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- PDB-6zhx: Cryo-EM structure of the regulatory linker of ALC1 bound to the n... -

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Entry
Database: PDB / ID: 6zhx
TitleCryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class.
Components
  • (DNA (145-MER) Widom 601 ...) x 2
  • Chromodomain-helicase-DNA-binding protein 1-like
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
KeywordsDNA BINDING PROTEIN / ALC1 / CHD1L / chromatin remodeler / DNA damage response / nucleosome / NUCLEAR PROTEIN / GENE REGULATION
Function / homology
Function and homology information


poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / site of DNA damage / nucleosome binding / DNA helicase activity / histone reader activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / structural constituent of chromatin ...poly-ADP-D-ribose modification-dependent protein binding / ATP-dependent chromatin remodeler activity / site of DNA damage / nucleosome binding / DNA helicase activity / histone reader activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / structural constituent of chromatin / nucleosome / site of double-strand break / chromatin remodeling / protein heterodimerization activity / nucleotide binding / DNA repair / DNA damage response / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 1-like / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Histone H2B signature. / Histone H2B / Histone H2B ...Chromodomain-helicase-DNA-binding protein 1-like / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Macro domain / Macro domain profile. / Macro domain-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Chromodomain-helicase-DNA-binding protein 1-like
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsBacic, L. / Gaullier, G. / Croll, T.I. / Deindl, S.
Funding support Sweden, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ChromatinRemodeling Sweden
Citation
Journal: Cell Rep / Year: 2020
Title: Mechanistic Insights into Regulation of the ALC1 Remodeler by the Nucleosome Acidic Patch.
Authors: Laura C Lehmann / Luka Bacic / Graeme Hewitt / Klaus Brackmann / Anton Sabantsev / Guillaume Gaullier / Sofia Pytharopoulou / Gianluca Degliesposti / Hanneke Okkenhaug / Song Tan / ...Authors: Laura C Lehmann / Luka Bacic / Graeme Hewitt / Klaus Brackmann / Anton Sabantsev / Guillaume Gaullier / Sofia Pytharopoulou / Gianluca Degliesposti / Hanneke Okkenhaug / Song Tan / Alessandro Costa / J Mark Skehel / Simon J Boulton / Sebastian Deindl /
Abstract: Upon DNA damage, the ALC1/CHD1L nucleosome remodeling enzyme (remodeler) is activated by binding to poly(ADP-ribose). How activated ALC1 recognizes the nucleosome, as well as how this recognition is ...Upon DNA damage, the ALC1/CHD1L nucleosome remodeling enzyme (remodeler) is activated by binding to poly(ADP-ribose). How activated ALC1 recognizes the nucleosome, as well as how this recognition is coupled to remodeling, is unknown. Here, we show that remodeling by ALC1 requires a wild-type acidic patch on the entry side of the nucleosome. The cryo-electron microscopy structure of a nucleosome-ALC1 linker complex reveals a regulatory linker segment that binds to the acidic patch. Mutations within this interface alter the dynamics of ALC1 recruitment to DNA damage and impede the ATPase and remodeling activities of ALC1. Full activation requires acidic patch-linker segment interactions that tether the remodeler to the nucleosome and couple ATP hydrolysis to nucleosome mobilization. Upon DNA damage, such a requirement may be used to modulate ALC1 activity via changes in the nucleosome acidic patches.
#1: Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Authors: Croll, T.I.
#3: Journal: IUCrJ / Year: 2020
Title: Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in
Authors: Zivanov, J. / Nakane, T. / Scheres, S.H.W.
#4: Journal: J. Struct. Biol. / Year: 2012
Title: RELION: implementation of a Bayesian approach to cryo-EM structure determination.
Authors: Scheres, S.H.
History
DepositionJun 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 14, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / audit_author ...atom_site / audit_author / chem_comp / em_entity_assembly / em_software / entity / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / software / struct_asym / struct_conf / struct_keywords
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _em_entity_assembly.entity_id_list / _em_software.category / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _ndb_struct_na_base_pair_step.helical_rise / _ndb_struct_na_base_pair_step.helical_twist / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.rise / _ndb_struct_na_base_pair_step.roll / _ndb_struct_na_base_pair_step.shift / _ndb_struct_na_base_pair_step.slide / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _ndb_struct_na_base_pair_step.twist / _ndb_struct_na_base_pair_step.x_displacement / _ndb_struct_na_base_pair_step.y_displacement / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.pdbx_keywords / _struct_keywords.text
Description: Model completeness
Details: Some protein chain termini were extended into density that had been left un-modeled in the initial deposition. Water molecules were placed where density supports them. Atomic displacement ...Details: Some protein chain termini were extended into density that had been left un-modeled in the initial deposition. Water molecules were placed where density supports them. Atomic displacement parameters are now correctly refined (they had been omitted in the initial deposition).
Provider: author / Type: Coordinate replacement

