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- PDB-3sjc: Crystal structure of S.cerevisiae Get3 in the semi-open state in ... -

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Basic information

Entry
Database: PDB / ID: 3sjc
TitleCrystal structure of S.cerevisiae Get3 in the semi-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


pheromone-dependent signal transduction involved in conjugation with cellular fusion / GET complex / 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 ...pheromone-dependent signal transduction involved in conjugation with cellular fusion / GET complex / 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 folding chaperone / protein-membrane adaptor activity / guanyl-nucleotide exchange factor activity / mitochondrial membrane / unfolded protein binding / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Golgi to ER traffic protein 1 / ATPase GET3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 1.3May 14, 2014Group: Refinement description
Revision 1.4Feb 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_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
E: ATPase GET3
F: ATPase GET3
G: Golgi to ER traffic protein 1
H: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,57710
Polymers193,4468
Non-polymers1312
Water0
1
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)96,7885
Polymers96,7234
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: ATPase GET3
F: ATPase GET3
G: Golgi to ER traffic protein 1
H: Golgi to ER traffic protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7885
Polymers96,7234
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.071, 112.243, 135.978
Angle α, β, γ (deg.)90.00, 103.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain B and (resseq 5:93 or resseq 131:182 or resseq 214:278 or resseq 285:352 )
211chain E and (resseq 5:93 or resseq 131:182 or resseq 214:278 or resseq 285:352 )
311chain F and (resseq 5:93 or resseq 131:182 or resseq 214:278 or resseq 285:352 )
112chain C and (resseq 38:91 )
212chain D and (resseq 38:91 )
312chain G and (resseq 38:91 )
412chain H and (resseq 38:91 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
ATPase GET3


