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- EMDB-4556: Truncated human R2TP complex, structure 5 (ADP-filled) -

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Basic information

Entry
Database: EMDB / ID: EMD-4556
TitleTruncated human R2TP complex, structure 5 (ADP-filled)
Map data
Sample
  • Complex: RUVBL1-RUVBL2 in a closed conformation with ADP
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: PIH1 domain-containing protein 1
    • Protein or peptide: RNA polymerase II-associated protein 3
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsMunoz-Hernandez H / Rodriguez CF / Llorca O
CitationJournal: Sci Adv / Year: 2019
Title: Structural mechanism for regulation of the AAA-ATPases RUVBL1-RUVBL2 in the R2TP co-chaperone revealed by cryo-EM.
Authors: Hugo Muñoz-Hernández / Mohinder Pal / Carlos F Rodríguez / Rafael Fernandez-Leiro / Chrisostomos Prodromou / Laurence H Pearl / Oscar Llorca /
Abstract: The human R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) is an HSP90 co-chaperone required for the maturation of several essential multiprotein complexes, including RNA polymerase II, small nucleolar ...The human R2TP complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) is an HSP90 co-chaperone required for the maturation of several essential multiprotein complexes, including RNA polymerase II, small nucleolar ribonucleoproteins, and PIKK complexes such as mTORC1 and ATR-ATRIP. RUVBL1-RUVBL2 AAA-ATPases are also primary components of other essential complexes such as INO80 and Tip60 remodelers. Despite recent efforts, the molecular mechanisms regulating RUVBL1-RUVBL2 in these complexes remain elusive. Here, we report cryo-EM structures of R2TP and show how access to the nucleotide-binding site of RUVBL2 is coupled to binding of the client recruitment component of R2TP (PIH1D1) to its DII domain. This interaction induces conformational rearrangements that lead to the destabilization of an N-terminal segment of RUVBL2 that acts as a gatekeeper to nucleotide exchange. This mechanism couples protein-induced motions of the DII domains with accessibility of the nucleotide-binding site in RUVBL1-RUVBL2, and it is likely a general mechanism shared with other RUVBL1-RUVBL2-containing complexes.
History
DepositionJan 18, 2019-
Header (metadata) releaseFeb 6, 2019-
Map releaseApr 10, 2019-
UpdateMay 15, 2019-
Current statusMay 15, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4556.png

Downloads & links

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Map

FileDownload / File: emd_4556.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 260 pix.
= 278.2 Å		1.07 Å/pix.
x 260 pix.
= 278.2 Å		1.07 Å/pix.
x 260 pix.
= 278.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.05577485 - 0.10785029
Average (Standard dev.)0.00005939254 (±0.003850617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 278.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z278.200278.200278.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0560.1080.000

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Supplemental data

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Sample components

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Entire : RUVBL1-RUVBL2 in a closed conformation with ADP

EntireName: RUVBL1-RUVBL2 in a closed conformation with ADP
Components
  • Complex: RUVBL1-RUVBL2 in a closed conformation with ADP
    • Protein or peptide: RuvB-like 1
    • Protein or peptide: RuvB-like 2
    • Protein or peptide: PIH1 domain-containing protein 1
    • Protein or peptide: RNA polymerase II-associated protein 3

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Supramolecule #1: RUVBL1-RUVBL2 in a closed conformation with ADP

SupramoleculeName: RUVBL1-RUVBL2 in a closed conformation with ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21

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Macromolecule #1: RuvB-like 1

MacromoleculeName: RuvB-like 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLA GPPGTGKTAL ALAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA I GLRIKETK EVYEGEVTEL TPCETENPMG GYGKTISHVI IGLKTAKGTK ...String:
MKIEEVKSTT KTQRIASHSH VKGLGLDESG LAKQAASGLV GQENAREACG VIVELIKSKK MAGRAVLLA GPPGTGKTAL ALAIAQELGS KVPFCPMVGS EVYSTEIKKT EVLMENFRRA I GLRIKETK EVYEGEVTEL TPCETENPMG GYGKTISHVI IGLKTAKGTK QLKLDPSIFE SL QKERVEA GDVIYIEANS GAVKRQGRCD TYATEFDLEA EEYVPLPKGD VHKKKEIIQD VTL HDLDVA NARPQGGQDI LSMMGQLMKP KKTEITDKLR GEINKVVNKY IDQGIAELVP GVLF VDEVH MLDIECFTYL HRALESSIAP IVIFASNRGN CVIRGTEDIT SPHGIPLDLL DRVMI IRTM LYTPQEMKQI IKIRAQTEGI NISEEALNHL GEIGTKTTLR YSVQLLTPAN LLAKIN GKD SIEKEHVEEI SELFYDAKSS AKILADQQDK YMK

