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- PDB-8ucz: Sterile Alpha Motif (SAM) domain from Tric1 from Arabidopsis thal... -

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Basic information

Entry
Database: PDB / ID: 8ucz
TitleSterile Alpha Motif (SAM) domain from Tric1 from Arabidopsis thaliana - D235A mutant
ComponentsChloroplastic import inner membrane translocase subunit HP30-1
KeywordsRNA BINDING PROTEIN / Mitochondria / tRNA import / Tric1 / SAM domain / oligomerization / PRAT domain / sterile alpha motif domain
Function / homology
Function and homology information


tRNA import into mitochondrion / protein targeting to chloroplast / chloroplast inner membrane / protein insertion into mitochondrial inner membrane / chloroplast envelope / plastid / protein transmembrane transporter activity / mitochondrion organization / chloroplast / : ...tRNA import into mitochondrion / protein targeting to chloroplast / chloroplast inner membrane / protein insertion into mitochondrial inner membrane / chloroplast envelope / plastid / protein transmembrane transporter activity / mitochondrion organization / chloroplast / : / mitochondrion / cytosol
Similarity search - Function
Mitochondrial import inner membrane translocase subunit TIM22 / SAM domain (Sterile alpha motif) / Tim17/Tim22/Tim23/Pmp24 family / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Chloroplastic import inner membrane translocase subunit HP30-1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsOlasz, B. / Vrielink, A. / Smithers, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural analysis of the SAM domain of the Arabidopsis mitochondrial tRNA import receptor.
Authors: Olasz, B. / Smithers, L. / Evans, G.L. / Anandan, A. / Murcha, M.W. / Vrielink, A.
History
DepositionSep 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloroplastic import inner membrane translocase subunit HP30-1
B: Chloroplastic import inner membrane translocase subunit HP30-1
C: Chloroplastic import inner membrane translocase subunit HP30-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4726
Polymers30,3653
Non-polymers1063
Water4,071226
1
A: Chloroplastic import inner membrane translocase subunit HP30-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1572
Polymers10,1221
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chloroplastic import inner membrane translocase subunit HP30-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1572
Polymers10,1221
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chloroplastic import inner membrane translocase subunit HP30-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1572
Polymers10,1221
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.676, 92.587, 94.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
DetailsThe assembly may be hexameric; however, the authors do not know the specific hexameric assembly.

