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- PDB-7epu: Crystal structure of HsALC1 -

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Basic information

Entry
Database: PDB / ID: 7epu
TitleCrystal structure of HsALC1
Components
  • Chromodomain-helicase-DNA-binding protein 1-like
  • non-immunized human scFv
KeywordsMOTOR PROTEIN / macrodomain / autoinhibition / DNA damage / PARP1
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 / site of double-strand break ...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 / site of double-strand break / chromatin remodeling / nucleotide binding / DNA repair / DNA damage response / ATP hydrolysis activity / 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. / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...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. / Helicase conserved C-terminal domain / 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
ADENOSINE-5'-DIPHOSPHATE / Chromodomain-helicase-DNA-binding protein 1-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsWang, L. / Chen, K.J.
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of ALC1/CHD1L autoinhibition and the mechanism of activation by the nucleosome.
Authors: Li Wang / Kangjing Chen / Zhucheng Chen /
Abstract: Chromatin remodeler ALC1 (amplification in liver cancer 1) is crucial for repairing damaged DNA. It is autoinhibited and activated by nucleosomal epitopes. However, the mechanisms by which ALC1 is ...Chromatin remodeler ALC1 (amplification in liver cancer 1) is crucial for repairing damaged DNA. It is autoinhibited and activated by nucleosomal epitopes. However, the mechanisms by which ALC1 is regulated remain unclear. Here we report the crystal structure of human ALC1 and the cryoEM structure bound to the nucleosome. The structure shows the macro domain of ALC1 binds to lobe 2 of the ATPase motor, sequestering two elements for nucleosome recognition, explaining the autoinhibition mechanism of the enzyme. The H4 tail competes with the macro domain for lobe 2-binding, explaining the requirement for this nucleosomal epitope for ALC1 activation. A dual-arginine-anchor motif of ALC1 recognizes the acidic pocket of the nucleosome, which is critical for chromatin remodeling in vitro. Together, our findings illustrate the structures of ALC1 and shed light on its regulation mechanisms, paving the way for the discovery of drugs targeting ALC1 for the treatment of cancer.
History
DepositionApr 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: non-immunized human scFv
B: Chromodomain-helicase-DNA-binding protein 1-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6134
Polymers127,1622
Non-polymers4522
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.480, 225.263, 106.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody non-immunized human scFv


Mass: 27769.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein Chromodomain-helicase-DNA-binding protein 1-like / Amplified in liver cancer protein 1


Mass: 99392.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1L, ALC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86WJ1, DNA helicase
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.62 Å3/Da / Density % sol: 66.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: MPD, sodium chloride, magnesium chloride, acetate

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 23523 / % possible obs: 99.4 % / Redundancy: 10.8 % / Biso Wilson estimate: 127.58 Å2 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.042 / Rrim(I) all: 0.137 / Χ2: 0.811 / Net I/σ(I): 5.5 / Num. measured all: 255064
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.569.91.49711490.5140.51.5830.69497.5
3.56-3.6310.91.3811160.5920.441.4510.68698
3.63-3.6911.11.05711740.6320.3381.1120.72598.6
3.69-3.7711.10.94411480.7820.3030.9940.7198.9
3.77-3.8511.10.80111380.7820.2580.8430.72998.4
3.85-3.9411.10.70911640.8260.2290.7460.7498.6
3.94-4.0411.10.58611350.8890.190.6180.73198.5
4.04-4.1510.80.45911720.9230.1510.4840.72499.6
4.15-4.2710.30.35811800.9480.1210.3790.75299.7
4.27-4.41110.23411660.9740.0770.2470.735100
4.41-4.5711.40.20111710.9810.0640.2110.75499.9
4.57-4.7511.40.17111580.9870.0550.180.796100
4.75-4.9711.30.15711890.9870.0510.1650.787100
4.97-5.2310.90.13911930.9910.0450.1470.792100
5.23-5.5510.20.12711750.9910.0430.1350.816100
5.55-5.9811.40.12211970.9930.0390.1280.821100
5.98-6.5811.30.09611880.9960.0310.1010.857100
6.58-7.5310.50.06812200.9980.0230.0720.918100
7.53-9.4810.80.04412080.9990.0140.0461.108100
9.48-509.40.03412820.9990.0120.0361.36299.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MWY, 5JXR, 2FG1, 5YAN

3mwy

5jxr

2fg1

5yan


Resolution: 3.5→45.402 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 35.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3157 1996 8.52 %
Rwork0.2675 21432 -
obs0.2715 23428 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 262.94 Å2 / Biso mean: 141.9093 Å2 / Biso min: 41.31 Å2
Refinement stepCycle: final / Resolution: 3.5→45.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7761 0 28 0 7789
Biso mean--129.26 --
Num. residues----978
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.5002-3.58770.41661340.3636144094
3.5877-3.68470.40591390.3336149198
3.6847-3.7930.36081400.3174149999
3.793-3.91540.39011400.3137150098
3.9154-4.05530.32491380.3025149699
4.0553-4.21750.34141450.29511546100
4.2175-4.40930.32041410.2471530100
4.4093-4.64160.2931440.23341532100
4.6416-4.93210.27751420.23661535100
4.9321-5.31230.29931440.24751546100
5.3123-5.84590.32981450.26791553100
5.8459-6.68950.321450.30481570100
6.6895-8.41930.35271460.2781574100
8.4193-45.40.26831530.2377162098

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