autophagosome maturation / autolysosome / Macroautophagy / Receptor Mediated Mitophagy / p38MAPK cascade / autophagosome maturation / autophagosome membrane / organelle membrane / autophagosome assembly / autophagosome / JNK cascade / cellular response to copper ion / cellular response to amino acid starvation / PINK1-PRKN Mediated Mitophagy / cellular response to starvation / macroautophagy / response to lead ion / phospholipid binding / cellular response to hydrogen peroxide / late endosome / microtubule binding / microtubule / lysosome / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / Golgi apparatus / membrane / metal ion binding / cytosol
Similarity search - Function
: / : / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger ...: / : / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / GOLD domain superfamily / GOLD domain / GOLD domain profile. / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger, FYVE/PHD-type / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Alpha Beta
Similarity search - Domain/homology
FYVE and coiled-coil domain-containing protein 1 / Microtubule-associated proteins 1A/1B light chain 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsCheng, X. / Pan, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31470749 China
National Basic Research Program of China (973 Program)2013CB836900 China
CitationJournal: Autophagy / Year: 2016
Title: Structural basis of FYCO1 and MAP1LC3A interaction reveals a novel binding mode for Atg8-family proteins.
Authors: Cheng, X. / Wang, Y. / Gong, Y. / Li, F. / Guo, Y. / Hu, S. / Liu, J. / Pan, L.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references / Structure summary
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3A
B: Microtubule-associated proteins 1A/1B light chain 3A
C: Microtubule-associated proteins 1A/1B light chain 3A
D: Microtubule-associated proteins 1A/1B light chain 3A
E: FYVE and coiled-coil domain-containing protein 1
F: FYVE and coiled-coil domain-containing protein 1
G: FYVE and coiled-coil domain-containing protein 1
H: FYVE and coiled-coil domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,86510
Polymers70,6808
Non-polymers1842
Water1,71195
1
A: Microtubule-associated proteins 1A/1B light chain 3A
C: Microtubule-associated proteins 1A/1B light chain 3A
E: FYVE and coiled-coil domain-containing protein 1
G: FYVE and coiled-coil domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4325
Polymers35,3404
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-20 kcal/mol
Surface area14910 Å2
MethodPISA
2
B: Microtubule-associated proteins 1A/1B light chain 3A
D: Microtubule-associated proteins 1A/1B light chain 3A
F: FYVE and coiled-coil domain-containing protein 1
H: FYVE and coiled-coil domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4325
Polymers35,3404
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-21 kcal/mol
Surface area14910 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-43 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.426, 115.257, 73.517
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14293.451 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H492
#2: Protein/peptide
FYVE and coiled-coil domain-containing protein 1 / Zinc finger FYVE domain-containing protein 7


Mass: 3376.661 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FYCO1, ZFYVE7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQS8