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-11220
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (145-MER) Widom 601 sequence
J: DNA (145-MER) Widom 601 sequence
K: Chromodomain-helicase-DNA-binding protein 1-like
L: Chromodomain-helicase-DNA-binding protein 1-like


Theoretical massNumber of molelcules
Total (without water)206,78512
Polymers206,78512
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Nucleosome-peptide complex ran similarly to free nucleosome and could be shifted by addition of streptavidin binding to the biotinylated peptide., microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area59490 Å2
ΔGint-391 kcal/mol
Surface area73960 Å2
MethodPISA

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3 /


Mass: 15403.062 Da / Num. of mol.: 2 / Mutation: C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1, UniProt: P84233*PLUS
#2: Protein Histone H4 /


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA (145-MER) Widom 601 ... , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER) Widom 601 sequence


Mass: 44520.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (145-MER) Widom 601 sequence


Mass: 44991.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 148 molecules KL

#7: Protein/peptide Chromodomain-helicase-DNA-binding protein 1-like / Amplified in liver cancer protein 1


Mass: 4073.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide biotinylated at its C-terminus. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86WJ1, DNA helicase
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Crosslinked complex of ALC1 regulatory linker and the nucleosomeCOMPLEX#1-#70MULTIPLE SOURCES
2HistonesHistoneCOMPLEX#1-#41RECOMBINANT
3DNACOMPLEX#5-#61RECOMBINANT
4Chromodomain-helicase-DNA-binding protein 1-likeCOMPLEX#71RECOMBINANT
Molecular weightValue: 0.206653 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Xenopus laevis (African clawed frog)8355
23synthetic construct (others)32630
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
34synthetic construct (others)32630
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
115 mMHEPES1
250 mMsodium chlorideNaClSodium chloride1
31 mMDTT1
SpecimenConc.: 1.32 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: current 20 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Blot time 2.5 s, blot force 0. Two sample applications and blots were performed before vitrification.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 19897
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
UCSF ChimeraX0.93/v8model building
EM software
IDNameVersionCategoryDetails
2EPU2.6.1image acquisition
4Gctf1.18b2CTF correction
7UCSF Chimera0.93model fittingChimeraX
9RELION3.1initial Euler assignmentcommit 5857e1
10RELION3.1final Euler assignmentcommit 5857e1
11RELION3.1classificationcommit 5857e1
12RELION3.13D reconstructioncommit 5857e1
13ISOLDE1.0b5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2968853
Details: Particles were picked with Warp's neural network picker, using model BoxNet2Mask_20180918.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 636544 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Real-space CC between model and map
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
13LZ0

3lz0

A1
23LZ0

3lz0

B1
33LZ0

3lz0

C1
43LZ0

3lz0

D1
53LZ0

3lz0

E1
63LZ0

3lz0

F1
73LZ0

3lz0

G1
83LZ0

3lz0

H1
93LZ0

3lz0

I1
103LZ0

3lz0

J1
111ZLA

1zla

K1

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