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- PDB-7lt6: Structure of Partial Beta-Hairpin LIR from FNIP2 Bound to GABARAP -

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Basic information

Entry
Database: PDB / ID: 7lt6
TitleStructure of Partial 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 / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / centriolar satellite / autophagosome assembly / autophagosome maturation / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / protein targeting / sperm midpiece / positive regulation of TORC1 signaling / autophagosome / positive regulation of protein-containing complex assembly / regulation of protein phosphorylation / microtubule cytoskeleton organization / intrinsic apoptotic signaling pathway in response to DNA damage / protein transport / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of peptidyl-serine phosphorylation / protein-folding chaperone binding / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / protein phosphorylation / lysosomal membrane / Golgi membrane / ubiquitin protein ligase binding / synapse / 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 / Ubiquitin-like domain superfamily
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 / molecular replacement / Resolution: 1.8 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: 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


Theoretical massNumber of molelcules
Total (without water)49,0013
Polymers49,0013
Non-polymers00
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.910, 44.750, 78.480
Angle α, β, γ (deg.)90.000, 118.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA-16 - 1176 - 139
21VALVALBB-16 - 1176 - 139
12GLUGLUAA-20 - 1172 - 139
22GLUGLUCC-20 - 1172 - 139
13GLUGLUBB-20 - 1172 - 139
23GLUGLUCC-20 - 1172 - 139

NCS ensembles :
ID
1
2
3
DetailsBiological assembly comprises of residues: -20:-2 of Chain A bound to 1:117 of Chain C, -20:-2 of Chain B bound to 1:117 of Chain A, -20:-2 of Chain C bound to 1:117 of Chain B

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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: 16333.598 Da / Num. of mol.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1 M magnesium acetate, 0.1 M MOPS pH 7.5, and 12% v/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→39.46 Å / Num. obs: 42191 / % possible obs: 97.5 % / Redundancy: 2.8 % / CC1/2: 0.748 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.193 / Rrim(I) all: 0.302 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.842.70.7162669525190.7030.5160.886298.4
9-39.432.90.0759513320.9580.0560.09426.388.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hyo

6hyo


Resolution: 1.8→39.46 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.304 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2734 2249 5.3 %RANDOM
Rwork0.2286 ---
obs0.2309 39930 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.66 Å2 / Biso mean: 27.092 Å2 / Biso min: 13.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å2-0 Å2-0.13 Å2
2--0.08 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 0 408 3798
Biso mean---35.24 -
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133555
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173353
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.6614794
X-RAY DIFFRACTIONr_angle_other_deg1.3821.5857789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7155417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69821.483209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83315656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9791528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A41450.13
12B41450.13
21A43640.15
22C43640.15
31B41580.16
32C41580.16
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 223 -
Rwork0.421 2903 -
all-3126 -
obs--98.49 %
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)
17.1015-3.00654.93211.2972-1.95744.6002-0.1991-0.4114-0.01870.09390.20140.0162-0.1459-0.2713-0.00240.04720.0522-0.02820.09550.00310.051739.271-5.770251.3725
20.73960.18740.16080.8330.15181.2239-0.0828-0.00490.0186-0.0020.10970.06530.0037-0.1712-0.0270.0162-0.0046-0.03250.1360.02970.164320.5071-6.342922.9946
37.92061.1957-0.68671.3538-0.80191.2832-0.08150.1491-0.02540.01660.15320.1189-0.085-0.2429-0.07170.01260.0074-0.01430.08830.05950.092615.383-2.876210.9468
40.9168-0.4861-0.27590.90070.32980.5865-0.01310.0975-0.0129-0.02250.0392-0.0236-0.0335-0.0004-0.02610.0134-0.0231-0.02410.0891-0.00950.146248.1573-8.80329.2802
51.6953-1.1749-2.36371.06932.75748.3956-0.05230.0262-0.0241-0.00060.0456-0.0156-0.11720.2370.00670.0161-0.0205-0.01380.0425-0.00690.074761.0602-7.538210.9957
60.899-0.07590.28413.7629-4.2425.62890.02270.06450.0167-0.1189-0.1524-0.29640.24870.4870.12970.02120.0387-0.03070.1668-0.00730.153656.2941-11.554343.7331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-21 - -5
2X-RAY DIFFRACTION2A-4 - 117
3X-RAY DIFFRACTION3B-20 - -5
4X-RAY DIFFRACTION4B0 - 117
5X-RAY DIFFRACTION5C-20 - -5
6X-RAY DIFFRACTION6C-4 - 11

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