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- PDB-2woj: ADP-AlF4 complex of S. cerevisiae GET3 -

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Basic information

Entry
Database: PDB / ID: 2woj
TitleADP-AlF4 complex of S. cerevisiae GET3
ComponentsATPASE GET3
KeywordsHYDROLASE / TAIL-ANCHORED / MEMBRANE PROTEIN / TARGETING FACTOR / ENDOPLASMIC RETICULUM / GET3 / ATPASE / TRC40 / ATP-BINDING / GOLGI APPARATUS / ER-GOLGI TRANSPORT / NUCLEOTIDE-BINDING / ARSENICAL RESISTANCE / NUCLEUS / CYTOPLASM / TRANSPORT / ARSA / ARSENITE
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
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / ATPase GET3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsMateja, A. / Szlachcic, A. / Downing, M.E. / Dobosz, M. / Mariappan, M. / Hegde, R.S. / Keenan, R.J.
CitationJournal: Nature / Year: 2009
Title: The Structural Basis of Tail-Anchored Membrane Protein Recognition by Get3.
Authors: Mateja, A. / Szlachcic, A. / Downing, M.E. / Dobosz, M. / Mariappan, M. / Hegde, R.S. / Keenan, R.J.
History
DepositionJul 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: 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_asym_id / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.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.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
C: ATPASE GET3
D: ATPASE GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,92318
Polymers157,5744
Non-polymers2,34914
Water9,224512
1
C: ATPASE GET3
D: ATPASE GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9629
Polymers78,7872
Non-polymers1,1747
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-98.29 kcal/mol
Surface area23490 Å2
MethodPISA
2
A: ATPASE GET3
B: ATPASE GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9629
Polymers78,7872
Non-polymers1,1747
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-100.44 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.612, 82.628, 167.282
Angle α, β, γ (deg.)90.00, 98.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ATPASE GET3 / GET3 / ARR4 / TRC40 / ASNA-1 / ATPASE SUBUNIT OF THE GET COMPLEX / ARSENICAL PUMP-DRIVING ATPASE / ...GET3 / ARR4 / TRC40 / ASNA-1 / ATPASE SUBUNIT OF THE GET COMPLEX / ARSENICAL PUMP-DRIVING ATPASE / ARSENITE-TRANSLOCATING ATPASE / ARSENICAL RESISTANCE ATPASE / ARSENITE-TRANSPORTING ATPASE


Mass: 39393.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)/PLYSS / References: UniProt: Q12154, EC: 3.6.3.16

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Non-polymers , 5 types, 526 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8.4
Details: 33% PEG3350, 0.1 M TRIS PH 8.4, 0.2 M AMMONIUM ACETATE, 75 MM NA/K TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 94446 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / % possible all: 86.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIAL MODEL DERIVED FROM SAD DATASET

Resolution: 1.994→37.441 Å / SU ML: 0 / σ(F): 1.34 / Phase error: 21.7 / Stereochemistry target values: ML
Details: DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.2127 4715 5 %
Rwork0.1759 --
obs0.1778 94446 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.944 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 47.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.9173 Å20 Å2-8.7466 Å2
2--0.0133 Å2-0 Å2
3----3.9307 Å2
Refinement stepCycle: LAST / Resolution: 1.994→37.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9368 0 134 512 10014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119694
X-RAY DIFFRACTIONf_angle_d1.33113068
X-RAY DIFFRACTIONf_dihedral_angle_d17.3853639
X-RAY DIFFRACTIONf_chiral_restr0.0881485
X-RAY DIFFRACTIONf_plane_restr0.0061641
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9937-2.01640.28791150.25422452X-RAY DIFFRACTION78
2.0164-2.04010.2811540.23662690X-RAY DIFFRACTION88
2.0401-2.0650.27391500.22882729X-RAY DIFFRACTION87
2.065-2.09110.24751250.21572892X-RAY DIFFRACTION93
2.0911-2.11860.25451500.20882856X-RAY DIFFRACTION92
2.1186-2.14770.25931630.19812863X-RAY DIFFRACTION92
2.1477-2.17830.22921650.1952907X-RAY DIFFRACTION94
2.1783-2.21080.23611750.18632832X-RAY DIFFRACTION94
2.2108-2.24540.22371340.17572958X-RAY DIFFRACTION93
2.2454-2.28220.23371600.17842910X-RAY DIFFRACTION94
2.2822-2.32150.21471600.17642918X-RAY DIFFRACTION94
2.3215-2.36380.22271470.1762928X-RAY DIFFRACTION94
2.3638-2.40920.22091650.17182984X-RAY DIFFRACTION96
2.4092-2.45840.21491670.17543000X-RAY DIFFRACTION96
2.4584-2.51180.24981630.17713003X-RAY DIFFRACTION97
2.5118-2.57020.21411500.16963052X-RAY DIFFRACTION97
2.5702-2.63450.2011370.16413078X-RAY DIFFRACTION99
2.6345-2.70570.21581650.1643127X-RAY DIFFRACTION99
2.7057-2.78530.2131480.16693104X-RAY DIFFRACTION99
2.7853-2.87520.21131560.17213106X-RAY DIFFRACTION99
2.8752-2.97790.24231630.17943125X-RAY DIFFRACTION99
2.9779-3.09710.20441640.16893099X-RAY DIFFRACTION100
3.0971-3.23790.21671760.16193082X-RAY DIFFRACTION100
3.2379-3.40850.181590.15843154X-RAY DIFFRACTION100
3.4085-3.62190.19661610.15153112X-RAY DIFFRACTION100
3.6219-3.90130.18591650.15233136X-RAY DIFFRACTION100
3.9013-4.29340.18331630.15923129X-RAY DIFFRACTION100
4.2934-4.91350.1991710.15673165X-RAY DIFFRACTION100
4.9135-6.1860.21821700.18733148X-RAY DIFFRACTION100
6.186-37.44750.20871740.20583192X-RAY DIFFRACTION99
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)
11.6791-0.52330.49782.22630.08112.57670.19690.2253-0.1987-0.3887-0.18080.09120.1213-0.0024-0.00010.21980.11640.02910.2267-0.03770.166415.024238.970449.9513
21.6772-0.54930.37181.7612-0.21092.62880.0091-0.1779-0.01660.1802-0.0893-0.0865-0.21960.0692-0.00010.1495-0.01830.06540.19150.00480.150822.191346.201573.5889
32.3496-0.48540.58352.26970.21741.9753-0.03830.1494-0.1345-0.03310.10880.0680.20770.021800.23810.0576-0.02020.2033-0.03460.200447.7993-13.244618.7067
41.9476-0.15930.29641.6370.25931.9044-0.2533-0.01490.4110.07530.13770.0827-0.3389-0.1133-00.34230.0916-0.09710.2291-0.03460.374241.224210.590823.3607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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