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- PDB-3sjd: Crystal structure of S. cerevisiae Get3 with bound ADP-Mg2+ in co... -

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Basic information

Entry
Database: PDB / ID: 3sjd
TitleCrystal structure of S. cerevisiae Get3 with bound ADP-Mg2+ in complex with Get2 cytosolic domain
Components
  • ATPase GET3
  • Golgi to ER traffic protein 2
KeywordsHYDROLASE/TRANSPORT PROTEIN / ATPase / receptor complex / TA-protein biogenesis / GET pathway / HYDROLASE-TRANSPORT PROTEIN complex
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 / mitophagy ...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 / mitophagy / protein-membrane adaptor activity / protein folding chaperone / guanyl-nucleotide exchange factor activity / unfolded protein binding / response to heat / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Golgi to ER traffic protein 2 / GET complex subunit Get2/sif1 / GET complex subunit GET2 / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Golgi to ER traffic protein 2 / ATPase GET3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 4.6 Å
AuthorsReitz, S. / Wild, K. / Sinning, I.
CitationJournal: Science / Year: 2011
Title: Structural basis for tail-anchored membrane protein biogenesis by the Get3-receptor complex.
Authors: Stefer, S. / Reitz, S. / Wang, F. / Wild, K. / Pang, Y.Y. / Schwarz, D. / Bomke, J. / Hein, C. / Lohr, F. / Bernhard, F. / Denic, V. / Dotsch, V. / Sinning, I.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_ref_seq_dif.details / _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: Golgi to ER traffic protein 2
E: Golgi to ER traffic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,85613
Polymers132,3715
Non-polymers1,4858
Water00
1
A: ATPase GET3
B: ATPase GET3
E: Golgi to ER traffic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3868
Polymers86,4183
Non-polymers9685
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATPase GET3
D: Golgi to ER traffic protein 2
hetero molecules

C: ATPase GET3
D: Golgi to ER traffic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,94010
Polymers91,9064
Non-polymers1,0346
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)149.640, 209.750, 133.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-363-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 4:88 or resseq 131: 188 or resseq 214:228 or resseq 230:278 or resseq 285:352 )
211chain B and (resseq 4:88 or resseq 131: 188 or resseq 214:228 or resseq 230:278 or resseq 285:352 )
311chain C and (resseq 4:88 or resseq 131: 188 or resseq 214:228 or resseq 230:278 or resseq 285:352 )
112chain D and (resseq 5:34 )
212chain E and (resseq 5:34 )

NCS ensembles :
ID
1
2
DetailsBIOLOGICAL ASSEMBLY-1 IS A TETRAMER, COMPOSED OF (ABEX). CHAIN X OF MOLECULE-2 IS MISSING IN THE COORDINATES

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Components

#1: Protein ATPase GET3


Mass: 40464.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET3, ARR4, YDL100C, D2371 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q12154, Hydrolases; Acting on acid anhydrides
#2: Protein/peptide Golgi to ER traffic protein 2


Mass: 5488.307 Da / Num. of mol.: 2 / Fragment: Get2 cytosolic domain from residue 1 to 35
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET2, HUR2, RMD7, YER083C / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40056
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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


Mass: 24.305 Da / Num. of mol.: 3 / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 40% (v/v) 1,2-propanediol, 0.1 M sodium acetate , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 4.6→66.6 Å / Num. obs: 11890 / % possible obs: 99.5 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 2.9 / Redundancy: 3.9 % / Rsym value: 0.052 / Net I/σ(I): 9.5
Reflection shellResolution: 4.6→4.85 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: PHASER / Resolution: 4.6→56.23 Å / SU ML: 0.7 / σ(F): 0.02 / Phase error: 38.45 / Stereochemistry target values: ML
Details: THE ELCTRON DENSITY/RESOLUTION IS WEAK IN THE REGIONS OF THE CLOSE CONTACTS
RfactorNum. reflection% reflection
Rfree0.388 538 4.75 %
Rwork0.323 --
obs0.326 11322 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 323.39 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.9541 Å20 Å20 Å2
2---12.7318 Å2-0 Å2
3----4.2223 Å2
Refinement stepCycle: LAST / Resolution: 4.6→56.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7295 0 86 0 7381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0237511
X-RAY DIFFRACTIONf_angle_d2.00510114
X-RAY DIFFRACTIONf_dihedral_angle_d22.9222819
X-RAY DIFFRACTIONf_chiral_restr0.0951150
X-RAY DIFFRACTIONf_plane_restr0.0091283
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2165X-RAY DIFFRACTIONPOSITIONAL
12B2165X-RAY DIFFRACTIONPOSITIONAL0.622
13C2179X-RAY DIFFRACTIONPOSITIONAL0.592
21D248X-RAY DIFFRACTIONPOSITIONAL
22E248X-RAY DIFFRACTIONPOSITIONAL0.001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.6-5.0630.37981390.33442485X-RAY DIFFRACTION90
5.063-5.7950.34731340.30362667X-RAY DIFFRACTION95
5.795-7.29850.36441390.30272751X-RAY DIFFRACTION97
7.2985-56.23770.40051260.32022881X-RAY DIFFRACTION97
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)
12.4821-1.61141.256-2.16351.6631-1.4436-0.47880.15670.0584-0.11160.2558-1.154-0.40990.171503.13030.20540.02912.7483-0.21072.414640.5582-54.2269-28.5149
210.3497-1.20086.5585-0.81932.75453.6959-0.4875-1.0498-1.1689-0.28790.7425-0.6670.1957-0.2488-0.00992.176-0.1314-0.57722.1991-0.28592.315529.3689-45.0139-3.8345
314.164-0.45712.47-0.1091-3.336-1.2668-1.2077-0.83910.35490.94961.25240.8452-0.53060.1499-02.2074-0.13910.22022.3899-0.09541.841427.0264-2.579913.8094
4-0.28490.04141.0509-0.49460.67050.26031.4214-0.8012-2.4414-0.9173.2648-3.5592.04361.410.23522.23780.1802-0.50861.8618-0.31554.489726.681-23.077415.5296
51.5327-0.30361.0569-0.3774-0.30040.9398-1.3826-0.6244-0.2054-0.7349-0.59841.7001-2.88683.7578-0.14193.05990.0641-1.34662.33380.614.145142.2531-74.1776-27.0902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E

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