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

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Basic information

Entry
Database: PDB / ID: 8hac
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


Hydrolases; Acting on acid anhydrides / protein insertion into ER membrane / endoplasmic reticulum / ATP hydrolysis activity / ATP 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
ADENOSINE-5'-DIPHOSPHATE / ATPase ASNA1 homolog
Similarity search - Component
Biological speciesPhaeodactylum tricornutum CCAP 1055/1 (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5776
Polymers77,6742
Non-polymers9034
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-53 kcal/mol
Surface area28800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.297, 125.212, 120.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21A-712-

HOH

31A-734-

HOH

41B-843-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 6 through 401)

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUPROPROAA6 - 3446 - 344
d_12ADPADPADPADPAC400
d_21LEULEUPROPROBB6 - 3446 - 344
d_22ADPADPADPADPBE400

NCS oper: (Code: givenMatrix: (-0.989357795723, 0.0995026866367, -0.10616198658), (0.0865293736108, -0.184228290163, -0.979067211486), (-0.116977859209, -0.97783390842, 0.173657789918)Vector: 31. ...NCS oper: (Code: given
Matrix: (-0.989357795723, 0.0995026866367, -0.10616198658), (0.0865293736108, -0.184228290163, -0.979067211486), (-0.116977859209, -0.97783390842, 0.173657789918)
Vector: 31.0542611279, -1.12053659388, 1.18835278792)

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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
Details: ADP, magnesium ion
Source: (gene. exp.) Phaeodactylum tricornutum CCAP 1055/1 (Diatom)
Production host: Escherichia coli (E. coli)
References: UniProt: B7G933, Hydrolases; Acting on acid anhydrides
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.085M sodium acetate, pH 4.7, 0.25M ammonium acetate, 18.5% glycerol, 0.25M sodium bromide, with 24.5% polyethylene glycol (PEG) 4000

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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: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. obs: 32898 / % possible obs: 98 % / Redundancy: 4.9 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 38.7
Reflection shellResolution: 2.32→2.4 Å / Rmerge(I) obs: 0.644 / Num. unique obs: 3227

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-20001.13_2998data collection
Cootmodel building
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WOJ

