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- PDB-7lsw: Structure of Full Beta-Hairpin LIR from FNIP2 Bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 7lsw
TitleStructure of Full Beta-Hairpin LIR from FNIP2 Bound to GABARAP
ComponentsFolliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / AUTOPHAGY / ATG8 / LIR
Function / homology
Function and homology information


FNIP-folliculin RagC/D GAP / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / Amino acids regulate mTORC1 / ATPase inhibitor activity / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex ...FNIP-folliculin RagC/D GAP / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / Amino acids regulate mTORC1 / ATPase inhibitor activity / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Macroautophagy / beta-tubulin binding / regulation of protein phosphorylation / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / smooth endoplasmic reticulum / protein targeting / mitophagy / positive regulation of peptidyl-serine phosphorylation / sperm midpiece / positive regulation of TORC1 signaling / autophagosome / GABA-ergic synapse / positive regulation of protein-containing complex assembly / centriolar satellite / microtubule cytoskeleton organization / intrinsic apoptotic signaling pathway in response to DNA damage / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / protein-folding chaperone binding / microtubule binding / cytoplasmic vesicle / chemical synaptic transmission / microtubule / lysosome / protein phosphorylation / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Folliculin-interacting protein family / Folliculin-interacting protein, N-terminal domain / Folliculin-interacting protein, middle domain / Folliculin-interacting protein, C-terminal domain / Folliculin-interacting protein N-terminus / Folliculin-interacting protein middle domain / Folliculin-interacting protein C-terminus / Tripartite DENN domain, FNIP1/2-type / Tripartite DENN FNIP1/2-type domain profile. / Autophagy protein Atg8 ubiquitin-like ...Folliculin-interacting protein family / Folliculin-interacting protein, N-terminal domain / Folliculin-interacting protein, middle domain / Folliculin-interacting protein, C-terminal domain / Folliculin-interacting protein N-terminus / Folliculin-interacting protein middle domain / Folliculin-interacting protein C-terminus / Tripartite DENN domain, FNIP1/2-type / Tripartite DENN FNIP1/2-type domain 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 / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Folliculin-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsAppleton, B.A.
CitationJournal: Sci Adv / Year: 2021
Title: GABARAP sequesters the FLCN-FNIP tumor suppressor complex to couple autophagy with lysosomal biogenesis.
Authors: Goodwin, J.M. / Walkup 4th, W.G. / Hooper, K. / Li, T. / Kishi-Itakura, C. / Ng, A. / Lehmberg, T. / Jha, A. / Kommineni, S. / Fletcher, K. / Garcia-Fortanet, J. / Fan, Y. / Tang, Q. / Wei, ...Authors: Goodwin, J.M. / Walkup 4th, W.G. / Hooper, K. / Li, T. / Kishi-Itakura, C. / Ng, A. / Lehmberg, T. / Jha, A. / Kommineni, S. / Fletcher, K. / Garcia-Fortanet, J. / Fan, Y. / Tang, Q. / Wei, M. / Agrawal, A. / Budhe, S.R. / Rouduri, S.R. / Baird, D. / Saunders, J. / Kiselar, J. / Chance, M.R. / Ballabio, A. / Appleton, B.A. / Brumell, J.H. / Florey, O. / Murphy, L.O.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
B: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
C: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
D: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
E: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
F: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,51913
Polymers101,8476
Non-polymers6727
Water00
1
A: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
C: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0453
Polymers33,9492
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
D: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4297
Polymers33,9492
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
E: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1414
Polymers33,9492
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
F: Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0453
Polymers33,9492
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.510, 202.510, 202.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 974 through 979 or (resid 980...
21(chain B and (resid 974 through 979 or (resid 980...
31(chain C and (resid 974 through 979 or (resid 980...
41(chain D and (resid 974 through 979 or (resid 980...
51(chain E and (resid 974 through 996 or resid 1001 through 1115))
61(chain F and (resid 974 through 979 or (resid 980...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 974 through 979 or (resid 980...A974 - 979
121(chain A and (resid 974 through 979 or (resid 980...A980 - 981
131(chain A and (resid 974 through 979 or (resid 980...A-26 - 117
141(chain A and (resid 974 through 979 or (resid 980...A-26 - 117
151(chain A and (resid 974 through 979 or (resid 980...A-26 - 117
161(chain A and (resid 974 through 979 or (resid 980...A-26 - 117
211(chain B and (resid 974 through 979 or (resid 980...B974 - 979
221(chain B and (resid 974 through 979 or (resid 980...B980 - 981
231(chain B and (resid 974 through 979 or (resid 980...B-26 - 117
241(chain B and (resid 974 through 979 or (resid 980...B-26 - 117
251(chain B and (resid 974 through 979 or (resid 980...B-26 - 117
261(chain B and (resid 974 through 979 or (resid 980...B-26 - 117
311(chain C and (resid 974 through 979 or (resid 980...C974 - 979
321(chain C and (resid 974 through 979 or (resid 980...C980 - 981
331(chain C and (resid 974 through 979 or (resid 980...C-27 - 117
341(chain C and (resid 974 through 979 or (resid 980...C-27 - 117
351(chain C and (resid 974 through 979 or (resid 980...C-27 - 117
361(chain C and (resid 974 through 979 or (resid 980...C-27 - 117
411(chain D and (resid 974 through 979 or (resid 980...D974 - 979
421(chain D and (resid 974 through 979 or (resid 980...D980 - 981
431(chain D and (resid 974 through 979 or (resid 980...D-27 - 117
441(chain D and (resid 974 through 979 or (resid 980...D-27 - 117
451(chain D and (resid 974 through 979 or (resid 980...D-27 - 117
461(chain D and (resid 974 through 979 or (resid 980...D-27 - 117
511(chain E and (resid 974 through 996 or resid 1001 through 1115))E974 - 996
521(chain E and (resid 974 through 996 or resid 1001 through 1115))E1001 - 1115
611(chain F and (resid 974 through 979 or (resid 980...F974 - 979
621(chain F and (resid 974 through 979 or (resid 980...F980 - 981
631(chain F and (resid 974 through 979 or (resid 980...F-26 - 115
641(chain F and (resid 974 through 979 or (resid 980...F-26 - 115
651(chain F and (resid 974 through 979 or (resid 980...F-26 - 115
661(chain F and (resid 974 through 979 or (resid 980...F-26 - 115
DetailsThe biologically relevant assembly interface is between residues -27 to -1 of one chain and residues 0 to 117 of the adjacent chain.

