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- PDB-3zs9: S. cerevisiae Get3-ADP-AlF4- complex with a cytosolic Get2 fragment -

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Basic information

Entry
Database: PDB / ID: 3zs9
TitleS. cerevisiae Get3-ADP-AlF4- complex with a cytosolic Get2 fragment
Components
  • ATPASE GET3
  • GOLGI TO ER TRAFFIC PROTEIN 2
KeywordsHYDROLASE/TRANSPORT PROTEIN / HYDROLASE-TRANSPORT PROTEIN COMPLEX / MEMBRANE PROTEIN / TARGETING FACTOR
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 / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / 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 / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to arsenic-containing substance / 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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / Golgi to ER traffic protein 2 / ATPase GET3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.095 Å
AuthorsMariappan, M. / Mateja, A. / Dobosz, M. / Bove, E. / Hegde, R.S. / Keenan, R.J.
CitationJournal: Nature / Year: 2011
Title: The Mechanism of Membrane-Associated Steps in Tail-Anchored Protein Insertion.
Authors: Mariappan, M. / Mateja, A. / Dobosz, M. / Bove, E. / Hegde, R.S. / Keenan, R.J.
History
DepositionJun 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _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 2
D: GOLGI TO ER TRAFFIC PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,65111
Polymers87,4774
Non-polymers1,1747
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-56.3 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.558, 77.317, 165.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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 / GET3


Mass: 39393.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PRIL / References: UniProt: Q12154, EC: 3.6.3.16
#2: Protein/peptide GOLGI TO ER TRAFFIC PROTEIN 2 / HYDROXYUREA RESISTANCE PROTEIN 2 / REQUIRED FOR MEIOTIC NUCLEAR DIVISION PROTEIN 7 / GET2


Mass: 4344.958 Da / Num. of mol.: 2
Fragment: CYTOSOLIC-FACING N-TERMINAL FRAGMENT, RESIDUES 1-38
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PRIL / References: UniProt: P40056

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Non-polymers , 5 types, 244 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growpH: 6
Details: 30% PEG 3350, 0.3 AMMONIUM ACETATE, 0.1 M BIS-TRIS, PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 39345 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 27.16 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.6 / % possible all: 89.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WOJ

2woj


Resolution: 2.095→36.537 Å / SU ML: 0.62 / σ(F): 1.35 / Phase error: 21.95 / Stereochemistry target values: ML
Details: DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.238 2023 5.1 %
Rwork0.1822 --
obs0.185 39345 96.92 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.472 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.062 Å2-0 Å2-0 Å2
2---3.1043 Å20 Å2
3---4.1663 Å2
Refinement stepCycle: LAST / Resolution: 2.095→36.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 67 237 5530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075385
X-RAY DIFFRACTIONf_angle_d1.0247243
X-RAY DIFFRACTIONf_dihedral_angle_d14.1242062
X-RAY DIFFRACTIONf_chiral_restr0.063817
X-RAY DIFFRACTIONf_plane_restr0.004914
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0953-2.14770.28131300.22812313X-RAY DIFFRACTION86
2.1477-2.20570.24151300.20262532X-RAY DIFFRACTION93
2.2057-2.27060.23751400.18772586X-RAY DIFFRACTION95
2.2706-2.34390.26881380.18572610X-RAY DIFFRACTION96
2.3439-2.42770.24131410.18482591X-RAY DIFFRACTION96
2.4277-2.52480.26231490.17922610X-RAY DIFFRACTION96
2.5248-2.63970.24141320.18252674X-RAY DIFFRACTION97
2.6397-2.77880.26491450.17562695X-RAY DIFFRACTION99
2.7788-2.95290.23011760.18582665X-RAY DIFFRACTION99
2.9529-3.18070.2321560.18022731X-RAY DIFFRACTION100
3.1807-3.50060.23311610.16752757X-RAY DIFFRACTION100
3.5006-4.00660.20891320.15852782X-RAY DIFFRACTION100
4.0066-5.04580.20991400.1642820X-RAY DIFFRACTION100
5.0458-36.54220.26641530.22162957X-RAY DIFFRACTION100
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)
11.9775-0.1716-0.10041.97880.01430.8844-0.03480.15190.1435-0.08260.0310.0426-0.0966-0.0687-0.0010.0676-0.0033-0.0470.05310.00970.0702-20.44529.3588-19.0523
20.9290.03110.03250.8780.25970.4323-0.00480.145-0.0289-0.03170.038-0.07990.01160.04060.0166-0.0781-0.0193-0.0914-0.0348-0.0234-0.1075-5.0369-11.0223-23.3535
30.01340.00690.03010.07510.00660.09780.10470.125-0.2039-0.0267-0.1166-0.01870.0461-0.036-0.00010.4017-0.02740.02260.2759-0.04850.4477-17.1746-27.9283-17.7287
40.0710.0435-0.03150.0610.05470.17130.0065-0.14750.07470.17660.03520.0008-0.31610.2183-0.00730.4078-0.0417-0.04530.1930.0210.4286-5.181925.0478-19.164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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