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- PDB-8q70: tRNA pseudouridine synthase A homodimer -

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Basic information

Entry
Database: PDB / ID: 8q70
TitletRNA pseudouridine synthase A homodimer
ComponentstRNA pseudouridine synthase A
KeywordsISOMERASE / pseudouridine / synthase / homodimer / pyrococcus / tRNA
Function / homology
Function and homology information


tRNA pseudouridine38-40 synthase / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / RNA binding
Similarity search - Function
Pseudouridine synthase I, TruA / Pseudouridine synthase I, TruA, C-terminal / Pseudouridine synthase I, TruA, alpha/beta domain / tRNA pseudouridine synthase / Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal / Pseudouridine synthase, catalytic domain superfamily
Similarity search - Domain/homology
tRNA pseudouridine synthase A
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPacesa, M. / Correia, B.E. / Levy, E.D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Cell / Year: 2024
Title: An atlas of protein homo-oligomerization across domains of life.
Authors: Hugo Schweke / Martin Pacesa / Tal Levin / Casper A Goverde / Prasun Kumar / Yoan Duhoo / Lars J Dornfeld / Benjamin Dubreuil / Sandrine Georgeon / Sergey Ovchinnikov / Derek N Woolfson / ...Authors: Hugo Schweke / Martin Pacesa / Tal Levin / Casper A Goverde / Prasun Kumar / Yoan Duhoo / Lars J Dornfeld / Benjamin Dubreuil / Sandrine Georgeon / Sergey Ovchinnikov / Derek N Woolfson / Bruno E Correia / Sucharita Dey / Emmanuel D Levy /
Abstract: Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their ...Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
History
DepositionAug 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA pseudouridine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2383
Polymers32,1781
Non-polymers602
Water2,342130
1
A: tRNA pseudouridine synthase A
hetero molecules

A: tRNA pseudouridine synthase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4766
Polymers64,3562
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4250 Å2
ΔGint-61 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.690, 61.690, 275.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21A-525-

HOH

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Components

#1: Protein tRNA pseudouridine synthase A


Mass: 32178.018 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: truA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U2C1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris 8.5, 0.2 M MgCl2.6H2O, 10% w/v PEG 8000, 10% w/v PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.846→53.43 Å / Num. obs: 27910 / % possible obs: 100 % / Redundancy: 21.3 % / Biso Wilson estimate: 35.39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.175 / Net I/σ(I): 11.7
Reflection shellResolution: 1.846→1.878 Å / Redundancy: 22.5 % / Rmerge(I) obs: 3.114 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1358 / CC1/2: 0.585 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4985refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→53.43 Å / SU ML: 0.1837 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6148
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 1419 5.08 %
Rwork0.1957 26490 -
obs0.1967 27909 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.28 Å2
Refinement stepCycle: LAST / Resolution: 1.85→53.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 2 130 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00372199
X-RAY DIFFRACTIONf_angle_d0.65552965
X-RAY DIFFRACTIONf_chiral_restr0.0489322
X-RAY DIFFRACTIONf_plane_restr0.0048381
X-RAY DIFFRACTIONf_dihedral_angle_d14.4816837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.30711410.28582563X-RAY DIFFRACTION100
1.91-1.990.30091420.25172595X-RAY DIFFRACTION100
1.99-2.080.29091290.23222568X-RAY DIFFRACTION100
2.08-2.190.24961640.20592566X-RAY DIFFRACTION100
2.19-2.330.21671380.20132601X-RAY DIFFRACTION100
2.33-2.510.27811410.20722608X-RAY DIFFRACTION100
2.51-2.760.21721320.20992643X-RAY DIFFRACTION100
2.76-3.160.26441410.20822681X-RAY DIFFRACTION99.96
3.16-3.980.1871280.1842736X-RAY DIFFRACTION99.97
3.98-53.430.18281630.17742929X-RAY DIFFRACTION99.94
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)
11.14176913284-0.400801053991-0.1126395890511.53288774088-0.1022342350381.82374264409-0.03334963212240.1539358058080.454708820642-0.1274477256070.1021414151140.253451810752-0.0555298075807-0.3340372626444.8755971434E-50.3438553040980.00765747549345-0.03655938681050.376036580443-0.01866729637820.468316423789-1.2193131686738.0633970157-0.399205964965
20.34394535057-0.2625406541480.1995176332820.570684042926-0.2276546580550.297108104019-0.09584933692950.2709010352670.0686927183959-0.186322153817-0.008644208670530.2683665369740.4221711779770.255986057194-4.45253218853E-50.503186136934-0.0262717840132-0.01088851540170.417098143565-0.03111346835950.4234141197564.3343077316331.9569965916-8.54082030943
31.230232322050.7996494272620.2610975725783.587277700860.6905551280072.165713623720.09792764563060.01242961472960.02191681199880.250018488924-0.125627445917-0.01233272490550.213445003765-0.1901982339130.0004724686629550.3440379438040.0009773753335270.007882705737760.270613901861-0.06689718215920.2498142516164.3267338412411.44538717349.21261188479
41.261124899670.069177169977-0.1000105202951.18125289380.3196824354410.944152448308-0.0161417767219-0.007041173402030.163925050002-0.0277187118008-0.128195208204-0.153696693355-0.07456276241580.09292521960146.12026354307E-50.337366202013-0.0284589036701-0.003706248499440.264902856069-0.0750252808620.36439475134510.886103534431.772879872612.517322494
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 82 )1 - 821 - 82
22chain 'A' and (resid 83 through 101 )83 - 10183 - 101
33chain 'A' and (resid 102 through 212 )102 - 212102 - 212
44chain 'A' and (resid 213 through 264 )213 - 264213 - 264

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