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- PDB-8had: A novel dimer configuration of a diatom Get3 forming a tetrameric... -

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Basic information

Entry
Database: PDB / ID: 8had
TitleA novel dimer configuration of a diatom Get3 forming a tetrameric complex with its tail-anchored membrane cargo
ComponentsATPase ASNA1 homolog
KeywordsCHAPERONE / Get3 / ArsA2 / ArsA1 / TRC40 / tail-anchored / post-translational pathway / diatom
Function / homology
Function and homology information


GET complex / tail-anchored membrane protein insertion into ER membrane / Hydrolases; Acting on acid anhydrides / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Arsenical pump ATPase, ArsA/GET3, eukaryotic / Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATPase ASNA1 homolog
Similarity search - Component
Biological speciesPhaeodactylum tricornutum CCAP 1055/1 (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å
AuthorsChang, H.Y. / Ko, T.P.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Bmc Biol. / Year: 2024
Title: A distinct dimer configuration of a diatom Get3 forming a tetrameric complex with its tail-anchored membrane cargo.
Authors: Chen, C.C. / Huang, Y.R. / Chan, Y.T. / Lin, H.Y. / Lin, H.J. / Hsiao, C.D. / Ko, T.P. / Lin, T.W. / Lan, Y.H. / Lin, H.Y. / Chang, H.Y.
History
DepositionOct 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 26, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATPase ASNA1 homolog
B: ATPase ASNA1 homolog


Theoretical massNumber of molelcules
Total (without water)77,6742
Polymers77,6742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-20 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.343, 115.468, 151.756
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 89 or resid 105 through 345))
d_2ens_1(chain "B" and resid 5 through 345)

NCS domain segments:

Ens-ID: ens_1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPAA5 - 895 - 89
d_12VALVALAA105 - 345105 - 345
d_21VALVALBB5 - 3455 - 345

NCS oper: (Code: givenMatrix: (-0.046842484256, 0.998516634614, 0.0277544963513), (0.998596916564, 0.0474970664476, -0.0234142458491), (-0.0246977711247, 0.0266187730347, -0.99934051305)Vector: -29. ...NCS oper: (Code: given
Matrix: (-0.046842484256, 0.998516634614, 0.0277544963513), (0.998596916564, 0.0474970664476, -0.0234142458491), (-0.0246977711247, 0.0266187730347, -0.99934051305)
Vector: -29.7899198124, 28.9542530666, 38.0800407986)

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Components

#1: Protein ATPase ASNA1 homolog / get3 / Arsenical pump-driving ATPase homolog / Arsenite-stimulated ATPase


Mass: 38836.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylum tricornutum CCAP 1055/1 (Diatom)
Production host: Escherichia coli (E. coli)
References: UniProt: B7G933, Hydrolases; Acting on acid anhydrides

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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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.07M sodium acetate, pH4.6, 5.6% PEG 4000, 30% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.81→30 Å / Num. obs: 9530 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 24.26 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 24.1
Reflection shellResolution: 3.81→3.95 Å / Rmerge(I) obs: 1.016 / Num. unique obs: 931

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-20001.19_4092data collection
CNSv1.0phasing
Cootmodel building
REFMACv1.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WOJ

2woj


Resolution: 3.81→29.82 Å / SU ML: 0.7159 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 38.3108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3694 393 4.36 %
Rwork0.3205 8624 -
obs0.3226 9017 94.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.87 Å2
Refinement stepCycle: LAST / Resolution: 3.81→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 0 0 5106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185202
X-RAY DIFFRACTIONf_angle_d0.4577046
X-RAY DIFFRACTIONf_chiral_restr0.0383809
X-RAY DIFFRACTIONf_plane_restr0.0044915
X-RAY DIFFRACTIONf_dihedral_angle_d12.60751926
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.936618950995 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.81-4.360.42021440.36612482X-RAY DIFFRACTION84.06
4.36-5.480.4021080.32313034X-RAY DIFFRACTION99.97
5.49-29.820.28441410.27673108X-RAY DIFFRACTION99.75
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)
10.134784176397-0.00422661440925-0.02038318506820.09643650592030.068274866240.163521497365-0.1642379337760.0715112266420.0327488463228-0.0171316439842-0.003298368739030.0115045807408-0.0476875891779-0.0771007279964-0.9875617869080.134601128498-0.0388756352769-0.2720248012070.142810992296-0.198124872740.185977287151-0.80066750356750.99573426297.06495403894
20.5765907864590.2344420127730.05083842932240.15340803503-0.1632050211990.799033965139-0.1252289396810.108525438393-0.182903257128-0.112315392997-0.0800324021321-0.05577646824180.1512299732640.0793106960014-0.853761438190.09116050173710.1103621152370.03659105828680.0531262417677-0.0927249366839-0.062417083236121.545673133930.307995932632.4374808884
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1 - 327

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 5 through 345)AA5 - 345
22(chain 'B' and resid 4 through 345)BB4 - 345

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