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- PDB-5yis: Crystal Structure of AnkB LIR/LC3B complex -

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Basic information

Entry
Database: PDB / ID: 5yis
TitleCrystal Structure of AnkB LIR/LC3B complex
Components
  • Ankyrin-2
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / Autophagy
Function / homology
Function and homology information


Receptor Mediated Mitophagy / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / TBC/RABGAPs / Macroautophagy / Pexophagy / protein localization to M-band ...Receptor Mediated Mitophagy / protein localization to T-tubule / atrial cardiac muscle cell to AV node cell communication / SA node cell to atrial cardiac muscle cell communication / regulation of calcium ion transmembrane transporter activity / positive regulation of calcium ion transmembrane transporter activity / TBC/RABGAPs / Macroautophagy / Pexophagy / protein localization to M-band / PINK1-PRKN Mediated Mitophagy / positive regulation of potassium ion transmembrane transporter activity / T-tubule organization / SA node cell action potential / membrane depolarization during SA node cell action potential / protein localization to organelle / paranodal junction assembly / mucus secretion / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / phosphorylation-dependent protein binding / positive regulation of cation channel activity / atrial cardiac muscle cell action potential / protein localization to endoplasmic reticulum / KEAP1-NFE2L2 pathway / sarcoplasmic reticulum calcium ion transport / cytoskeletal anchor activity / atrial septum development / positive regulation of potassium ion transport / costamere / ventricular cardiac muscle cell action potential / regulation of release of sequestered calcium ion into cytosol / response to methylmercury / positive regulation of calcium ion transport / phosphatidylethanolamine binding / regulation of ventricular cardiac muscle cell membrane repolarization / M band / regulation of cardiac muscle contraction by calcium ion signaling / regulation of cardiac muscle cell contraction / protein localization to cell surface / cellular response to nitrogen starvation / Interaction between L1 and Ankyrins / A band / microtubule associated complex / positive regulation of mucus secretion / autolysosome / spectrin binding / regulation of heart rate by cardiac conduction / axoneme / regulation of calcium ion transport / autophagosome membrane / autophagosome maturation / intercalated disc / mitophagy / autophagosome assembly / regulation of cardiac muscle contraction / autophagosome / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / endomembrane system / COPI-mediated anterograde transport / T-tubule / regulation of heart rate / cellular response to starvation / tubulin binding / protein localization to plasma membrane / establishment of localization in cell / mitochondrial membrane / regulation of protein stability / recycling endosome / structural constituent of cytoskeleton / sarcolemma / Z disc / autophagy / intracellular calcium ion homeostasis / endocytosis / protein localization / protein transport / protein-macromolecule adaptor activity / ATPase binding / cytoplasmic vesicle / microtubule binding / basolateral plasma membrane / postsynaptic membrane / transmembrane transporter binding / microtubule / early endosome / lysosome / cytoskeleton / protein stabilization / neuron projection / apical plasma membrane / protein domain specific binding / axon / neuronal cell body / ubiquitin protein ligase binding / dendrite / positive regulation of gene expression / protein kinase binding / enzyme binding / mitochondrion
Similarity search - Function
: / Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Death domain profile. ...: / Ankyrin, UPA domain / UPA domain / Domain present in ZO-1 and Unc5-like netrin receptors / ZU5 domain / ZU5 domain / ZU5 domain profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Ankyrin repeats (many copies) / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ankyrin-2 / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsLi, J. / Zhu, R. / Chen, K. / Zheng, H. / Yuan, C. / Zhang, H. / Wang, C. / Zhang, M.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
Research Grants Council (RGC)AoE-M09-12 Hong Kong
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins.
Authors: Li, J. / Zhu, R. / Chen, K. / Zheng, H. / Zhao, H. / Yuan, C. / Zhang, H. / Wang, C. / Zhang, M.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 3B
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Ankyrin-2
C: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0287
Polymers35,7494
Non-polymers2793
Water64936
1
A: Microtubule-associated proteins 1A/1B light chain 3B
C: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9663
Polymers17,8742
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-10 kcal/mol
Surface area8090 Å2
MethodPISA
2
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Ankyrin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0614
Polymers17,8742
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-16 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.802, 66.866, 74.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 13 or (resid 14...
21(chain B and (resid 5 through 23 or (resid 24...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPHEPHE(chain A and (resid 5 through 13 or (resid 14...AA5 - 135 - 13
12GLUGLUGLNGLN(chain A and (resid 5 through 13 or (resid 14...AA14 - 1514 - 15
13LYSLYSGLUGLU(chain A and (resid 5 through 13 or (resid 14...AA5 - 1175 - 117
14LYSLYSGLUGLU(chain A and (resid 5 through 13 or (resid 14...AA5 - 1175 - 117
15LYSLYSGLUGLU(chain A and (resid 5 through 13 or (resid 14...AA5 - 1175 - 117
16LYSLYSGLUGLU(chain A and (resid 5 through 13 or (resid 14...AA5 - 1175 - 117
21LYSLYSILEILE(chain B and (resid 5 through 23 or (resid 24...BB5 - 235 - 23
22ARGARGARGARG(chain B and (resid 5 through 23 or (resid 24...BB2424
23GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
24GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
25GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
26GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
27GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125
28GLUGLUVALVAL(chain B and (resid 5 through 23 or (resid 24...BB4 - 1254 - 125