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES sodium
PH range: 6.9-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 25680 / % possible obs: 99.1 % / Redundancy: 3 % / Net I/σ(I): 16.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029phasing
RefinementResolution: 2.3→34.615 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1235 5.14 %
Rwork0.1776 --
obs0.1811 24033 93.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→34.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4551 0 12 95 4658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094703
X-RAY DIFFRACTIONf_angle_d1.1616353
X-RAY DIFFRACTIONf_dihedral_angle_d16.3471841
X-RAY DIFFRACTIONf_chiral_restr0.053698
X-RAY DIFFRACTIONf_plane_restr0.006841
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.3257950.22521741X-RAY DIFFRACTION64
2.3921-2.5010.30961100.23082338X-RAY DIFFRACTION87
2.501-2.63280.2721510.21472623X-RAY DIFFRACTION98
2.6328-2.79760.32231530.22482649X-RAY DIFFRACTION99
2.7976-3.01350.29971440.20662676X-RAY DIFFRACTION99
3.0135-3.31660.30041490.19672676X-RAY DIFFRACTION99
3.3166-3.7960.23671480.16882688X-RAY DIFFRACTION100
3.796-4.78050.18331420.13512679X-RAY DIFFRACTION99
4.7805-34.61860.19141430.1522728X-RAY DIFFRACTION99
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)
15.32784.5936-4.27164.307-2.75635.6709-0.30120.06960.0572-0.32820.1437-0.0410.53150.65910.17340.39530.0423-0.0040.4293-0.01950.232520.6115-30.192662.5532
25.62021.00691.28083.98991.17113.17440.07750.01390.01590.3019-0.0109-0.0844-0.15630.0356-0.07980.22320.02680.03190.23070.04440.170422.3536-23.09578.0553
35.3337-4.0608-5.61413.26633.41858.9745-0.45080.1789-0.27980.18920.19760.16910.6101-0.22190.22250.41010.03150.02770.50160.08040.305331.9632-29.022150.6025
42.4448-2.0825-0.0373.8457-0.38363.62460.08080.1254-0.3478-0.3105-0.07620.19330.098-0.1584-0.07170.2503-0.0448-0.02180.3685-0.03630.222330.594-23.264835.5804
52.44714.05690.88957.67533.20655.4829-0.15460.2647-0.1668-0.45550.02310.8258-0.3915-0.49460.04580.27920.018-0.07890.4319-0.0270.323728.1089-14.997133.0781
64.7939-1.367-0.97616.4714-1.43934.6008-0.0742-0.39520.076-0.01220.1233-0.1393-0.4980.32180.00830.2492-0.01790.04020.3213-0.11060.17830.8681-16.067141.6181
71.26651.17081.36176.3575-1.87384.14660.5199-0.06430.0919-0.2143-0.1670.48610.1925-0.3508-0.35410.32970.0110.070.3346-0.03180.436421.076211.361569.7107
81.72720.8895-1.23048.585-0.29857.31320.0572-0.0464-0.01661.1103-0.17980.1866-0.1863-0.07840.11460.46540.00430.00590.23440.06020.557626.88784.374282.5066
93.0434-0.5935-2.26432.06662.50175.9803-0.1235-0.05890.35730.62910.00350.36420.38130.40910.03490.6386-0.03610.18180.2630.00260.439326.4303-4.212484.4869
102.79131.40310.02384.2042-4.32745.2676-0.12970.20860.08630.0644-0.0173-0.10060.1730.24110.01880.4132-0.00450.09030.2559-0.03770.465326.081-2.269176.0038
114.1413-6.2307-4.57339.49946.94925.09070.1086-0.3060.9709-0.92470.4104-2.2625-0.26131.167-0.51610.47610.03560.20660.5579-0.07930.757138.166910.727348.547
123.99543.99524.12157.92780.99488.5652-0.627-1.30180.6344-0.1206-0.16510.0175-0.5067-0.17410.71960.49230.0720.00750.5013-0.0290.362126.212713.570455.964
132.4715-1.6549-2.66887.46883.59447.39520.36840.32010.1771-1.3503-0.0435-0.2616-1.3809-0.4029-0.24020.69580.07410.01130.32840.00950.416926.71388.841840.3135
143.60763.7421-2.2215.45030.34916.31710.68670.47760.3526-2.0415-0.66421.0198-0.1081-0.6475-0.1191.230.4278-0.12310.5314-0.11390.596320.68777.619333.6048
