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- PDB-3zs8: S. cerevisiae Get3 complexed with a cytosolic Get1 fragment -

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Basic information

Entry
Database: PDB / ID: 3zs8
TitleS. cerevisiae Get3 complexed with a cytosolic Get1 fragment
Components
  • ATPASE GET3
  • GOLGI TO ER TRAFFIC PROTEIN 1
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 / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / 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 / response to arsenic-containing substance / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / response to metal ion / mitophagy / protein-membrane adaptor activity / protein folding chaperone / 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 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 / 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 / _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_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 1
D: GOLGI TO ER TRAFFIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9815
Polymers98,9164
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-65.1 kcal/mol
Surface area34630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.276, 110.276, 315.956
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 5:90 OR RESSEQ 135:154 OR RESSEQ 158:170 OR RESSEQ 232:279 OR RESSEQ 285:350 )
211CHAIN B AND (RESSEQ 5:90 OR RESSEQ 135:155 OR RESSEQ 158:170 OR RESSEQ 232:279 OR RESSEQ 285:350 )
112CHAIN C AND (RESSEQ 545:580 )
212CHAIN D AND (RESSEQ 545:580 )

NCS ensembles :
ID
1
2

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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 / 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 GOLGI TO ER TRAFFIC PROTEIN 1 / GUIDED ENTRY OF TAIL-ANCHORED PROTEINS 1 / MITOCHONDRIAL DISTRIBUTION AND MORPHOLOGY PROTEIN 39 / GET1


Mass: 10064.349 Da / Num. of mol.: 2 / Fragment: CYTOSOLIC-FACING FRAGMENT, RESIDUES 21-104
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: P53192
#3: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 7.2
Details: 0.2 M K/NA TARTRATE, 16% PEG3350, 0.1 M HEPES, PH 7.2 AND 6% POLYPROPYLENE GLYCOL P400

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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: Jul 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 23431 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 86.66 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24.1
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.7 / % possible all: 87.3

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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 3H84

3h84


Resolution: 3→47.215 Å / SU ML: 0.97 / σ(F): 1.34 / Phase error: 28.18 / Stereochemistry target values: ML
Details: ELECTRON DENSITY IS WEAKEST IN THE HELICAL SUBDOMAINS. DISORDERED SIDECHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.2807 2334 10 %
Rwork0.2202 --
obs0.2261 23431 98.85 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.117 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.4602 Å20 Å20 Å2
2--14.4602 Å20 Å2
3----28.9205 Å2
Refinement stepCycle: LAST / Resolution: 3→47.215 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5644 0 1 0 5645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045736
X-RAY DIFFRACTIONf_angle_d0.837719
X-RAY DIFFRACTIONf_dihedral_angle_d14.6632165
X-RAY DIFFRACTIONf_chiral_restr0.062873
X-RAY DIFFRACTIONf_plane_restr0.003988
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1853X-RAY DIFFRACTIONPOSITIONAL
12B1853X-RAY DIFFRACTIONPOSITIONAL0.02
21C306X-RAY DIFFRACTIONPOSITIONAL
22D306X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.06130.40351150.33061094X-RAY DIFFRACTION88
3.0613-3.12790.36451240.28491167X-RAY DIFFRACTION96
3.1279-3.20060.31651370.26851206X-RAY DIFFRACTION100
3.2006-3.28070.31971490.23641216X-RAY DIFFRACTION100
3.2807-3.36930.29251280.23671227X-RAY DIFFRACTION100
3.3693-3.46850.29211340.21751235X-RAY DIFFRACTION100
3.4685-3.58040.28281380.21791222X-RAY DIFFRACTION100
3.5804-3.70830.2621320.2131249X-RAY DIFFRACTION100
3.7083-3.85670.31971380.21511215X-RAY DIFFRACTION100
3.8567-4.03210.27861420.21291241X-RAY DIFFRACTION100
4.0321-4.24460.25441350.19911266X-RAY DIFFRACTION100
4.2446-4.51030.27011410.18111232X-RAY DIFFRACTION100
4.5103-4.85820.20311370.15751261X-RAY DIFFRACTION100
4.8582-5.34650.25081440.19541263X-RAY DIFFRACTION100
5.3465-6.11880.34711420.26281296X-RAY DIFFRACTION100
6.1188-7.70360.33521440.25521301X-RAY DIFFRACTION100
7.7036-47.22060.25711540.22911406X-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)
11.04010.458-1.42410.3017-0.51180.89720.0364-0.252-0.0590.2599-0.28170.10870.35540.0818-0.00740.3744-0.0475-0.00170.91270.06340.526332.9905-55.104316.5555
2-0.0906-0.123-0.00380.2770.12010.0465-0.08760.2302-0.01740.12570.5317-0.1306-0.42130.18220.00010.75790.1381-0.10070.8762-0.25750.94424.2474-27.857435.2644
30.994-0.31460.69040.28650.90790.2854-0.098-0.19-0.05730.0580.00370.0431-0.16810.0762-0.08740.263-0.0116-0.02640.6794-0.01160.49960.4544-35.486114.6992
4-0.14070.0779-0.12870.3873-0.28490.08580.25860.0310.30070.47640.0556-0.66120.1493-0.2014-0.00010.6721-0.0378-0.01710.67260.14170.61638.1647-58.438137.5428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 1:354
2X-RAY DIFFRACTION2CHAIN C AND RESID 521:604
3X-RAY DIFFRACTION3CHAIN B AND RESID 1:354
4X-RAY DIFFRACTION4CHAIN D AND RESID 521:604

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