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Components

#1: Protein 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: 14637.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map1lc3b, Map1alc3, Map1lc3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CQV6
#2: Protein/peptide Ankyrin-2 / ANK-2 / Ankyrin-B / Brain ankyrin / Non-erythroid ankyrin


Mass: 3236.489 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1588-1614
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANK2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01484
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 2.4 M ammonium phosphate dibasic, 0.1 M Tris buffer (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 16051 / % possible obs: 99.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 35.52 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.048 / Rrim(I) all: 0.122 / Χ2: 1.791 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.246.40.9547780.8090.4071.041.392100
2.24-2.286.40.8667850.7940.370.9441.433100
2.28-2.326.40.7067950.8970.3010.7691.429100
2.32-2.376.40.6977990.8840.2960.7591.486100
2.37-2.426.40.5457840.9280.2320.5941.441100
2.42-2.486.30.4977930.9360.2130.5421.444100
2.48-2.546.40.4418020.9450.1880.481.464100
2.54-2.616.40.4017870.9580.1720.4371.404100
2.61-2.696.40.3287990.9660.140.3581.495100
2.69-2.776.40.2637960.9760.1130.2871.511100
2.77-2.876.40.2297880.9820.0970.2491.559100
2.87-2.996.30.1817950.9810.0780.1981.63599.9
2.99-3.126.30.158220.9890.0650.1641.91999.9
3.12-3.296.20.1227880.990.0530.1342.21899.9
3.29-3.496.20.1028070.9930.0450.1122.5399.8
3.49-3.765.90.0797980.9970.0350.0862.77999.5
3.76-4.1460.0698270.9960.030.0762.90999.4
4.14-4.745.90.0448140.9980.0190.0482.05599.3
4.74-5.976.30.0418250.9980.0180.0451.79198.7
5.97-505.80.0428690.9980.0190.0472.06395.4

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIX1.12_2829refinement
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UGM

