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- PDB-5bw8: 2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex ... -

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Basic information

Entry
Database: PDB / ID: 5bw8
Title2.8 A crystal structure of a Get3-Get4-Get5 intermediate complex from S.cerevisiae
Components
  • ATPase GET3
  • Golgi to ER traffic protein 4
  • Ubiquitin-like protein MDY2
  • Unknown Protein
KeywordsHydrolase/Transport / Tail-anchored targeting / ATPase / electrostatic interaction / Hydrolase-Transport complex
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / TRC 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 ...cell morphogenesis involved in conjugation with cellular fusion / GET complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / TRC 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 / protein folding chaperone / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / cytoplasmic stress granule / unfolded protein binding / protein-folding chaperone binding / response to heat / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase ...Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Ubiquitin-like protein MDY2, C-terminal domain / Golgi to ER traffic protein 4 / Golgi to ER traffic protein 4 / Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATPase GET3 / Golgi to ER traffic protein 4 / ATPase GET3 / Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGristick, H.B. / Chartron, J.W. / Clemons, W.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Mechanism of Assembly of a Substrate Transfer Complex during Tail-anchored Protein Targeting.
Authors: Gristick, H.B. / Rome, M.E. / Chartron, J.W. / Rao, M. / Hess, S. / Shan, S.O. / Clemons, W.M.
History
DepositionJun 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Sep 27, 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 4
D: Ubiquitin-like protein MDY2
Z: Unknown Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,1816
Polymers126,1155
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-89 kcal/mol
Surface area46400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.960, 238.050, 52.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 4 - 352 / Label seq-ID: 23 - 371

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein ATPase GET3 / Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Golgi to ER traffic protein 3 / Guided ...Arsenical pump-driving ATPase / Arsenite-stimulated ATPase / Golgi to ER traffic protein 3 / Guided entry of tail-anchored proteins 3


Mass: 41576.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast)
Strain: RM11-1a / Gene: GET3, SCRG_00595 / Production host: Escherichia coli (E. coli)
References: UniProt: B3LGZ3, UniProt: Q12154*PLUS, Hydrolases; Acting on acid anhydrides
#2: Protein Golgi to ER traffic protein 4 / Guided entry of tail-anchored proteins 4


Mass: 35803.250 Da / Num. of mol.: 1 / Fragment: UNP residues 1-290 / Mutation: K258A, K260A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GET4, YOR164C, O3580 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12125
#3: Protein Ubiquitin-like protein MDY2 / Golgi to ER traffic protein 5 / Mating-deficient protein 2 / Translation machinery-associated protein 24


Mass: 6034.042 Da / Num. of mol.: 1 / Fragment: UNP residues 1-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MDY2, GET5, TMA24, YOL111C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12285
#4: Protein/peptide Unknown Protein


Mass: 1124.378 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
#5: 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: 55.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 17% PEG 3350, 0.24 M Na citrate, and 30 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→29.8 Å / Num. obs: 34114 / % possible obs: 97 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.6 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0043refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A37 and 3LKU

