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- PDB-5bwk: 6.0 A Crystal structure of a Get3-Get4-Get5 intermediate complex ... -

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Basic information

Entry
Database: PDB / ID: 5bwk
Title6.0 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
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 / TRC 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 ...cell morphogenesis involved in conjugation with cellular fusion / GET complex / TRC 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 / vesicle-mediated transport / protein folding chaperone / guanyl-nucleotide exchange factor activity / cytoplasmic stress granule / unfolded protein binding / response to heat / cellular response to oxidative stress / protein-macromolecule adaptor activity / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding / nucleus / 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 ...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 / Ubiquitin family / Ubiquitin homologues / Tetratricopeptide-like helical domain superfamily / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
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: 6 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 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: ATPase GET3
E: Golgi to ER traffic protein 4
F: Ubiquitin-like protein MDY2
G: Golgi to ER traffic protein 4
H: Ubiquitin-like protein MDY2
I: Golgi to ER traffic protein 4
J: Ubiquitin-like protein MDY2
K: Golgi to ER traffic protein 4
L: Ubiquitin-like protein MDY2
M: ATPase GET3
N: ATPase GET3
O: ATPase GET3
P: ATPase GET3
Q: Golgi to ER traffic protein 4
R: Ubiquitin-like protein MDY2
S: Golgi to ER traffic protein 4
T: Ubiquitin-like protein MDY2
U: Golgi to ER traffic protein 4
V: Ubiquitin-like protein MDY2
W: Golgi to ER traffic protein 4
X: Ubiquitin-like protein MDY2
C: ATPase GET3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)681,28728
Polymers681,02524
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area71940 Å2
ΔGint-614 kcal/mol
Surface area237520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.430, 127.330, 210.260
Angle α, β, γ (deg.)90.00, 110.23, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 8
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: 37245.977 Da / Num. of mol.: 8 / Fragment: UNP residues 11-311
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: 6305.339 Da / Num. of mol.: 8 / Fragment: UNP residues 1-56
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 3350 and 0.1 M Na malonate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 6→30 Å / Num. obs: 18388 / % possible obs: 96.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.9
Reflection shellResolution: 6→6.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.4 / % possible all: 98.7

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Processing

Software
NameClassification
CNSrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3A37 and 3LKU

3a37

3lku


Resolution: 6→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3025 917 4.8 %
Rwork0.2739 17462 -
obs0.274 18379 96.5 %
Solvent computationBsol: 295.14 Å2
Displacement parametersBiso max: 386.38 Å2 / Biso mean: 361.6852 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-34.317 Å20 Å2-14.815 Å2
2---47.101 Å20 Å2
3---12.785 Å2
Refinement stepCycle: final / Resolution: 6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41920 0 4 0 41924
Biso mean--357.54 --
Num. residues----5192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_d0.737
X-RAY DIFFRACTIONc_mcbond_it015
X-RAY DIFFRACTIONc_scbond_it020
X-RAY DIFFRACTIONc_mcangle_it020
X-RAY DIFFRACTIONc_scangle_it025
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
6-6.210.4169930.43941748184199.1
6.21-6.460.43791020.39161754185697.7
6.46-6.750.40291000.38771740184097.5
6.75-7.10.3784970.37331757185497.4
7.1-7.540.3981090.33341727183696.8
7.54-8.110.3714680.32941608167688.8
8.11-8.910.2961760.26891761183796.5
8.91-10.150.2239790.21851824190399.3
10.15-12.630.1937990.19461775187497.6
12.63-300.3515940.28021768186294.8

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