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- PDB-8x8a: Crystal structure of STBD1 LIR motif in complex with GABARAPL1 -

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Basic information

Entry
Database: PDB / ID: 8x8a
TitleCrystal structure of STBD1 LIR motif in complex with GABARAPL1
Components
  • Gamma-aminobutyric acid receptor-associated protein-like 1
  • Starch-binding domain-containing protein 1
KeywordsPROTEIN BINDING / STBD1 / LIR / GABARAPL1
Function / homology
Function and homology information


substrate localization to autophagosome / glycogen binding / glycophagy / starch binding / phagophore assembly site membrane / GABA receptor binding / Tat protein binding / phosphatidylethanolamine binding / RHOD GTPase cycle / glycogen catabolic process ...substrate localization to autophagosome / glycogen binding / glycophagy / starch binding / phagophore assembly site membrane / GABA receptor binding / Tat protein binding / phosphatidylethanolamine binding / RHOD GTPase cycle / glycogen catabolic process / cellular response to nitrogen starvation / cargo receptor activity / Macroautophagy / polysaccharide binding / autophagosome membrane / tertiary granule membrane / ficolin-1-rich granule membrane / RHOG GTPase cycle / autophagosome assembly / RHOA GTPase cycle / autophagosome maturation / RAC2 GTPase cycle / RAC3 GTPase cycle / intracellular transport / beta-tubulin binding / mitophagy / T-tubule / autophagosome / cytoplasmic vesicle membrane / phospholipid binding / microtubule / cilium / ciliary basal body / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / Golgi apparatus / membrane / plasma membrane / cytosol
Similarity search - Function
Starch-binding domain-containing protein 1, CBM20 domain / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Starch-binding domain-containing protein 1 / Gamma-aminobutyric acid receptor-associated protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsZhang, Y.C. / Pan, L.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Decoding the molecular mechanism of selective autophagy of glycogen mediated by autophagy receptor STBD1.
Authors: Zhang, Y. / Sun, Y. / Shi, J. / Xu, P. / Wang, Y. / Liu, J. / Gong, X. / Wang, Y. / Tang, Y. / Liu, H. / Zhou, X. / Lin, Z. / Baba, O. / Morita, T. / Yu, B. / Pan, L.
History
DepositionNov 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein-like 1
B: Starch-binding domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)16,0942
Polymers16,0942
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-5 kcal/mol
Surface area7430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.395, 100.395, 100.395
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein-like 1 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular ...Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1


Mass: 14068.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0R8
#2: Protein/peptide Starch-binding domain-containing protein 1 / Genethonin-1 / Glycophagy cargo receptor STBD1


Mass: 2026.129 Da / Num. of mol.: 1 / Fragment: LIR motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STBD1, GENX-3414 / Production host: Escherichia coli (E. coli) / References: UniProt: O95210
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 25% w/v Pentaerythritol Propoxylate (5/4 PO/OH), 0.1 M Sodium acetate pH 4.6, 0.05 M Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.529→50.198 Å / Num. obs: 25598 / % possible obs: 100 % / Redundancy: 38.8 % / Biso Wilson estimate: 26.72 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 24.9
Reflection shellResolution: 1.529→1.555 Å / Num. unique obs: 25582 / Rpim(I) all: 0.37

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
PHENIX1.19rc4_4035refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LXI

5lxi


Resolution: 1.53→25.1 Å / SU ML: 0.1416 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1097
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1868 1294 5.06 %
Rwork0.1727 24288 -
obs0.1735 25582 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.89 Å2
Refinement stepCycle: LAST / Resolution: 1.53→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1096 0 0 144 1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781181
X-RAY DIFFRACTIONf_angle_d1.04521605
X-RAY DIFFRACTIONf_chiral_restr0.0652160
X-RAY DIFFRACTIONf_plane_restr0.0146212
X-RAY DIFFRACTIONf_dihedral_angle_d5.5545164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.590.23431480.2272654X-RAY DIFFRACTION100
1.59-1.660.24291570.18212695X-RAY DIFFRACTION100
1.66-1.750.20221450.19312647X-RAY DIFFRACTION100
1.75-1.860.23071280.19462704X-RAY DIFFRACTION100
1.86-20.20281210.19682705X-RAY DIFFRACTION100
2-2.20.20241440.19662667X-RAY DIFFRACTION100
2.2-2.520.19881620.19012706X-RAY DIFFRACTION100
2.52-3.170.17711350.18772715X-RAY DIFFRACTION100
3.18-25.10.17141540.14282795X-RAY DIFFRACTION99.7
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)
18.338274340362.964648663365.740096549639.298581971695.088065577438.7183036497-0.418134581877-0.1320666203451.07802425648-0.0678407728612-0.1688411262610.268244608835-1.23469801323-0.257401482320.7242405042520.3752736638870.0411085794351-0.03854604765830.261953128034-0.03083342700790.456587010080.264332366392-21.2083219395-20.4092838978
27.46468193329-0.7560946425753.0664900631.48562965691-0.8412079248222.80457909268-0.227921294773-0.6136671812840.4183307029840.1311631537290.09488304324970.0172249026615-0.333934358533-0.2696719328740.1271168254440.240485405690.02035307155680.01577897798990.244958803258-0.01366150400530.1770703574240.556266436425-30.1838877957-18.7036113136
37.02421360104-0.03698960490192.495912256261.334959748920.306176804312.594800044860.0921854670875-0.113878634708-0.4686228340140.0864283556878-0.03271079849370.03746765405930.0301098833241-0.115124625427-0.04018351721970.247269513818-0.007754734963260.02263267945570.2243205339580.05241842591460.253481936752-8.22856203909-39.2295767169-23.1962435442
46.459924324511.758217043730.5791556595653.13191716903-1.140461627245.789087109180.01195449511420.284370093330.423463237870.1145288369960.1457340749430.410531416909-0.0463506366771-0.850463649268-0.1581433484480.199855282420.03037951667980.02440206807050.2526858699340.03422791487920.221544833763-18.8090546956-32.3088919666-29.1152410747
56.687940455580.3452974426342.409108592150.5798561278880.3065967989482.13635496165-0.1323413230270.4028678892710.295169420232-0.0416351094688.68048158233E-5-0.107421544081-0.1705544980470.1674598605310.1364549727890.259218468858-0.01416376775830.01656629734940.2311114948440.04435878814650.221025061406-1.53898311375-31.4221283432-30.1308013597
69.31539810384.736131305226.358957972612.978027131282.956509938839.755494921490.66695629252-0.735600050294-0.859674121880.134151656514-0.676167694030.3301502829560.648430965173-1.37562532509-0.0526013219570.31946090795-0.01106868200050.0352711739350.413050850210.05299719050070.4128657301-5.99600921628-41.0663675229-17.2548490871
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 10 )AA1 - 101 - 10
22chain 'A' and (resid 11 through 47 )AA11 - 4711 - 47
33chain 'A' and (resid 48 through 68 )AA48 - 6848 - 68
44chain 'A' and (resid 69 through 79 )AA69 - 7969 - 79
55chain 'A' and (resid 80 through 117 )AA80 - 11780 - 117
66chain 'B' and (resid 201 through 213 )BB201 - 2131 - 13

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