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- PDB-1gnu: GABA(A) receptor associated protein GABARAP -

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Basic information

Entry
Database: PDB / ID: 1gnu
TitleGABA(A) receptor associated protein GABARAP
ComponentsGABARAP
KeywordsTRANSPORT / UBIQUITIN-LIKE / RECEPTOR
Function / homology
Function and homology information


positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / autophagy of mitochondrion / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / autophagy of mitochondrion / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / smooth endoplasmic reticulum / axoneme / autophagosome membrane / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome / protein targeting / sperm midpiece / macroautophagy / microtubule cytoskeleton organization / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / chemical synaptic transmission / cytoplasmic vesicle / microtubule binding / microtubule / lysosome / Golgi membrane / synapse / ubiquitin protein ligase binding / plasma membrane / 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
NICKEL (II) ION / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKnight, D. / Harris, R. / Moss, S. / Driscoll, P.C. / Keep, N.H.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The X-Ray Crystal Structure and Putative Ligand-Derived Peptide Binding Properties of Gamma-Aminobutyric Acid Receptor Type a Receptor-Associated Protein
Authors: Knight, D. / Harris, R. / Mcalister, M. / Phelan, J. / Geddes, S. / Moss, S. / Driscoll, P.C. / Keep, N.H.
History
DepositionOct 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2001Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GABARAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0012
Polymers13,9421
Non-polymers591
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.013, 55.124, 64.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GABARAP / / GABA(A) RECEPTOR ASSOCIATED PROTEIN / GABARAP / FLC3B / MM46 (HT004 PROTEIN) (MAP1 LIGHT CHAIN 3 ...GABA(A) RECEPTOR ASSOCIATED PROTEIN / GABARAP / FLC3B / MM46 (HT004 PROTEIN) (MAP1 LIGHT CHAIN 3 RELATED PROTEIN)


Mass: 13942.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: NEURONALNeuron / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95166
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.91 Å3/Da / Density % sol: 69 %
Crystal growpH: 8.5
Details: 18MG/ML GABARAP, 50MM TRIS PH8.5, 0.25M NACL,10%(W/V) PEGMONO, pH 8.50
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
136 mg/mlprotein1drop
210 mMTris1drop
30.5 M1droppH7.0NaCl
40.1 MTris1reservoirpH8.5
520 %(w/v)PEG2000MME1reservoir
610 mMnickel(II) chloride hexahydrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.75→22 Å / Num. obs: 11007 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.2 / % possible all: 95.1
Reflection
*PLUS
Lowest resolution: 22 Å / Num. measured all: 82560
Reflection shell
*PLUS
% possible obs: 95.1 % / Num. unique obs: 1540 / Num. measured obs: 11020

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EO6

1eo6


Resolution: 1.75→41.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.97 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CONSTANT COMPONENT OF SCATTERING FACTOR FOR NI(II) SET TO -7.00 IN ATOMSF.LIB TO COMPENSATE FOR BEING NEAR THE NICKEL EDGE
RfactorNum. reflection% reflectionSelection details
Rfree0.23 533 4.9 %RANDOM
Rwork0.201 ---
obs0.203 10450 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.75→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 1 100 1088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221025
X-RAY DIFFRACTIONr_bond_other_d0.0010.02934
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg2.1071.9631379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.95632179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1490.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021111
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02230
X-RAY DIFFRACTIONr_nbd_refined0.2340.3224
X-RAY DIFFRACTIONr_nbd_other0.2210.3919
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2920.5106
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.34503
X-RAY DIFFRACTIONr_metal_ion_refined0.1702
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.512
X-RAY DIFFRACTIONr_symmetry_hbond_other0.33901
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2641.5590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2042962
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3743435
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4054.5417
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 33
Rwork0.375 746
Refinement TLS params.Method: refined / Origin x: 25.952 Å / Origin y: 1.026 Å / Origin z: 6.919 Å
111213212223313233
T0.0178 Å20.0063 Å2-0.011 Å2-0.0293 Å20.0096 Å2--0.0136 Å2
L1.974 °2-1.0566 °20.0508 °2-4.5831 °20.9782 °2--1.482 °2
S0.0506 Å °0.0993 Å °0.0058 Å °-0.2357 Å °-0.0698 Å °-0.0358 Å °-0.0846 Å °-0.0069 Å °0.0192 Å °
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 22 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Lowest resolution: 1.8 Å / Rfactor obs: 0.375

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