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- PDB-2r2q: Crystal structure of human Gamma-Aminobutyric Acid Receptor-Assoc... -

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Basic information

Entry
Database: PDB / ID: 2r2q
TitleCrystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1 (GABARAP1), Isoform CRA_a
ComponentsGamma-aminobutyric acid receptor-associated protein-like 1
KeywordsSIGNALING PROTEIN / PROTEIN TRANSPORT / autophagy / ubiquitin homolog / Structural Genomics Consortium / SGC / Microtubule
Function / homology
Function and homology information


glycophagy / Tat protein binding / GABA receptor binding / cellular response to nitrogen starvation / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome assembly / autophagosome / phospholipid binding ...glycophagy / Tat protein binding / GABA receptor binding / cellular response to nitrogen starvation / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome assembly / autophagosome / phospholipid binding / macroautophagy / cytoplasmic vesicle membrane / microtubule / ubiquitin protein ligase binding / Golgi apparatus / endoplasmic reticulum / cytosol
Similarity search - Function
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-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsTempel, W. / Paramanathan, R. / Davis, T. / Mujib, S. / Butler-Cole, C. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. ...Tempel, W. / Paramanathan, R. / Davis, T. / Mujib, S. / Butler-Cole, C. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human Gamma-Aminobutyric Acid Receptor-Associated Protein-like 1 (GABARAP1), Isoform CRA_a.
Authors: Paramanathan, R. / Davis, T. / Tempel, W. / Mujib, S. / Butler-Cole, C. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionAug 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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: Gamma-aminobutyric acid receptor-associated protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5186
Polymers26,4002
Non-polymers1184
Water2,000111
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1


Theoretical massNumber of molelcules
Total (without water)13,2004
Polymers13,2001
Non-polymers03
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein-like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3182
Polymers13,2001
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.860, 38.193, 45.746
Angle α, β, γ (deg.)111.090, 95.910, 108.050
Int Tables number1
Space group name H-MP1
DetailsAuthors state that the biological unit of this protein is unknown

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Components

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


Mass: 13200.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Plasmid: pET28-MHL / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0R8
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 25% PEG 3350, 0.2M Sodium chloride, 0.1M Hepes, 5% MPD, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E+ DW11.5418
ROTATING ANODERIGAKU FR-E+ DW21.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS1IMAGE PLATEAug 10, 2007
RIGAKU RAXIS2IMAGE PLATEAug 16, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 24587 / % possible obs: 94.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.042 / Χ2: 1.889 / Net I/σ(I): 27.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.712.20.08216890.54865
1.71-1.782.70.08122851.41388.6
1.78-1.863.60.07125571.82298.6
1.86-1.963.60.05425551.47499
1.96-2.083.60.03925781.18299.7
2.08-2.243.70.03226002.18899.9
2.24-2.463.70.02925921.37100
2.46-2.823.80.02825901.183100
2.82-3.553.80.03325811.778100
3.55-303.80.05225604.70498.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å18.51 Å
Translation1.8 Å18.51 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GNU

1gnu


Resolution: 1.65→18.5 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.216 / SU B: 2.137 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Arp/warp, coot, molprobity programs have also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 910 3.707 %thin shells
Rwork0.2 ---
all0.201 ---
obs0.201 24551 95.045 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.432 Å2-0.07 Å2-1.123 Å2
2---0.474 Å2-0.43 Å2
3----0.542 Å2
Refinement stepCycle: LAST / Resolution: 1.65→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1905 0 3 119 2027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221982
X-RAY DIFFRACTIONr_bond_other_d0.0040.021401
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9772710
X-RAY DIFFRACTIONr_angle_other_deg0.90233402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.96723.551107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14715332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2661516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
X-RAY DIFFRACTIONr_nbd_refined0.2130.2354
X-RAY DIFFRACTIONr_nbd_other0.1950.21400
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2967
X-RAY DIFFRACTIONr_nbtor_other0.0820.21000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.212
X-RAY DIFFRACTIONr_mcbond_it2.68921274
X-RAY DIFFRACTIONr_mcbond_other0.7872445
X-RAY DIFFRACTIONr_mcangle_it3.48231904
X-RAY DIFFRACTIONr_scbond_it2.812909
X-RAY DIFFRACTIONr_scangle_it3.8053795
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.6930.3971510.2791029190761.877
1.693-1.73900.2521506185081.405
1.739-1.78800.2451658177493.461
1.788-1.8430.32180.2311558179998.722
1.843-1.90300.211646166698.8
1.903-1.96900.2041608161799.443
1.969-2.04200.1911599160499.688
2.042-2.1250.2591770.1961331151199.801
2.125-2.21800.1961478147999.932
2.218-2.3240.40310.1961397139999.929
2.324-2.4480.2381240.19612051329100
2.448-2.59300.20212591259100
2.593-2.7690.226890.20310911180100
2.769-2.98500.21811031103100
2.985-3.2610.228690.2049621031100
3.261-3.63200.20391391499.891
3.632-4.1670.167380.17178282199.878
4.167-5.0410.156110.15268369899.427
5.041-6.8780.192140.21535549100
6.878-18.50.173180.2329834192.669

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