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Components

#1: Protein Chloroplastic import inner membrane translocase subunit HP30-1


Mass: 10121.772 Da / Num. of mol.: 3 / Fragment: SAM domain / Mutation: D235A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HP30-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q9SCK3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.5 M ammonium sulphate, 0.1 M Tris / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.07→47.05 Å / Num. obs: 15930 / % possible obs: 97.3 % / Redundancy: 13.9 % / Biso Wilson estimate: 18.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.03 / Net I/σ(I): 19.5
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4 / Num. unique obs: 1505 / CC1/2: 0.91 / Rpim(I) all: 0.019 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→47.05 Å / SU ML: 0.3163 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2766 811 5.23 %
Rwork0.2475 14702 -
obs0.249 15513 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.14 Å2
Refinement stepCycle: LAST / Resolution: 2.07→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 3 226 1755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521621
X-RAY DIFFRACTIONf_angle_d0.83292199
X-RAY DIFFRACTIONf_chiral_restr0.0462251
X-RAY DIFFRACTIONf_plane_restr0.0386285
X-RAY DIFFRACTIONf_dihedral_angle_d16.92651
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.20.33461480.28942352X-RAY DIFFRACTION95.53
2.2-2.370.43421000.42132128X-RAY DIFFRACTION84.91
2.37-2.610.26191410.24812499X-RAY DIFFRACTION100
2.61-2.980.28581470.24832483X-RAY DIFFRACTION100
2.98-3.760.24721390.2312543X-RAY DIFFRACTION99.37
3.76-47.050.24581360.1932697X-RAY DIFFRACTION99.79
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)
17.89478287649-2.478125244870.9174659391397.23662969861-4.356700796378.111163283930.004330675153180.210107039797-0.788427173269-0.7038630535450.09615755828950.1988309217650.598437691138-0.305026912598-0.07201979070440.135983874023-0.03843523422110.01609580108070.211201350229-0.08315544032150.2299830361124.402592759453.49156887-21.8309705074
26.97192434828-4.542750996623.917629572116.06251242079-2.126642187314.471246647190.5612999515750.8488785514220.155611889701-0.880620796583-0.762992745446-0.7214019211330.3806354175010.8144593804060.1993038562210.150232696994-0.03390833081370.05999691383860.296462085880.01790947409750.22769105621611.39625179979.30869859917-20.8091250952
31.74312992032-1.228310809550.9680317324824.23916441617-2.27107409691.83623220993-0.109469286345-0.2056702904930.2415370037690.5014695017160.0220078765977-0.178943404367-0.2994437100540.07873981333810.0637540106720.206490494202-0.0337957015196-0.03831879464380.180969469174-0.02446464000710.1622417749125.0579798889612.2403979919-13.8633646151
46.279887488392.41601105712.487755880684.95064715842-0.5574173976013.973143306450.7378938089791.0592933959-1.21374086579-0.85519731758-0.673166973526-0.05290873838581.28516769625-0.9924746116160.01913201820940.2305164847870.1969641380890.0249832228860.319242318285-0.1073462993770.552473949742-7.029962715467.58052600242-17.195779337
54.375179517124.80446737817-2.924511966256.78017601839-3.142994055116.63556059861-0.219295787458-1.07042405827-0.1530021999471.191004185990.233308455404-0.969627551330.05149579602460.06944035132280.1843878934940.2539230391910.0473518677991-0.06038597021630.4193924730760.006234462090780.2698745540480.583991567038-14.1948501927-19.1654396016
65.862274737891.37813264369-0.2817667071876.31545088346-2.326288655743.8306114973-0.115398693983-0.02062685899120.183117658672-0.1073570936390.06157999922490.130057300848-0.0694616838537-0.03619250433990.04374327362230.1339011394320.00880651229556-0.03104093214390.152317800847-0.02530000936960.135408511666-1.3204962087-15.1634460047-29.0590774716
77.049866254165.21861868155-4.409157072557.72303891448-6.206746283689.652548115260.992994743696-2.67277512799-0.5758832915432.046439636690.910540139510.4748682345340.0886881913086-0.38062509481-1.381456577160.4880027109780.0662084954047-0.02440692189670.9400735181820.03319373060760.36443577330211.0539101516-17.9734601448-22.0173855451
8-0.1535035052860.00752336335795-0.1292054795285.25318158825-2.941042397977.340411520510.0723101884127-0.468149637362-0.226841500061-0.00647776105232-0.01446957921850.4584844233910.682356348815-0.548822431519-0.08178165865550.240580340467-0.03995760696990.06981574225220.2956041861580.01772787679490.2002273747429.63087490692-5.617633065947.74228020066
95.953222537660.67151280942.760585339873.12167847997-1.037474500932.246959792660.04808835652750.097947704008-0.766381201533-0.5091220825240.134929391165-0.1958061514191.065833401750.818893926878-0.02705046337650.1723224403020.03824531734640.08117963550620.414352438881-0.05118187308110.16018289162715.385026459-2.057747365690.804217400991
101.42824457849-0.3763480513622.2314301431.28372748468-0.826725558145.04647035166-0.2076430677950.1799738892330.197516775937-0.009263126426040.0612005934499-0.113520252412-0.3231202015710.2210161287390.108706555320.15023249771-0.05017863554850.01445144856270.22053777684-0.01909430887970.14091848487310.03949675955.657116951132.61761674171
113.600134189952.365324186143.057251258737.629786192460.6888541560753.276842778450.6335588051710.314871622936-0.2109191775460.167743253798-0.2809477402620.96377309517-0.1498682385640.310910723345-0.1815450917160.438618090767-0.0235173948021-0.07297113843820.5558121080540.1288157558660.479621562548-2.158105533880.7597687885275.8759248555
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 194 through 206 )AA194 - 2061 - 13
22chain 'A' and (resid 207 through 218 )AA207 - 21814 - 25
33chain 'A' and (resid 219 through 250 )AA219 - 25026 - 57
44chain 'A' and (resid 251 through 257 )AA251 - 25758 - 64
55chain 'B' and (resid 194 through 206 )BB194 - 2061 - 13
66chain 'B' and (resid 207 through 252 )BB207 - 25214 - 59
77chain 'B' and (resid 253 through 257 )BB253 - 25760 - 64
88chain 'C' and (resid 193 through 205 )CC193 - 2051 - 13
99chain 'C' and (resid 206 through 217 )CC206 - 21714 - 25
1010chain 'C' and (resid 218 through 250 )CC218 - 25026 - 58
1111chain 'C' and (resid 251 through 257 )CC251 - 25759 - 65

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