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- PDB-8ucy: Sterile Alpha Motif (SAM) domain from Tric1, Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 8ucy
TitleSterile Alpha Motif (SAM) domain from Tric1, Arabidopsis thaliana
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


protein targeting to chloroplast / chloroplast inner membrane / tRNA import into mitochondrion / protein insertion into mitochondrial inner membrane / chloroplast envelope / plastid / chloroplast / mitochondrion organization / 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 / MAD / Resolution: 1.48 Å
AuthorsOlasz, B. / Vrielink, A. / Evans, G.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 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Experimental preparation
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / exptl / exptl_crystal / exptl_crystal_grow
Item: _exptl.crystals_number

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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)30,5334
Polymers30,4973
Non-polymers351
Water3,243180
1
A: Chloroplastic import inner membrane translocase subunit HP30-1


Theoretical massNumber of molelcules
Total (without water)10,1661
Polymers10,1661
Non-polymers00
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)10,2012
Polymers10,1661
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chloroplastic import inner membrane translocase subunit HP30-1


Theoretical massNumber of molelcules
Total (without water)10,1661
Polymers10,1661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.639, 92.121, 93.310
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: 10165.782 Da / Num. of mol.: 3 / Fragment: SAM domain
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.: 1 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.0339.33rod shaped crystals, abundant in all crystallisation drops
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
293.151vapor diffusion, hanging drop8.52.0 M ammonium sulphate, 0.1 M Tris, 12 mg/mL SAM protein
293.152microbatch8.51.0 M ammonium sulphate, 0.1 M Tris, 6.15 mg/mL SeMet SAM protein (0.5uL:0.5uL drop under paratone oil)

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
31002N
41002N
51002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX110.9537
SYNCHROTRONAustralian Synchrotron MX120.9793
SYNCHROTRONAustralian Synchrotron MX130.9795
SYNCHROTRONAustralian Synchrotron MX140.9537
SYNCHROTRONAustralian Synchrotron MX150.9871
Detector
TypeIDDetectorDateID
ADSC QUANTUM 210r1CCDDec 11, 2015
ADSC QUANTUM 210r2CCDNov 11, 20161
ADSC QUANTUM 210r3CCDNov 11, 20161
ADSC QUANTUM 210r4CCDNov 11, 20161
ADSC QUANTUM 210r5CCDNov 11, 20161
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
3MADMx-ray3
4MADMx-ray4
5MADMx-ray5
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97931
30.97951
40.98711
51
ReflectionResolution: 1.48→29.2 Å / Num. obs: 42224 / % possible obs: 99.9 % / Redundancy: 14.3 % / Biso Wilson estimate: 19.28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.015 / Net I/σ(I): 28.1
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2085 / CC1/2: 0.671 / Rpim(I) all: 0.403 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.48→29.17 Å / SU ML: 0.1539 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: The structure was solved by MAD using a SeMet mutant; however, the final refined structure was obtained using a native data set.
RfactorNum. reflection% reflection
Rfree0.1981 2115 5.02 %
Rwork0.1792 40031 -
obs0.1801 42146 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.3 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 1 180 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121633
X-RAY DIFFRACTIONf_angle_d1.1632213
X-RAY DIFFRACTIONf_chiral_restr0.0807251
X-RAY DIFFRACTIONf_plane_restr0.0383289
X-RAY DIFFRACTIONf_dihedral_angle_d15.1575654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.29091230.2572618X-RAY DIFFRACTION99.24
1.51-1.550.25531260.23042639X-RAY DIFFRACTION100
1.55-1.590.22671190.22042658X-RAY DIFFRACTION99.93
1.59-1.640.21841130.2152641X-RAY DIFFRACTION100
1.64-1.690.23431430.22212638X-RAY DIFFRACTION99.89
1.69-1.760.21411540.21752593X-RAY DIFFRACTION99.96
1.76-1.830.22721790.19922604X-RAY DIFFRACTION100
1.83-1.910.22891090.17932705X-RAY DIFFRACTION100
1.91-2.010.20481430.1822622X-RAY DIFFRACTION100
2.01-2.140.19721450.18382653X-RAY DIFFRACTION99.93
2.14-2.30.18031320.16132682X-RAY DIFFRACTION100
2.3-2.530.19981540.16262674X-RAY DIFFRACTION100
2.53-2.90.21361470.1712713X-RAY DIFFRACTION100
2.9-3.650.19191620.18182718X-RAY DIFFRACTION100
3.65-29.170.17471660.16472873X-RAY DIFFRACTION100

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