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- PDB-8eb5: Tandem of Hermes transposase BED domain in complex with the quasi... -

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Basic information

Entry
Database: PDB / ID: 8eb5
TitleTandem of Hermes transposase BED domain in complex with the quasi palindrome of its transposon left-end
Components
  • (Hermes transposon left-end subterminal repeats 1 and 2) x 2
  • Hermes transposase BED domain
KeywordsDNA BINDING PROTEIN/DNA / BED domain / zinc-binding domain / transposase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


protein dimerization activity / DNA binding / zinc ion binding / identical protein binding / nucleus
Similarity search - Function
: / Hermes trasposase, DNA-binding domain / Hermes transposase DNA-binding domain / HAT, C-terminal dimerisation domain / hAT family C-terminal dimerisation region / Zinc finger, BED-type / Zinc finger BED-type profile. / BED zinc finger / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposase
Similarity search - Component
Biological speciesMusca domestica (house fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsLannes, L. / Dyda, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036153-16 United States
CitationJournal: Nat Commun / Year: 2023
Title: Zinc-finger BED domains drive the formation of the active Hermes transpososome by asymmetric DNA binding.
Authors: Laurie Lannes / Christopher M Furman / Alison B Hickman / Fred Dyda /
Abstract: The Hermes DNA transposon is a member of the eukaryotic hAT superfamily, and its transposase forms a ring-shaped tetramer of dimers. Our investigation, combining biochemical, crystallography and cryo- ...The Hermes DNA transposon is a member of the eukaryotic hAT superfamily, and its transposase forms a ring-shaped tetramer of dimers. Our investigation, combining biochemical, crystallography and cryo-electron microscopy, and in-cell assays, shows that the full-length Hermes octamer extensively interacts with its transposon left-end through multiple BED domains of three Hermes protomers contributed by three dimers explaining the role of the unusual higher-order assembly. By contrast, the right-end is bound to no BED domains at all. Thus, this work supports a model in which Hermes multimerizes to gather enough BED domains to find its left-end among the abundant genomic DNA, facilitating the subsequent interaction with the right-end.
History
DepositionAug 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Oct 2, 2024Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hermes transposase BED domain
C: Hermes transposon left-end subterminal repeats 1 and 2
D: Hermes transposon left-end subterminal repeats 1 and 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6284
Polymers19,5633
Non-polymers651
Water905
1
A: Hermes transposase BED domain
C: Hermes transposon left-end subterminal repeats 1 and 2
D: Hermes transposon left-end subterminal repeats 1 and 2
hetero molecules

A: Hermes transposase BED domain
D: Hermes transposon left-end subterminal repeats 1 and 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0557
Polymers33,9245
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)55.271, 55.271, 212.573
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-9-

DG

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Components

#1: Protein Hermes transposase BED domain


Mass: 9150.765 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Musca domestica (house fly) / Plasmid: pET15b / Details (production host): no purification tag / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q25442
#2: DNA chain Hermes transposon left-end subterminal repeats 1 and 2


Mass: 5201.396 Da / Num. of mol.: 1 / Mutation: None / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#3: DNA chain Hermes transposon left-end subterminal repeats 1 and 2


Mass: 5210.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Musca domestica (house fly)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, Bis-TRIS

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.28335 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28335 Å / Relative weight: 1
ReflectionResolution: 2.5→27.64 Å / Num. obs: 7292 / % possible obs: 99.8 % / Redundancy: 19.2 % / Biso Wilson estimate: 100.25 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04434 / Rpim(I) all: 0.01086 / Rrim(I) all: 0.04575 / Net I/σ(I): 35.47
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 19.23 % / Rmerge(I) obs: 1.224 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 694 / CC1/2: 0.85 / CC star: 0.959 / Rpim(I) all: 0.2717 / Rrim(I) all: 1.224 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (11-DEC-2020)refinement
Coot0.8.9model building
Omodel building
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→27.64 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.472 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.647 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.251
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 743 10.19 %RANDOM
Rwork0.2308 ---
obs0.2316 7292 99.8 %-
Displacement parametersBiso mean: 98.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.2075 Å20 Å20 Å2
2---3.2075 Å20 Å2
3---6.415 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 691 1 5 1298
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081425HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.942067HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d407SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes142HARMONIC5
X-RAY DIFFRACTIONt_it1425HARMONIC5
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion27.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion188SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle4HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact686SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.52 Å / Total num. of bins used: 38
RfactorNum. reflection% reflection
Rfree0.3255 -7.58 %
Rwork0.3017 183 -
all0.3034 198 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.60933.32681.39175.6090.40889.0815-0.20530.57670.7413-0.7830.0732-0.24910.31470.1640.13210.3867-0.13930.0996-0.01940.0543-0.083317.194430.17541.3939
26.02541.695-2.1899.446-2.55532.23050.4002-0.24230.1584-0.1986-0.76250.78190.0499-0.06290.36230.1693-0.36070.0212-0.02-0.0609-0.092413.160924.777218.8006
34.56312.1326-0.960311.6649-1.79167.17530.2116-0.19520.373-0.6529-0.1180.00960.0317-0.026-0.09360.0144-0.35490.0442-0.162-0.09580.11613.24524.521218.9323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }
3X-RAY DIFFRACTION3{ D|* }

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