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- PDB-3h84: Crystal structure of GET3 -

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Basic information

Entry
Database: PDB / ID: 3h84
TitleCrystal structure of GET3
ComponentsATPase GET3
KeywordsCHAPERONE / beta-alpha-barrels / Arsenical resistance / ATP-binding / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Hydrolase / Nucleotide-binding / Transport
Function / homology
Function and homology information


GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / protein folding chaperone ...GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / protein folding chaperone / guanyl-nucleotide exchange factor activity / unfolded protein binding / response to heat / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHu, J. / Li, J. / Qian, X. / Sha, B.
CitationJournal: Plos One / Year: 2009
Title: The crystal structures of yeast Get3 suggest a mechanism for tail-anchored protein membrane insertion.
Authors: Hu, J. / Li, J. / Qian, X. / Denic, V. / Sha, B.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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: ATPase GET3
B: ATPase GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,04110
Polymers78,7872
Non-polymers2548
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-119 kcal/mol
Surface area31480 Å2
MethodPISA
2
A: ATPase GET3
B: ATPase GET3
hetero molecules

A: ATPase GET3
B: ATPase GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,08220
Polymers157,5744
Non-polymers50816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7980 Å2
ΔGint-267 kcal/mol
Surface area60500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.400, 113.743, 48.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ATPase GET3 / Arsenical pump-driving ATPase / Arsenite-translocating ATPase / Arsenical resistance ATPase / ...Arsenical pump-driving ATPase / Arsenite-translocating ATPase / Arsenical resistance ATPase / Arsenite-transporting ATPase / Golgi to ER traffic protein 3


Mass: 39393.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GET3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12154, EC: 3.6.3.16

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Non-polymers , 5 types, 332 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6
Details: 13% PEG 4K, 0.2M Ammonium sulfate, 20% Ethylene Glycol, 0.1% n-octyl-[beta]-D-glucopyranoside, pH 6.0, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 54963 / Num. obs: 54963 / % possible obs: 100 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2 / Redundancy: 6.2 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 32.77
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2524 / Rsym value: 0.586 / % possible all: 97.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.928 / SU B: 10.552 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2.2 / σ(I): 2.2 / ESU R: 0.22 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2763 5.1 %RANDOM
Rwork0.22168 ---
obs0.22297 51794 99.29 %-
all-54963 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2---0.94 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 8 324 5405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225157
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9666957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3535645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80125.941239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49415950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951517
X-RAY DIFFRACTIONr_chiral_restr0.080.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023836
X-RAY DIFFRACTIONr_nbd_refined0.1910.22414
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0920.212
X-RAY DIFFRACTIONr_mcbond_it0.4161.53215
X-RAY DIFFRACTIONr_mcangle_it0.78625186
X-RAY DIFFRACTIONr_scbond_it0.92631973
X-RAY DIFFRACTIONr_scangle_it1.5224.51771
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 204 -
Rwork0.291 3567 -
obs--95.4 %
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)
12.25991.2279-0.60351.8485-0.58982.1980.0615-0.16270.03270.1913-0.0091-0.05960.0763-0.1896-0.0524-0.11530.020.0039-0.21290.0116-0.271742.272416.967816.4731
22.2464-1.0853-0.25992.6540.43722.06820.02070.07640.0753-0.04940.03230.6784-0.2181-0.3732-0.053-0.13910.03910.0474-0.19550.03820.173534.6263-13.254-3.4789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 348
2X-RAY DIFFRACTION2B6 - 350

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