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- EMDB-19894: Arabidopsis thaliana R2T complex -

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Basic information

Entry
Database: EMDB / ID: EMD-19894
TitleArabidopsis thaliana R2T complex
Map dataArabidopsis thaliana R2T complex
Sample
  • Complex: AtR2T complex
    • Protein or peptide: RuvB-like protein 1
    • Protein or peptide: RuvB-like helicase
    • Protein or peptide: At1g56440
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsRUVBL1 / RUVBL2 / R2TP / HSP90 / Chaperone
Function / homology
Function and homology information


meristem development / regulation of defense response to fungus / flower development / R2TP complex / Swr1 complex / Ino80 complex / box C/D snoRNP assembly / plastid / NuA4 histone acetyltransferase complex / ATP-dependent activity, acting on DNA ...meristem development / regulation of defense response to fungus / flower development / R2TP complex / Swr1 complex / Ino80 complex / box C/D snoRNP assembly / plastid / NuA4 histone acetyltransferase complex / ATP-dependent activity, acting on DNA / DNA helicase activity / helicase activity / DNA helicase / cell differentiation / hydrolase activity / chromatin remodeling / DNA repair / regulation of transcription by RNA polymerase II / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Tetratricopeptide repeat / TPR repeat profile. ...RNA-polymerase II-associated protein 3-like, C-terminal domain / Potential Monad-binding region of RPAP3 / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
At1g56440 / RuvB-like helicase / RuvB-like protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsLopez-Perrote A / Llorca O
Funding support Spain, 1 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2020-114429RB-I00 Spain
CitationJournal: Structure / Year: 2025
Title: The structure of the R2T complex reveals a different architecture from the related HSP90 cochaperone R2TP.
Authors: Alberto Palacios-Abella / Andrés López-Perrote / Jasminka Boskovic / Sandra Fonseca / Cristina Úrbez / Vicente Rubio / Oscar Llorca / David Alabadí /
Abstract: The R2TP complex is a specialized HSP90 cochaperone essential for the maturation of macromolecular complexes such as RNAPII and TORC1. R2TP is formed by a hetero-hexameric ring of AAA-ATPases RuvBL1 ...The R2TP complex is a specialized HSP90 cochaperone essential for the maturation of macromolecular complexes such as RNAPII and TORC1. R2TP is formed by a hetero-hexameric ring of AAA-ATPases RuvBL1 and RuvBL2, which interact with RPAP3 and PIH1D1. Several R2TP-like complexes have been described, but these are less well characterized. Here, we identified, characterized and determined the cryo-electron microscopy (cryo-EM) structure of R2T from Arabidopsis thaliana, which lacks PIH1D1 and is probably the only form of the complex in seed plants. In contrast to R2TP, R2T is organized as two rings of AtRuvBL1-AtRuvBL2a interacting back-to-back, with one AtRPAP3 anchored per ring. AtRPAP3 has no effect on the ATPase activity of AtRuvBL1-AtRuvBL2a and binds with a different stoichiometry than in human R2TP. We show that the interaction of AtRPAP3 with AtRuvBL2a and AtHSP90 occurs via a conserved mechanism. However, the distinct architectures of R2T and R2TP suggest differences in their functions and mechanisms.
History
DepositionMar 20, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19894.png

Downloads & links

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Map

FileDownload / File: emd_19894.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationArabidopsis thaliana R2T complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 320 pix.
= 294.72 Å		0.92 Å/pix.
x 320 pix.
= 294.72 Å		0.92 Å/pix.
x 320 pix.
= 294.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.921 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.012261973 - 0.040693942
Average (Standard dev.)0.0000053762565 (±0.0018697606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 294.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened map (Postprocess) for the Arabidopsis thaliana R2T complex

Fileemd_19894_additional_1.map
AnnotationSharpened map (Postprocess) for the Arabidopsis thaliana R2T complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Arabidopsis thaliana dodecameric R2T complex II (containing a...

Fileemd_19894_additional_2.map
AnnotationArabidopsis thaliana dodecameric R2T complex II (containing a AtRUVBL1-AtRUVBL2 hetero-dodecamer in complex with 1 AtRPAP3 RBD domain)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Arabidopsis thaliana dodecameric R2T complex I (containing a...

Fileemd_19894_additional_3.map
AnnotationArabidopsis thaliana dodecameric R2T complex I (containing a AtRUVBL1-AtRUVBL2 hetero-dodecamer in complex with 2 AtRPAP3 RBD domains)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 (unfil) for the Arabidopsis thaliana R2T complex

Fileemd_19894_half_map_1.map
AnnotationHalf map 1 (unfil) for the Arabidopsis thaliana R2T complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 (unfil) for the Arabidopsis thaliana R2T complex

Fileemd_19894_half_map_2.map
AnnotationHalf map 2 (unfil) for the Arabidopsis thaliana R2T complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : AtR2T complex

EntireName: AtR2T complex
Components
  • Complex: AtR2T complex
    • Protein or peptide: RuvB-like protein 1
    • Protein or peptide: RuvB-like helicase
    • Protein or peptide: At1g56440
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: AtR2T complex

SupramoleculeName: AtR2T complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: AtRuvBL1-AtRuvBL2a in complex with AtRPAP3
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: RuvB-like protein 1