Mass: 40464.730 Da / Num. of mol.: 4
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: 7896.763 Da / Num. of mol.: 4 / Fragment: Get1 cytosolic domain from residue 36 to 93
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-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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 M LiCl, 21% PEG 6000, 0.1 M Tris/HCl, pH 7.5, 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
DetectorDate: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.2→56.3 Å / Num. obs: 31634 / % possible obs: 100 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8 / Redundancy: 3.8 % / Rsym value: 0.124 / Net I/σ(I): 7.3
Reflection shellResolution: 3.2→3.37 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→47.436 Å / SU ML: 0.51 / σ(F): 0 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1443 5.05 %random
Rwork0.2093 ---
obs0.2119 28576 90.82 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.834 Å2 / ksol: 0.26 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.066 Å2-0 Å211.5655 Å2
2--0.745 Å20 Å2
3----0.7539 Å2
Refinement stepCycle: LAST / Resolution: 3.2→47.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10557 0 2 0 10559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110745
X-RAY DIFFRACTIONf_angle_d1.18914462
X-RAY DIFFRACTIONf_dihedral_angle_d16.1874059
X-RAY DIFFRACTIONf_chiral_restr0.0711636
X-RAY DIFFRACTIONf_plane_restr0.0041854
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2158X-RAY DIFFRACTIONPOSITIONAL
12E2158X-RAY DIFFRACTIONPOSITIONAL0.035
13F2170X-RAY DIFFRACTIONPOSITIONAL0.032
21C453X-RAY DIFFRACTIONPOSITIONAL
22D453X-RAY DIFFRACTIONPOSITIONAL0.033
23G453X-RAY DIFFRACTIONPOSITIONAL0.03
24H453X-RAY DIFFRACTIONPOSITIONAL0.033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.31440.32631300.30132494X-RAY DIFFRACTION84
3.3144-3.44710.29451400.24462522X-RAY DIFFRACTION86
3.4471-3.60390.2821280.2162688X-RAY DIFFRACTION89
3.6039-3.79380.24131310.20672677X-RAY DIFFRACTION91
3.7938-4.03140.2391510.18662781X-RAY DIFFRACTION92
4.0314-4.34250.21181500.17192753X-RAY DIFFRACTION93
4.3425-4.77910.23821320.15362829X-RAY DIFFRACTION95
4.7791-5.46980.26021570.19222838X-RAY DIFFRACTION95
5.4698-6.8880.30061620.2492753X-RAY DIFFRACTION93
6.888-47.44080.25441620.23092798X-RAY DIFFRACTION92
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)
10.2288-0.3178-0.00630.7018-0.03810.07740.1420.0944-0.0666-0.215-0.063-0.07260.0058-0.1078-0.0331-0.12810.1559-0.0867-0.27740.0379-0.017530.7596-19.683661.3894
20.2210.1294-0.10080.23610.15770.3249-0.01790.0364-0.0202-0.2199-0.2011-0.0025-0.4589-0.34210.12190.46140.1990.14130.2396-0.0678-0.003318.3971-14.438340.9186
30.4672-0.8480.09382.2634-0.47420.2269-0.01790.2127-0.20880.34770.10010.5792-0.2356-0.0296-0.05090.11450.01850.0524-0.11590.00760.10174.5826-29.198375.7272
40.1609-0.04970.20470.0152-0.07440.24620.05870.135-0.0608-0.02310.12640.09390.04160.0427-0.1402-0.1024-0.0056-0.15460.2194-0.03720.2445-6.5741-33.953354.05
50.091-0.1559-0.04580.5909-0.17910.40710.0393-0.0060.05310.13310.20090.08860.1751-0.0327-0.1830.16530.0038-0.11020.01020.02920.16572.1248-0.23157.9343
60.6680.78710.07021.55970.09980.0053-0.20130.13730.0286-0.31280.2922-0.02560.15440.0347-0.05920.23620.0079-0.1286-0.0617-0.1162-0.063816.828-48.382749.5787
70.1597-0.136-0.05010.5810.42950.36410.05220.015-0.1233-0.32140.0189-0.6276-0.0511-0.0181-0.07120.68650.0250.05340.0975-0.0051.016914.5611-18.7024127.4992
80.0785-0.2318-0.17510.82580.42810.6498-0.0121-0.02960.02890.03770.0418-0.2069-0.3567-0.0555-0.07480.41580.13020.09040.0887-0.19840.13982.001-13.6951106.3949
90.4165-0.33690.10440.4304-0.00960.2286-0.1207-0.02140.01710.17780.09960.8383-0.10580.00470.03430.8210.05250.20650.1290.00190.8382-11.6931-28.325141.6057
100.1361-0.25440.03961.0973-0.08280.29160.201-0.0274-0.22980.41330.03630.41520.07760.0349-0.22360.34390.0065-0.23950.0789-0.07850.8876-22.5431-33.2301119.9395
110.15160.0046-0.01350.0015-0.01610.2051-0.10880.0209-0.0397-0.19250.17140.45660.18690.0154-0.07440.8519-0.0026-0.1020.0714-0.05110.8795-14.10150.6991123.8696
120.10230.0040.09630.0030.04680.5288-0.00980.0038-0.06240.02570.2458-0.3246-0.0611-0.0241-0.230.86650.0305-0.01370.08720.0090.61520.7355-47.4694115.5582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )A4 - 88
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )A158 - 170
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )A233 - 352
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 89:157 OR RESID 172:232 ) )A89 - 157
5X-RAY DIFFRACTION2( CHAIN A AND ( RESID 89:157 OR RESID 172:232 ) )A172 - 232
6X-RAY DIFFRACTION3( CHAIN B AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )B4 - 88
7X-RAY DIFFRACTION3( CHAIN B AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )B158 - 170
8X-RAY DIFFRACTION3( CHAIN B AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )B233 - 352
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 89:157 OR RESID 172:232 ) )B89 - 157
10X-RAY DIFFRACTION4( CHAIN B AND ( RESID 89:157 OR RESID 172:232 ) )B172 - 232
11X-RAY DIFFRACTION5( CHAIN C AND RESID 38:91 )C38 - 91
12X-RAY DIFFRACTION6( CHAIN D AND RESID 38:91 )D38 - 91
13X-RAY DIFFRACTION7( CHAIN E AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )E4 - 88
14X-RAY DIFFRACTION7( CHAIN E AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )E158 - 170
15X-RAY DIFFRACTION7( CHAIN E AND ( RESID 4:88 OR RESID 158:170 OR RESID 233:352 ) )E233 - 352
16X-RAY DIFFRACTION8( CHAIN E AND ( RESID 89:157 OR RESID 172:232 ) )E89 - 157
17X-RAY DIFFRACTION8( CHAIN E AND ( RESID 89:157 OR RESID 172:232 ) )E172 - 232
18X-RAY DIFFRACTION9( CHAIN F AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:352 ) )F5 - 88
19X-RAY DIFFRACTION9( CHAIN F AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:352 ) )F158 - 170
20X-RAY DIFFRACTION9( CHAIN F AND ( RESID 5:88 OR RESID 158:170 OR RESID 233:352 ) )F233 - 352
21X-RAY DIFFRACTION10( CHAIN F AND ( RESID 89:157 OR RESID 172:232 ) )F89 - 157
22X-RAY DIFFRACTION10( CHAIN F AND ( RESID 89:157 OR RESID 172:232 ) )F172 - 232
23X-RAY DIFFRACTION11( CHAIN G AND RESID 38:91 )G38 - 91
24X-RAY DIFFRACTION12( CHAIN H AND RESID 38:91 )H38 - 91

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