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Macromolecule #2: RuvB-like 2

MacromoleculeName: RuvB-like 2 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIA GRAVLIAGQP GTGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL T QAFRRSIG VRIKEETEII EGEVVEIQID RPATGTGSKV GKLTLKTTEM ...String:
MATVTATTKV PEIRDVTRIE RIGAHSHIRG LGLDDALEPR QASQGMVGQL AARRAAGVVL EMIREGKIA GRAVLIAGQP GTGKTAIAMG MAQALGPDTP FTAIAGSEIF SLEMSKTEAL T QAFRRSIG VRIKEETEII EGEVVEIQID RPATGTGSKV GKLTLKTTEM ETIYDLGTKM IE SLTKDKV QAGDVITIDK ATGKISKLGR SFTRARDYDA MGSQTKFVQC PDGELQKRKE VVH TVSLHE IDVINSRTQG FLALFSGDTG EIKSEVREQI NAKVAEWREE GKAEIIPGVL FIDE VHMLD IESFSFLNRA LESDMAPVLI MATNRGITRI RGTSYQSPHG IPIDLLDRLL IVSTT PYSE KDTKQILRIR CEEEDVEMSE DAYTVLTRIG LETSLRYAIQ LITAASLVCR KRKGTE VQV DDIKRVYSLF LDESRSTQYM KEYQDAFLFN ELKGETMDTS

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Macromolecule #3: PIH1 domain-containing protein 1

MacromoleculeName: PIH1 domain-containing protein 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MANPKLLGMG LSEAEAIGAD SARFEELLLQ ASKELQQAQT TRPESTQIQP QPGFCIKTNS SEGKVFINI CHSPSIPPPA DVTEEELLQM LEEDQAGFRI PMSLGEPHAE LDAKGQGCTA Y DVAVNSDF YRRMQNSDFL RELVITIARE GLEDKYNLQL NPEWRMMKNR ...String:
MANPKLLGMG LSEAEAIGAD SARFEELLLQ ASKELQQAQT TRPESTQIQP QPGFCIKTNS SEGKVFINI CHSPSIPPPA DVTEEELLQM LEEDQAGFRI PMSLGEPHAE LDAKGQGCTA Y DVAVNSDF YRRMQNSDFL RELVITIARE GLEDKYNLQL NPEWRMMKNR PFMGSISQQN IR SEQRPRI QELGDLYTPA PGRAESGPEK PHLNLWLEAP DLLLAEVDLP KLDGALGLSL EIG ENRLVM GGPQQLYHLD AYIPLQINSH ESKAAFHRKR KQLMVAMPLL PVPS

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Macromolecule #4: RNA polymerase II-associated protein 3

MacromoleculeName: RNA polymerase II-associated protein 3 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KGHWDDVFLD STQRQNVVKP IDNPPHPGST KPLKKVIIEE TGNLIQTIDV PDSTTAAAPE NNPINLANV IAATGTTSKK NSSQDDLFPT SDTPRAKVLK IEEVSDTSSL QPQASLKQDV C QSYSEKMP IEIEQKPAQF ATTVLPPIPA NSFQLESDFR QLKSSPDMLY ...String:
KGHWDDVFLD STQRQNVVKP IDNPPHPGST KPLKKVIIEE TGNLIQTIDV PDSTTAAAPE NNPINLANV IAATGTTSKK NSSQDDLFPT SDTPRAKVLK IEEVSDTSSL QPQASLKQDV C QSYSEKMP IEIEQKPAQF ATTVLPPIPA NSFQLESDFR QLKSSPDMLY QYLKQIEPSL YP KLFQKNL DPDVFNQIVK ILHDFYIEKE KPLLIFEILQ RLSELKRFDM AVMFMSETEK KIA RALFNH IDKSGLKDSS VEELKKRYGG

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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

BufferpH: 7.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 408781
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 102100
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

6fo1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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