1ugm


Resolution: 2.201→28.712 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.12
RfactorNum. reflection% reflection
Rfree0.2496 763 4.76 %
Rwork0.1973 --
obs0.1997 16013 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.54 Å2 / Biso mean: 44.7684 Å2 / Biso min: 20.42 Å2
Refinement stepCycle: final / Resolution: 2.201→28.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 17 36 2214
Biso mean--72.42 38.03 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092233
X-RAY DIFFRACTIONf_angle_d1.0163027
X-RAY DIFFRACTIONf_chiral_restr0.063353
X-RAY DIFFRACTIONf_plane_restr0.006386
X-RAY DIFFRACTIONf_dihedral_angle_d7.1521599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A964X-RAY DIFFRACTION12.45TORSIONAL
12B964X-RAY DIFFRACTION12.45TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2013-2.37120.32031530.26332955310898
2.3712-2.60970.30811700.243230083178100
2.6097-2.98690.27461470.225630333180100
2.9869-3.76190.26941300.19930913221100
3.7619-28.71460.20521630.16383163332699
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)
14.3975-0.11621.52382.2454-2.01684.45030.05090.3293-0.0742-0.1591-0.08860.1522-0.2605-0.0703-0.04450.26330.03040.01630.23230.00620.29884.148174.264312.5927
23.94841.09123.00382.94980.12544.4889-0.0507-1.33730.861.20150.40050.0303-1.5826-0.69680.12510.93250.1399-0.09870.1831-0.12120.59459.562583.998529.3438
35.0747-2.0426-0.99072.8029-0.45464.2444-0.2467-0.53590.280.36450.4409-0.2218-0.49080.1775-0.19190.3310.0590.00830.3036-0.01570.342314.656871.371127.97
42.69810.2922.56862.9592-0.21564.8276-0.3337-0.6893-0.26210.69210.2250.545-0.0934-0.85070.11380.36960.0770.10050.37070.03410.37762.766767.197128.1873
53.0121-0.77590.69773.23330.56756.0055-0.2433-0.4695-0.01790.52330.38550.18960.0567-0.1669-0.02780.31860.08170.03470.2892-0.00670.24751.863673.868623.5434
65.9745-0.03071.45117.1386-1.36618.6117-0.76320.018-0.213-0.3119-0.0278-0.6679-0.05120.86640.72310.4365-0.01760.04870.37440.00310.459431.036258.578920.5149
73.70550.84531.53994.45140.3812.7321-0.06581.4426-0.2822-1.56670.5873-0.6274-0.07830.6527-0.38440.7475-0.05150.16370.6676-0.07080.361625.197651.56299.5528
81.73390.78181.24422.74740.63454.5201-0.06620.0353-0.2185-0.10220.2503-0.38670.1190.3654-0.20950.22170.0553-0.01950.3833-0.06080.268627.534649.104927.2504
97.38470.2592-1.72683.9153-1.25844.87630.6620.8870.0246-0.2494-0.09090.27390.87190.4452-0.52110.35290.0613-0.04720.3563-0.09480.362720.947140.71920.1803
105.63942.54111.35674.64151.03753.30370.5724-0.29560.18570.4061-0.3057-0.01540.94930.2606-0.12140.39980.0449-0.07840.33370.01840.367324.312440.210930.0414
114.6938-1.83360.05074.199-0.56972.7841-0.1655-0.2985-0.30241.0678-0.116-0.33840.12470.49480.23380.4528-0.0693-0.07650.47980.0520.36223.387245.971836.0909
121.71421.0163-0.82113.3929-0.11450.9396-0.12740.02410.31480.18070.02380.278-0.0239-0.226-0.01730.23480.0072-0.00870.291-0.01930.323712.370947.415725.2685
134.1134-3.1121-2.96073.32021.81033.46740.037-0.35950.5426-1.27080.3415-0.2253-0.60210.5474-0.42150.4463-0.05610.020.39610.02880.342219.031255.154616.0384
141.3610.64261.35753.0578-0.32834.63390.0032-0.27110.08690.4180.0480.1072-0.0301-0.6735-0.0290.2620.0435-0.02470.3938-0.01760.285820.702754.025336.4359
152.8132-0.9668-0.07981.357-2.49386.15480.17710.8754-0.69360.153-0.34230.1529-0.2214-0.0017-0.20410.410.22840.11540.4878-0.16660.775329.651542.043117.9791
166.9216-0.3023.46024.28831.61976.00540.6119-0.2893-2.00420.79080.54691.44931.3140.2416-0.87390.70690.09160.13690.60240.02051.907223.810931.228123.4502
171.1409-0.78461.02871.9984-1.68464.2501-0.12330.16780.669-0.3378-0.1711-0.1797-0.02050.59980.22450.30220.009-0.04440.40440.07460.384415.665975.885112.786
185.43283.1522-0.49687.3624-4.41117.5792-0.63980.0849-0.4242-0.2865-0.1823-1.08430.35810.71010.72550.26540.02580.0240.4590.07060.443621.736864.885125.4081
194.3389-1.32391.64174.4086-3.21163.1887-1.0216-0.2057-0.20220.45140.5078-0.1952-0.6622-0.8830.52040.5430.17890.03140.7581-0.06910.414815.833259.76634.9026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 37 )A5 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 50 )A38 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 79 )A51 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 102 )A80 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 117 )A103 - 117
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 12 )B4 - 12
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 26 )B13 - 26
8X-RAY DIFFRACTION8chain 'B' and (resid 27 through 50 )B27 - 50
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 59 )B51 - 59
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 71 )B60 - 71
11X-RAY DIFFRACTION11chain 'B' and (resid 72 through 85 )B72 - 85
12X-RAY DIFFRACTION12chain 'B' and (resid 86 through 102 )B86 - 102
13X-RAY DIFFRACTION13chain 'B' and (resid 103 through 108 )B103 - 108
14X-RAY DIFFRACTION14chain 'B' and (resid 109 through 125 )B109 - 125
15X-RAY DIFFRACTION15chain 'D' and (resid 122 through 128 )D122 - 128
16X-RAY DIFFRACTION16chain 'D' and (resid 129 through 134 )D129 - 134
17X-RAY DIFFRACTION17chain 'C' and (resid 121 through 128 )C121 - 128
18X-RAY DIFFRACTION18chain 'C' and (resid 129 through 136 )C129 - 136
19X-RAY DIFFRACTION19chain 'C' and (resid 137 through 145 )C137 - 145

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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