2woj


Resolution: 2.32→24.7 Å / SU ML: 0.2603 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2442 1592 5 %
Rwork0.1929 30230 -
obs0.1955 31822 94.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.58 Å2
Refinement stepCycle: LAST / Resolution: 2.32→24.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5092 0 56 632 5780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00395246
X-RAY DIFFRACTIONf_angle_d0.78547116
X-RAY DIFFRACTIONf_chiral_restr0.0452813
X-RAY DIFFRACTIONf_plane_restr0.005915
X-RAY DIFFRACTIONf_dihedral_angle_d15.15961944
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.00542746166 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.390.30311050.24892001X-RAY DIFFRACTION70.39
2.39-2.480.29631380.23592616X-RAY DIFFRACTION91.31
2.48-2.580.27961470.23562781X-RAY DIFFRACTION97.47
2.58-2.70.25621490.22722835X-RAY DIFFRACTION98.55
2.7-2.840.34581490.22062833X-RAY DIFFRACTION98.64
2.84-3.020.2621490.21522831X-RAY DIFFRACTION98.48
3.02-3.250.2541490.21342827X-RAY DIFFRACTION98.48
3.25-3.570.25761510.17832867X-RAY DIFFRACTION98.79
3.57-4.090.21411510.16182870X-RAY DIFFRACTION98.89
4.09-5.140.19241520.15882884X-RAY DIFFRACTION98.25
5.14-24.70.22481520.18682885X-RAY DIFFRACTION94.73
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)
14.025566102020.4781213048922.170870659843.493979610190.7901685776842.032582194030.373109735963-0.350455766946-0.4514046631180.2563531539420.013189605646-1.199412895750.7860769173890.3817077307920.1058404190920.2799339364890.09104466063690.05381509009840.231850193215-0.07075252231360.55000205661236.9410966844-8.53758697461-21.2989079213
20.6294666234630.6998922693180.7821779630131.885962496861.449300987951.1138327905-0.0840755086495-0.464099408136-0.2811507749290.9673737314330.403322192393-0.6143593234840.6649621901830.3177756453930.08372145383130.4301424648190.0919975731322-0.1089706075430.4755417281240.02645981619210.3791735681333.66703539013.6584838001-9.54467818812
31.14035269766-0.565730603937-0.3111718133984.37456969312.035523080651.211792265050.0727639631274-0.1408205273070.220577480721-0.259594776246-0.0820454879171-0.215748447202-0.2076674842210.138903026029-0.009569437854790.245187574033-0.01407480986020.03710369335940.2170206594280.001777916703620.18756497426127.928937754914.7713711186-17.7420018495
42.675800523162.903995925810.5434294901163.674061081631.304110791561.122367410610.0602928910784-0.0225974721692-0.65674406617-0.111121251806-0.0012811450634-0.4634879136090.18300611119-0.1123407644890.02598312328910.3885746798210.07001296547220.1005073670680.306380964471-0.0295700212290.4201856851423.7202435782-20.8622942014-31.4273076595
54.401398142521.616369239630.2831886550361.330582544640.6110908541213.566408734870.0886719357886-0.599884701440.03144062152110.353681879532-0.4048185212880.574134374659-0.126247016072-0.54543566943-0.05338169005290.1518109606260.06850372238910.09869624559840.306973744471-0.1911537396940.307363840816-3.9432801970225.29549133221.72112822418
60.653686138070.108886412561-0.3885103408151.155956920141.462879769141.95589011267-0.0744118046935-0.386664440856-0.2966941192860.449245381227-0.1665352457540.4908038124930.483591758624-0.23149540542-0.004134418618520.2877732283230.005628086885040.08241384365280.385627535066-0.02292834313120.325910339965-1.1033807453910.3642741598-8.10999981375
73.27506412571.14563875556-0.5319749847711.91274046881-1.386468297651.05309279985-0.4262666325860.219588010092-0.302393107349-0.231152114059-0.1013337472940.3327131210390.4882894881620.600348889781-0.1553482720360.2928335924990.0983963756427-0.0687375706750.278621670097-0.01815025911060.28717232660311.174097587310.8995861361-26.2044295539
85.11919773909-0.3993049027270.3596461717814.85804621102-0.2909413013984.70968448709-0.1077739335990.385680857579-0.461695691567-0.396027868106-0.02904823502980.552888389740.0732606310818-0.23321462066-0.4339305351120.108290340044-0.0477603852631-0.09140789620670.202469686641-0.04374536689380.07654918936161.42370045147.12024143946-26.5633142401
92.76730930375-0.1433994403330.3261787734952.31257340426-0.9201687541142.42467341449-0.300454894872-0.4115492190390.210384890189-0.0614159344162-0.2761841685650.351144403673-0.7006141779530.462337893569-0.902905871330.1975707409210.03374833026380.03311290042960.0297579029785-0.3857130855870.04265682418616.7261491547531.9216824818-1.64680071465
100.5803553604490.566962665151.48018751221.015113144291.744802195243.7387010826-0.0909393664682-0.226778307648-0.01911668333310.0923269381251-0.0253039349683-0.0477892075259-0.277072365659-0.311726888629-0.003545021880810.4274804828180.02505479522810.006552490525390.345355130387-0.1236823280660.337076075289.7744959778835.964487139515.5304040626
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 66 )AA6 - 661 - 61
22chain 'A' and (resid 67 through 148 )AA67 - 14862 - 129
33chain 'A' and (resid 149 through 249 )AA149 - 249130 - 230
44chain 'A' and (resid 250 through 344 )AA250 - 344231 - 325
55chain 'B' and (resid 4 through 66 )BD4 - 661 - 63
66chain 'B' and (resid 67 through 148 )BD67 - 14864 - 131
77chain 'B' and (resid 149 through 184 )BD149 - 184132 - 167
88chain 'B' and (resid 185 through 218 )BD185 - 218168 - 201
99chain 'B' and (resid 219 through 268 )BD219 - 268202 - 251
1010chain 'B' and (resid 269 through 344 )BD269 - 344252 - 327

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