6FML

CryoEM Structure INO80core Nucleosome complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for ATP-dependent chromatin remodelling by the INO80 complex.

Eustermann, S.Schall, K.Kostrewa, D.Lakomek, K.Strauss, M.Moldt, M.Hopfner, K.P.

(2018) Nature 556: 386-390

  • DOI: 10.1038/s41586-018-0029-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chro ...

    In the eukaryotic nucleus, DNA is packaged in the form of nucleosomes, each of which comprises about 147 base pairs of DNA wrapped around a histone protein octamer. The position and histone composition of nucleosomes is governed by ATP-dependent chromatin remodellers 1-3 such as the 15-subunit INO80 complex 4 . INO80 regulates gene expression, DNA repair and replication by sliding nucleosomes, the exchange of histone H2A.Z with H2A, and the positioning of + 1 and -1 nucleosomes at promoter DNA 5-8 . The structures and mechanisms of these remodelling reactions are currently unknown. Here we report the cryo-electron microscopy structure of the evolutionarily conserved core of the INO80 complex from the fungus Chaetomium thermophilum bound to a nucleosome, at a global resolution of 4.3 Å and with major parts at 3.7 Å. The INO80 core cradles one entire gyre of the nucleosome through multivalent DNA and histone contacts. An Rvb1/Rvb2 AAA + ATPase heterohexamer is an assembly scaffold for the complex and acts as a 'stator' for the motor and nucleosome-gripping subunits. The Swi2/Snf2 ATPase motor binds to nucleosomal DNA at superhelical location -6, unwraps approximately 15 base pairs, disrupts the H2A-DNA contacts and is poised to pump entry DNA into the nucleosome. Arp5 and Ies6 bind superhelical locations -2 and -3 to act as a counter grip for the motor, on the other side of the H2A-H2B dimer. The Arp5 insertion domain forms a grappler element that binds the nucleosome dyad, connects the Arp5 actin-fold and entry DNA over a distance of about 90 Å and packs against histone H2A-H2B near the 'acidic patch'. Our structure together with biochemical data 8 suggests a unified mechanism for nucleosome sliding and histone editing by INO80. The motor is part of a macromolecular ratchet, persistently pumping entry DNA across the H2A-H2B dimer against the Arp5 grip until a large nucleosome translocation step occurs. The transient exposure of H2A-H2B by motor activity as well as differential recognition of H2A.Z and H2A may regulate histone exchange.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.,the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India. Electronic address: tpsingh.aiims@gmail.com.,Department of Rheumatology & Clinical Immunology, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.,Biomedical Center and Center for Integrated Protein Science, Ludwig-Maximilians-University, 82152 Martinsried, Germany.,Multidiscipline Research Center, Institute of High Energy Physics Chinese Academy of Sciences, Beijing, China.,Institute for chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany. hopfner@genzentrum.lmu.de.,Institute of Biochemistry and Biotechnology, Martin-Luther-University, 06120, Halle (Saale), Germany.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.,Department of Biochemistry & Molecular Biology, The University of Georgia, Athens, Georgia, 30602, USA.,Chemistry Department, Faculty of Science, Suez Canal University, 41522, Ismailia, Egypt.,Department of Biochemistry , University of Bayreuth , 95447 Bayreuth , Germany.,Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea. Electronic address: saylim@kaeri.re.kr.,IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France.,Science for Life Laboratory, Stockholm University, Solna, Sweden.,CBS, University of Montpellier, CNRS, INSERM, Montpellier, 34090, France.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China. yuanqp@mail.buct.edu.cn.,Department of Optoelectronic Information, School of Science, Qilu University of Technology, Jinan, China.,the Department of Biochemistry, McGill Centre for Structural Biology, McGill University, Montreal, Quebec H3G 0B1, Canada kalle.gehring@mcgill.ca.,Center for Integrated Protein Science, Munich, Germany. hopfner@genzentrum.lmu.de.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France. sebastien.granier@igf.cnrs.fr.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Microbiology, University of Illinois, Urbana, IL 61801, USA.,Department of Chemistry, Fudan University, Shanghai, China.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. martin.ott@dbb.su.se.,Institute of Molecular Biology and Pathology, CNR, Rome, Italy.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: tatiana.kutateladze@ucdenver.edu.,State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.,Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea. Electronic address: mkkim@kaeri.re.kr.,Department of Enzymology, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany. hopfner@genzentrum.lmu.de.,Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,CeSI-MeT, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.,National Center for Protein Science, Shanghai, China.,Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, China.,Key Laboratory of Structural Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,From the Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada and.,Synthesis and Solid State Pharmaceutical Centre (SSPC), School of Chemistry, University College Dublin, Dublin, Ireland.,Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China. yuanqp@mail.buct.edu.cn.,School of Chemistry, University of Nottingham, Nottingham, United Kingdom.