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- PDB-4co7: Crystal structure of human GATE-16 -

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Basic information

Entry
Database: PDB / ID: 4co7
TitleCrystal structure of human GATE-16
ComponentsGAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2
KeywordsPROTEIN TRANSPORT / AUTOPHAGY / BETA-GRASP FOLD / UBIQUITIN SUPERFAMILY
Function / homology
Function and homology information


protein localization to endoplasmic reticulum / negative regulation of proteasomal protein catabolic process / intra-Golgi vesicle-mediated transport / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / TBC/RABGAPs / Macroautophagy / beta-tubulin binding ...protein localization to endoplasmic reticulum / negative regulation of proteasomal protein catabolic process / intra-Golgi vesicle-mediated transport / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / TBC/RABGAPs / Macroautophagy / beta-tubulin binding / autophagosome membrane / autophagosome assembly / autophagosome / SNARE binding / macroautophagy / autophagy / protein transport / ATPase binding / cytoplasmic vesicle / microtubule binding / Golgi membrane / ubiquitin protein ligase binding / endoplasmic reticulum membrane / Golgi apparatus / cytosol / cytoplasm
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 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWeiergraeber, O.H. / Ma, P. / Willbold, D.
CitationJournal: Biochemistry / Year: 2015
Title: Conformational Polymorphism in Autophagy-Related Protein Gate-16.
Authors: Ma, P. / Schillinger, O. / Schwarten, M. / Lecher, J. / Hartmann, R. / Stoldt, M. / Mohrluder, J. / Olubiyi, O. / Strodel, B. / Willbold, D. / Weiergraber, O.H.
History
DepositionJan 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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 2
B: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2


Theoretical massNumber of molelcules
Total (without water)27,6622
Polymers27,6622
Non-polymers00
Water2,720151
1
A: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2


Theoretical massNumber of molelcules
Total (without water)13,8311
Polymers13,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2


Theoretical massNumber of molelcules
Total (without water)13,8311
Polymers13,8311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.730, 67.440, 58.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9998, -0.01669, 0.008549), (0.01655, -0.9997, -0.01662), (0.008824, -0.01648, 0.9998)
Vector: 38.28, 74.79, 29.62)

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Components

#1: Protein GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 2 / GABA(A) RECEPTOR-ASSOCIATED PROTEIN-LIKE 2 / GANGLIOSIDE EXPRESSION FACTOR 2 / GEF-2 / GENERAL ...GABA(A) RECEPTOR-ASSOCIATED PROTEIN-LIKE 2 / GANGLIOSIDE EXPRESSION FACTOR 2 / GEF-2 / GENERAL PROTEIN TRANSPORT FACTOR P16 / GOLGI-ASSOCIATED ATPASE ENHANCER OF 16 KDA / GATE-16 / MAP1 LIGHT CHAIN 3-RELATED PROTEIN


Mass: 13830.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P60520
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPURIFIED PROTEIN CONTAINS CLONING ARTIFACT (GS) AT N- TERMINUS

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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: 40 % / Description: NONE
Crystal growpH: 7
Details: 100 MM SODIUM PHOSPHATE PH 7.0, 50 MM POTASSIUM CHLORIDE, 10 MM DITHIOTHREITOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0092
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 22, 2011 / Details: FOCUSSING MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0092 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.49
ReflectionResolution: 2→44.29 Å / Num. obs: 14406 / % possible obs: 94.8 % / Redundancy: 2.2 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 5.8 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EO6

1eo6


Resolution: 2→29.36 Å / σ(F): 1.43 / Phase error: 23.96 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2117 1051 7.3 %
Rwork0.1805 --
obs0.1878 14392 94.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 2→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 0 151 2073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051966
X-RAY DIFFRACTIONf_angle_d0.8172649
X-RAY DIFFRACTIONf_dihedral_angle_d12.825743
X-RAY DIFFRACTIONf_chiral_restr0.039286
X-RAY DIFFRACTIONf_plane_restr0.004335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0005-2.10590.29491390.27961913X-RAY DIFFRACTION88
2.1059-2.23780.29591400.2431929X-RAY DIFFRACTION89
2.2378-2.41050.241470.23371939X-RAY DIFFRACTION89
2.4105-2.65280.22351430.22061895X-RAY DIFFRACTION89
2.6528-3.03620.22251440.19391949X-RAY DIFFRACTION89
3.0362-3.82320.20581430.15441904X-RAY DIFFRACTION88
3.8232-25.80880.16911360.13741855X-RAY DIFFRACTION83

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