MacromoleculeName: RuvB-like protein 1 / type: protein_or_peptide / ID: 1
Details: Protein sequence contains a N-terminal 10xHistidine tag and TEV protease cleavage site that do not affect protein activity nor structure
Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 53.750754 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH HHSSGENLYF QGSHMLEDPM EKVKIEEIQS TAKKQRIATH THIKGLGLEP TGIPIKLAAG FVGQLEAREA AGLVVDMIK QKKMAGKALL LAGPPGTGKT ALALGISQEL GSKVPFCPMV GSEVYSSEVK KTEVLMENFR RAIGLRIKET K EVYEGEVT ...String:
MGSSHHHHHH HHSSGENLYF QGSHMLEDPM EKVKIEEIQS TAKKQRIATH THIKGLGLEP TGIPIKLAAG FVGQLEAREA AGLVVDMIK QKKMAGKALL LAGPPGTGKT ALALGISQEL GSKVPFCPMV GSEVYSSEVK KTEVLMENFR RAIGLRIKET K EVYEGEVT ELSPEETESL TGGYGKSISH VVITLKTVKG TKHLKLDPTI YDALIKEKVA VGDVIYIEAN SGAVKRVGRS DA FATEFDL EAEEYVPLPK GEVHKKKEIV QDVTLQDLDA ANARPQGGQD ILSLMGQMMK PRKTEITDKL RQEINKVVNR YID EGVAEL VPGVLFIDEV HMLDMECFSY LNRALESSLS PIVIFATNRG VCNVRGTDMP SPHGVPIDLL DRLVIIRTQI YDPS EMIQI IAIRAQVEEL TVDEECLVLL GEIGQRTSLR HAVQLLSPAS IVAKMNGRDN ICKADIEEVT SLYLDAKSSA KLLHE QQEK YIS

UniProtKB: RuvB-like protein 1

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Macromolecule #2: RuvB-like helicase

MacromoleculeName: RuvB-like helicase / type: protein_or_peptide / ID: 2
Details: Protein sequence contains a stretch of 18 residues extra at the N-terminus due to cloning design that does not affect protein activity nor structure
Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 54.007848 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADLNWISAG HAIADVGTMA ELKLSESRDL TRVERIGAHS HIRGLGLDSA LEPRAVSEGM VGQVKARKAA GVILQMIREG KIAGRAILI AGQPGTGKTA IAMGMAKSLG LETPFAMIAG SEIFSLEMSK TEALTQSFRK AIGVRIKEET EVIEGEVVEV Q IDRPASSG ...String:
MADLNWISAG HAIADVGTMA ELKLSESRDL TRVERIGAHS HIRGLGLDSA LEPRAVSEGM VGQVKARKAA GVILQMIREG KIAGRAILI AGQPGTGKTA IAMGMAKSLG LETPFAMIAG SEIFSLEMSK TEALTQSFRK AIGVRIKEET EVIEGEVVEV Q IDRPASSG VASKSGKMTM KTTDMETVYD MGAKMIEALN KEKVQSGDVI AIDKATGKIT KLGRSFSRSR DYDAMGAQTK FV QCPEGEL QKRKEVVHCV TLHEIDVINS RTQGFLALFT GDTGEIRSEV REQIDTKVAE WREEGKAEIV PGVLFIDEVH MLD IECFSF LNRALENEMS PILVVATNRG VTTIRGTNQK SPHGIPIDLL DRLLIITTQP YTDDDIRKIL EIRCQEEDVE MNEE AKQLL TLIGRDTSLR YAIHLITAAA LSCQKRKGKV VEVEDIQRVY RLFLDVRRSM QYLVEYQSQY MFSEPIKNDE AAAED EQDA MQI

UniProtKB: RuvB-like helicase

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Macromolecule #3: At1g56440

MacromoleculeName: At1g56440 / type: protein_or_peptide / ID: 3
Details: Protein sequence contains a N-terminal His-tag followed by an IF2D1 tag and a TEV protease site, and C-terminal Strep-II tag with HRV 3C protease site that do not affect protein activity nor structure
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 59.14498 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH HHHHMTDVTI KGGENLYFQG MARSPSKHGR DQTQDFQGFF NDLQDWELSL KDKDKKIKQQ PANSSNPSSE TFRPSGSGK YDFAKKYRSI RDLSSSLIGE SLLDSSSEKE QGNEFFKQKK FNEAIDCYSR SIALSPNAVT YANRAMAYLK I KRYREAEV ...String:
MGSSHHHHHH HHHHMTDVTI KGGENLYFQG MARSPSKHGR DQTQDFQGFF NDLQDWELSL KDKDKKIKQQ PANSSNPSSE TFRPSGSGK YDFAKKYRSI RDLSSSLIGE SLLDSSSEKE QGNEFFKQKK FNEAIDCYSR SIALSPNAVT YANRAMAYLK I KRYREAEV DCTEALNLDD RYIKAYSRRA TARKELGMIK EAKEDAEFAL RLEPESQELK KQYADIKSLL EKEIIEKATG AM QSTAQEL LKTSGLDKKI QKPKTEMTSK PVTLVAKTNR DIVQPVLGSN ESSGKKLIEN IQPEEKSKEG SMKIPAITEI LDS KKVTPG SQSYEKEAKP SDRNGTQPSG PENQVSKQLE LKPSVQELAA HAASLAMTEA SKNIKTPKSA YEFENSWRSF SGDS ALRSQ LLKVTTPSSL PQIFKNALTS PVLVDIIKCV ASFFTEDMDL AVKYIENLTK VPRFNMLVMC LTSTEKNELL KIWED VFCN KATPMEYAEV LDKLRSRYCL KQLEVLFQGP WSHPQFEK

UniProtKB: At1g56440

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMHEPESN-(2-Hydroxyethyl)piperazine-N-(2-ethanesulfonic acid)
300.0 mMNaClSodium chloride
1.0 mMDTT1,4-Dithiothreitol
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 100.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.12 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2334954
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC Ab Initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 185042
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. v4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-9eq2:
Arabidopsis thaliana R2T complex

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