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA.,Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany. matthias.schmidt@uni-ulm.de.,Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland.,Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA bnolen@uoregon.edu.,Department of Biochemistry & Molecular Biology, The University of Georgia, Athens, Georgia, 30602, USA. jprose@uga.edu.,School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA. yajunyan@uga.edu.,Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China. Electronic address: yinyuxin@hsc.pku.edu.cn.,IGF, University of Montpellier, CNRS, INSERM, Montpellier, 34094, France. cedric.leyrat@igf.cnrs.fr.,Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences.,Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Biotechnology and Bioengineering, Interdisciplinary Program for Bioenergy and Biomaterials, Chonnam National University, Gwangju, 61186, Republic of Korea.,Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea; Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Republic of Korea.,Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany.,Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany. marcus.faendrich@uni-ulm.de.,Department of Medical Chemistry, Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany.,Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.,Department of Natural Product Biochemistry, Institute of Biochemistry and Biotechnology , Martin-Luther-University Halle-Wittenberg , 06120 Halle/Saale , Germany.,Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel. Electronic address: noam@ch.technion.ac.il.,Department of Microbiology, University of Illinois, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA.,Department of Medical Cell Biology, Uppsala University, SE-75123, Uppsala, Sweden.,Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, SE-751 85, Sweden.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China.,School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA, 30602, USA.,Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RuvB-like helicase
A, B, C
462Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
EC: 3.6.4.12
Find proteins for G0RYI5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RYI5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RuvB-like helicase
D, E, F
488Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
EC: 3.6.4.12
Find proteins for G0RYC2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RYC2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ino80
G
1856N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
les2
H
491Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0RY01 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0RY01
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ies6
I
219Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S590 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S590
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Actin related protein 5
J
770Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)Mutation(s): 0 
Find proteins for G0S589 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Go to UniProtKB:  G0S589
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
M, Q
135Homo sapiensMutation(s): 0 
Gene Names: HIST2H3A, HIST2H3C, HIST2H3D (H3F2, H3FM)
Find proteins for Q71DI3 (Homo sapiens)
Go to Gene View: HIST2H3A HIST2H3C HIST2H3D
Go to UniProtKB:  Q71DI3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Histone H4
N, R
102Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
O, S
129Homo sapiensMutation(s): 0 
Gene Names: H2AC11, H2AC13, H2AC15, H2AC16, H2AC17 (H2AFP, HIST1H2AG, H2AFC, HIST1H2AI, H2AFD, HIST1H2AK, H2AFI, HIST1H2AL, H2AFN, HIST1H2AM)
Find proteins for P0C0S8 (Homo sapiens)
Go to UniProtKB:  P0C0S8
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Histone H2B type 1-C/E/F/G/I
P, T
125Homo sapiensMutation(s): 0 
Gene Names: H2BC4, H2BC6, H2BC7, H2BC8, H2BC10 (H2BFL, HIST1H2BC, H2BFH, HIST1H2BE, H2BFG, HIST1H2BF, H2BFA, HIST1H2BG, H2BFK, HIST1H2BI)
Find proteins for P62807 (Homo sapiens)
Go to UniProtKB:  P62807
Entity ID: 7
MoleculeChainsLengthOrganism
Nucleosomal DNA Strand 1K196synthetic construct
Entity ID: 8
MoleculeChainsLengthOrganism
Nucleosomal DNA Strand 2L196synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
J
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
H, J
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Molecular Biology OrganizationGermanyEMBO ALTF 1098-2012
European Research CouncilGermanyATMMACHINE
German Research FoundationGermanyCRC1064, GRK1721

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references
  • Version 1.2: 2019-12-11
    Type: Other