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- PDB-5hoo: Crystal structure of the Mos1 Strand Transfer Complex -

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Basic information

Entry
Database: PDB / ID: 5hoo
TitleCrystal structure of the Mos1 Strand Transfer Complex
Components
  • Mariner Mos1 transposase
  • Mos1 IR DNA NTS
  • Mos1 IR TS joined to Target DNA,Mos1 IR TS joined to Target DNA
  • Target DNA
KeywordsDNA / protein-DNA complex / DNA transposase / recombinase / integrase / helix-turn-helix / base flipping
Function / homology
Function and homology information


mitotic DNA integrity checkpoint signaling / DNA topoisomerase binding / DNA double-strand break processing / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / replication fork processing / condensed chromosome / DNA integration / double-strand break repair via nonhomologous end joining ...mitotic DNA integrity checkpoint signaling / DNA topoisomerase binding / DNA double-strand break processing / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / replication fork processing / condensed chromosome / DNA integration / double-strand break repair via nonhomologous end joining / site of double-strand break / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / Hydrolases; Acting on ester bonds / nucleus / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Ribonuclease H-like superfamily/Ribonuclease H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily ...Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Ribonuclease H-like superfamily/Ribonuclease H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Mariner Mos1 transposase
Similarity search - Component
Biological speciesDrosophila mauritiana (fry)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
Model detailsrepresents the Mos1 transposition machinery after transposon integration into target DNA
AuthorsRichardson, J.M. / Morris, E.R.
CitationJournal: Elife / Year: 2016
Title: A bend, flip and trap mechanism for transposon integration.
Authors: Morris, E.R. / Grey, H. / McKenzie, G. / Jones, A.C. / Richardson, J.M.
History
DepositionJan 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mariner Mos1 transposase
B: Mariner Mos1 transposase
C: Mos1 IR DNA NTS
D: Mos1 IR TS joined to Target DNA,Mos1 IR TS joined to Target DNA
E: Mos1 IR DNA NTS
F: Mos1 IR TS joined to Target DNA,Mos1 IR TS joined to Target DNA
G: Target DNA
H: Target DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,41610
Polymers125,3678
Non-polymers492
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27950 Å2
ΔGint-159 kcal/mol
Surface area49820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.340, 58.830, 110.140
Angle α, β, γ (deg.)90.000, 94.910, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mariner Mos1 transposase / Transposable element Mos1 transposase


Mass: 40865.316 Da / Num. of mol.: 2 / Fragment: full-length Mos1 transposase / Mutation: T216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila mauritiana (fry) / Gene: mariner / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7JQ07, Hydrolases; Acting on ester bonds

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DNA chain , 3 types, 6 molecules CEDFGH

#2: DNA chain Mos1 IR DNA NTS


Mass: 7768.030 Da / Num. of mol.: 2 / Fragment: Mos1 IR DNA NTS / Source method: obtained synthetically / Details: synthetic DNA / Source: (synth.) synthetic construct (others)
#3: DNA chain Mos1 IR TS joined to Target DNA,Mos1 IR TS joined to Target DNA


Mass: 11044.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic DNA
Source: (synth.) synthetic construct (others), (synth.) Drosophila mauritiana (fry)
#4: DNA chain Target DNA


Mass: 3005.969 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (v/v) MPD, 0.1 M sodium cacodylate pH 6.5,0.2 M magnesium acetate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.29→86.99 Å / Num. obs: 25201 / % possible obs: 99.6 % / Redundancy: 3.1 % / Rsym value: 0.077 / Net I/σ(I): 8.1
Reflection shellResolution: 3.29→3.52 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.152 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HOS

3hos


Resolution: 3.3→60.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.943 / SU B: 90.635 / SU ML: 0.582 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.55
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 1239 5 %RANDOM
Rwork0.2319 ---
obs0.2339 23767 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145 Å2 / Biso mean: 73.034 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-9.43 Å2
2--10.82 Å2-0 Å2
3----8.06 Å2
Refinement stepCycle: final / Resolution: 3.3→60.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5591 2895 2 2 8490
Biso mean--145 145 -
Num. residues----813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0168991
X-RAY DIFFRACTIONr_bond_other_d0.0040.027003
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.6412743
X-RAY DIFFRACTIONr_angle_other_deg1.467316217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4495667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6923.333309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.031151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1581554
X-RAY DIFFRACTIONr_chiral_restr0.0790.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028152
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022120
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 108 -
Rwork0.318 1701 -
all-1809 -
obs--99.29 %
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)
11.15630.33620.58440.70260.29950.9979-0.1148-0.05170.02290.13880.0404-0.1731-0.06850.27310.07440.3459-0.0878-0.08221.01510.06050.134946.5871-13.10796.101
20.643-0.28280.39350.4630.03592.9158-0.097-0.14940.09380.1840.14610.0206-0.05750.0717-0.04920.2669-0.0657-0.08090.91550.06960.083725.624-20.250617.1368
31.0808-0.15591.181.2966-0.35822.3703-0.040.03650.02270.04630.08330.118-0.28550.289-0.04320.1477-0.1819-0.05070.91170.10370.060620.771-16.9117-15.9502
43.48760.7624-0.76241.3141-1.10271.0145-0.2437-0.3086-0.07070.29420.2983-0.0657-0.0770.0179-0.05460.8618-0.047-0.39491.8769-0.01950.208853.1407-16.674943.406
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 345
2X-RAY DIFFRACTION2B3 - 345
3X-RAY DIFFRACTION3C4 - 28
4X-RAY DIFFRACTION3D29 - 56
5X-RAY DIFFRACTION3E4 - 28
6X-RAY DIFFRACTION3F29 - 56
7X-RAY DIFFRACTION4D0 - 7
8X-RAY DIFFRACTION4F0 - 7
9X-RAY DIFFRACTION4G-10 - -1
10X-RAY DIFFRACTION4H-10 - -1

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