152.94350.4966-0.562.3537-2.45478.47570.30350.29970.164-0.5306-0.3625-0.0058-0.2214-0.53650.32690.70050.21520.0310.3745-0.08550.438625.64580.615434.693
163.86553.42424.11539.46355.04034.69020.1915-0.8686-0.91280.394-1.16090.98120.8292-1.50071.08240.5850.08530.18920.6423-0.02580.531419.40240.070249.1503
173.1793-0.8914-1.6475.57616.20357.70090.033-0.0525-0.0353-0.31590.178-0.0159-0.19480.0785-0.26590.50090.05710.09110.27940.06670.335929.54390.55740.7541
182.1629-0.9464-1.13833.15041.54667.04410.14390.7417-0.46970.2594-0.1639-0.99540.53620.538-0.01820.35330.1313-0.02910.5330.03120.561324.0162-35.500974.2536
194.6944-1.64793.26114.8781-2.85942.94920.3737-2.20061.08082.023-1.32760.002-0.605-0.75520.80530.699-0.20030.12940.9383-0.11180.461112.9323-33.242389.7296
204.94435.0869-5.25835.4839-5.55595.6949-0.36370.5001-0.7169-0.7775-0.00880.87951.1399-0.41860.53840.41470.0050.06080.387-0.04030.535431.6671-32.415838.5197
212.89240.179-1.71573.6777-3.31043.8347-1.10881.0953-1.4806-0.44370.0272-0.41340.94120.2550.90790.55080.00710.04010.5522-0.09510.494538.2773-26.816524.6023
229.83166.9758-6.35.2661-4.31574.11041.3568-0.92880.59572.4953-1.11340.6003-0.18620.5166-0.11590.6347-0.14410.02410.5404-0.07050.377743.3434-13.93518.6926
237.3531-6.8146.99686.3409-6.50086.6674-0.2786-1.37890.78861.25610.2944-0.4625-0.4029-0.94640.2270.47520.0155-0.10570.4743-0.01980.527726.355114.441380.0789
248.8357-4.26163.03194.2421-3.61533.2153-0.6931-0.13410.13230.8222-0.6716-1.1348-0.19010.04941.7350.7761-0.042-0.08730.75270.1240.709839.28886.674890.456
259.65794.4548-0.63463.80290.83510.9458-0.3361-0.9575-0.6203-1.16820.1581-0.10530.6022-0.05380.00511.76840.5986-0.1971.03230.31851.126224.592817.516643.2194
264.12072.66493.92092.59351.91524.16020.8613-0.3827-0.8909-0.36230.13810.2708-1.0651-0.7099-0.90071.04930.2452-0.04891.158-0.00040.848112.893713.68632.79
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 121 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 26 )
4X-RAY DIFFRACTION4chain 'B' and (resid 27 through 70 )
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 121 )
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 26 )
8X-RAY DIFFRACTION8chain 'C' and (resid 27 through 71 )
9X-RAY DIFFRACTION9chain 'C' and (resid 72 through 94 )
10X-RAY DIFFRACTION10chain 'C' and (resid 95 through 121 )
11X-RAY DIFFRACTION11chain 'D' and (resid 5 through 12 )
12X-RAY DIFFRACTION12chain 'D' and (resid 13 through 26 )
13X-RAY DIFFRACTION13chain 'D' and (resid 27 through 59 )
14X-RAY DIFFRACTION14chain 'D' and (resid 60 through 70 )
15X-RAY DIFFRACTION15chain 'D' and (resid 71 through 94 )
16X-RAY DIFFRACTION16chain 'D' and (resid 95 through 102 )
17X-RAY DIFFRACTION17chain 'D' and (resid 103 through 121 )
18X-RAY DIFFRACTION18chain 'E' and (resid 1273 through 1284 )
19X-RAY DIFFRACTION19chain 'E' and (resid 1285 through 1292 )
20X-RAY DIFFRACTION20chain 'F' and (resid 1276 through 1284 )
21X-RAY DIFFRACTION21chain 'F' and (resid 1285 through 1292 )
22X-RAY DIFFRACTION22chain 'F' and (resid 1293 through 1300 )
23X-RAY DIFFRACTION23chain 'G' and (resid 1276 through 1284 )
24X-RAY DIFFRACTION24chain 'G' and (resid 1285 through 1294 )
25X-RAY DIFFRACTION25chain 'H' and (resid 1277 through 1284 )
26X-RAY DIFFRACTION26chain 'H' and (resid 1285 through 1292 )

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