3a37

3lku


Resolution: 2.8→29.8 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 39.837 / SU ML: 0.347 / Cross valid method: THROUGHOUT / ESU R: 1.562 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26161 1710 5 %RANDOM
Rwork0.22404 ---
obs0.2259 32332 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 111.032 Å2
Baniso -1Baniso -2Baniso -3
1-5.29 Å20 Å2-0 Å2
2---1.23 Å2-0 Å2
3----4.05 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7741 0 1 0 7742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197900
X-RAY DIFFRACTIONr_bond_other_d0.0040.027508
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.96910664
X-RAY DIFFRACTIONr_angle_other_deg1.033317340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.57425.442373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.384151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0291525
X-RAY DIFFRACTIONr_chiral_restr0.1160.21198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028868
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021765
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7124.4763876
X-RAY DIFFRACTIONr_mcbond_other3.7054.4743875
X-RAY DIFFRACTIONr_mcangle_it6.1186.6884831
X-RAY DIFFRACTIONr_mcangle_other6.126.6914832
X-RAY DIFFRACTIONr_scbond_it3.0394.574024
X-RAY DIFFRACTIONr_scbond_other3.0394.5734025
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1196.8015833
X-RAY DIFFRACTIONr_long_range_B_refined13.18442.37435370
X-RAY DIFFRACTIONr_long_range_B_other13.18542.37735371
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17758 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 127 -
Rwork0.357 2296 -
obs--93.84 %
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)
13.40341.3052-0.60162.9022-0.27853.6168-0.0292-0.0148-0.4132-0.2866-0.1713-0.13680.47450.03630.20050.09390.03720.040.75450.02471.070112.12944.107-5.987
20.58411.2342-0.89096.868-1.8373.5138-0.29270.3326-0.5434-0.79390.00280.09711.0616-0.31090.28980.3458-0.08640.10250.8232-0.14051.48546.56928.495-8.527
355.418-22.95240.63929.509-0.270.0298-0.7161-2.0636-4.54540.23130.82271.93820.04740.197-0.10662.75240.0646-0.47012.3779-0.12442.87593.622-6.0949.024
42.31620.9916-0.86692.9287-0.97761.19490.0318-0.0729-0.2130.017-0.05780.16350.03350.0570.0260.0034-0.004-0.00720.80510.05080.97254.73948.0121.557
52.3371-0.57750.54353.27651.15884.541-0.0671-0.17960.24980.59360.0563-0.05850.18590.27290.01080.1113-0.0227-0.03430.80260.01730.8024-28.07952.73619.723
60.5140.4732-0.49512.0891-1.55232.7867-0.0112-0.1068-0.00580.2066-0.1888-0.15820.29040.25710.20.1428-0.0074-0.0060.83820.04460.9014-25.41537.49119.463
729.9444-23.992118.433834.398-5.194517.3958-0.8776-1.1139-0.1895-1.93860.53870.8354-2.2113-0.98850.33890.74280.30550.19921.32590.46421.5548-13.84364.881-8.247
82.9006-1.42020.69741.5045-0.93752.1806-0.12940.16260.3611-0.0648-0.0111-0.2538-0.11140.14050.14060.0475-0.0762-0.01240.83450.06650.9911-24.25958.1661.432
97.18582.81520.80574.11042.54614.408-0.2035-0.26860.70510.0274-0.27530.6818-0.0115-0.33550.47880.4070.00790.00920.54090.12170.9336-36.29734.746-8.852
103.01390.57021.1676.94491.99461.1120.11450.1115-0.54980.45870.05620.61590.42550.0335-0.17070.4383-0.0908-0.01460.5860.10420.9512-34.59212.704-7.117
111.2278-1.12091.54426.69011.35177.6460.13350.3541-0.99440.1295-0.25441.09471.1261-0.44350.12090.4492-0.2224-0.4020.4899-0.26992.3748-46.128-17.977-15.409
1210.9436-3.26052.40032.1296-0.46490.83940.21440.4818-1.9611-0.9814-0.03530.36570.06980.3809-0.17911.3140.0754-0.260.9851-0.31352.6154-31.912-25.075-12.636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 60
2X-RAY DIFFRACTION2A61 - 192
3X-RAY DIFFRACTION3A193 - 206
4X-RAY DIFFRACTION4A212 - 352
5X-RAY DIFFRACTION5B3 - 98
6X-RAY DIFFRACTION6B99 - 276
7X-RAY DIFFRACTION7B277 - 291
8X-RAY DIFFRACTION8B292 - 351
9X-RAY DIFFRACTION9C11 - 37
10X-RAY DIFFRACTION10C38 - 170
11X-RAY DIFFRACTION11C171 - 262
12X-RAY DIFFRACTION12C263 - 292

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