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- PDB-3sjb: Crystal structure of S. cerevisiae Get3 in the open state in comp... -

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Basic information

Entry
Database: PDB / ID: 3sjb
TitleCrystal structure of S. cerevisiae Get3 in the open state in complex with Get1 cytosolic domain
Components
  • ATPase GET3
  • Golgi to ER traffic protein 1
KeywordsHYDROLASE/TRANSPORT PROTEIN / Coiled-coil / receptor complex / TA-protein biogenesis / GET pathway / HYDROLASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


establishment of protein localization to endoplasmic reticulum membrane / 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 / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / response to metal ion ...establishment of protein localization to endoplasmic reticulum membrane / 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 / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / response to metal ion / protein transmembrane transporter activity / mitophagy / protein-membrane adaptor activity / protein folding chaperone / guanyl-nucleotide exchange factor activity / mitochondrial membrane / unfolded protein binding / cellular response to oxidative stress / response to heat / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Get 1, fungi / Helix hairpin bin / Get1 family / CHD5-like protein / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Helix hairpin bin domain superfamily / Helix Hairpins ...Get 1, fungi / Helix hairpin bin / Get1 family / CHD5-like protein / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Helix hairpin bin domain superfamily / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Golgi to ER traffic protein 1 / ATPase GET3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_conn.ptnr2_label_seq_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: Golgi to ER traffic protein 1
D: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,9509
Polymers103,5054
Non-polymers4455
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-96 kcal/mol
Surface area34910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.900, 112.900, 310.481
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein ATPase GET3


Mass: 40464.730 Da / Num. of mol.: 2
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 Golgi to ER traffic protein 1


Mass: 11287.648 Da / Num. of mol.: 2 / Fragment: Get1 cytosolic domain from residue 19 to 103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET1, MDM39, YGL020C / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53192
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1 M LiCl, 20% PEG 6000, 0.1 M Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3.3→93.3 Å / Num. obs: 18481 / % possible obs: 99.7 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 4.9 % / Rsym value: 0.092
Reflection shellResolution: 3.3→3.48 Å / % possible all: 95.1

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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: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WOJ

2woj


Resolution: 3.3→48.887 Å / SU ML: 0.35 / σ(F): 1.35 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 941 5.11 %random
Rwork0.1946 ---
obs0.197 18397 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 103.091 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1929 Å20 Å20 Å2
2---2.1929 Å2-0 Å2
3---4.3857 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.887 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5802 0 21 0 5823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095917
X-RAY DIFFRACTIONf_angle_d1.1947969
X-RAY DIFFRACTIONf_dihedral_angle_d19.3722213
X-RAY DIFFRACTIONf_chiral_restr0.075886
X-RAY DIFFRACTIONf_plane_restr0.0041029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.4740.29381550.23572399X-RAY DIFFRACTION100
3.474-3.69160.23331310.19812436X-RAY DIFFRACTION100
3.6916-3.97650.23761280.16652453X-RAY DIFFRACTION100
3.9765-4.37640.2341250.15212478X-RAY DIFFRACTION100
4.3764-5.00920.20451260.14632495X-RAY DIFFRACTION100
5.0092-6.30890.2081420.18742533X-RAY DIFFRACTION100
6.3089-48.89250.27451340.23482662X-RAY DIFFRACTION98
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)
12.1432-0.6934-0.72781.1653-0.06411.1641-0.22510.0046-0.16810.0287-0.04590.16360.03570.18940.26410.296-0.020.02750.65420.14810.570530.6348-54.25059.0478
21.3570.00111.16281.32230.01521.30610.3118-0.9221-0.216-0.3881-0.10440.42720.0683-0.5793-0.1410.8631-0.0445-0.12541.5850.31991.074330.0448-62.244133.9007
31.9155-0.02331.06571.9573-0.07651.5501-0.2375-0.08270.14520.0165-0.0878-0.0802-0.0624-0.08940.30950.23610.017-0.02140.5920.04730.5235-1.1104-40.84926.7329
42.40560.29980.69911.2476-0.00851.4367-0.4849-1.35630.6812-0.23730.38650.07970.0452-0.43550.24740.89620.3692-0.25341.4147-0.44861.0895-0.0796-25.890229.7652
50.7317-0.6906-0.96271.947-0.82292.8361-0.00910.06780.0753-0.07660.50960.17110.27820.4809-0.25460.6024-0.1010.14080.84960.22790.64176.4568-58.633937.3594
6-0.27290.18450.7844-0.1953-0.09191.08220.21150.14330.49060.05580.0929-0.0595-0.02990.3186-0.38740.9748-0.1336-0.11611.1808-0.31380.903423.3108-28.263637.3276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and ((resseq 4:88) or (resseq 158:170) or (resseq 233:354))
2X-RAY DIFFRACTION2chain A and ((resseq 89:157) or (resseq 172:232))
3X-RAY DIFFRACTION3chain B and ((resseq 4:88) or (resseq 158:170) or (resseq 233:354))
4X-RAY DIFFRACTION4chain B and ((resseq 89:157) or (resseq 172:232))
5X-RAY DIFFRACTION5chain C and resseq 20:82
6X-RAY DIFFRACTION6chain D and resseq 19:90

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