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Components

#1: Protein
Folliculin-interacting protein 2,Gamma-aminobutyric acid receptor-associated protein / FNIP1-like protein / O6-methylguanine-induced apoptosis 1 protein / GABA(A) receptor-associated protein / MM46


Mass: 16974.434 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FNIP2, FNIPL, KIAA1450, MAPO1, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P278, UniProt: O95166
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 3.4 Å3/Da / Density % sol: 63.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 2.0 M ammonium sulfate, 0.1 M HEPES pH 7.5, and 2% v/v PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→49.12 Å / Num. obs: 27664 / % possible obs: 100 % / Redundancy: 78.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.494 / Rpim(I) all: 0.056 / Rrim(I) all: 0.498 / Net I/σ(I): 11.5 / Num. measured all: 2171504
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.05-3.2481.39.4220.843630.5111.0479.481100
9.15-49.1267.10.10411790.9990.0130.10599.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hyo

6hyo


Resolution: 3.05→49.12 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2468 1406 5.09 %
Rwork0.2278 26203 -
obs0.2289 27609 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.18 Å2 / Biso mean: 92.6965 Å2 / Biso min: 47.03 Å2
Refinement stepCycle: final / Resolution: 3.05→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7083 0 35 0 7118
Biso mean--111.86 --
Num. residues----856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047281
X-RAY DIFFRACTIONf_angle_d0.6959816
X-RAY DIFFRACTIONf_dihedral_angle_d20.866958
X-RAY DIFFRACTIONf_chiral_restr0.0531042
X-RAY DIFFRACTIONf_plane_restr0.0051255
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2496X-RAY DIFFRACTION6.947TORSIONAL
12B2496X-RAY DIFFRACTION6.947TORSIONAL
13C2496X-RAY DIFFRACTION6.947TORSIONAL
14D2496X-RAY DIFFRACTION6.947TORSIONAL
15E2496X-RAY DIFFRACTION6.947TORSIONAL
16F2496X-RAY DIFFRACTION6.947TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.05-3.160.40731350.344325502685
3.16-3.290.35381250.319725842709
3.29-3.430.31941430.290925612704
3.44-3.620.35271260.277426022728
3.62-3.840.30751370.250425732710
3.84-4.140.23341510.226725902741
4.14-4.550.21641520.196425922744
4.56-5.210.23261360.188726502786
5.21-6.560.25081390.23526722811
6.57-49.120.20181620.206828292991

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