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- PDB-6pqn: Crystal structure of HzTransib transposase -

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Basic information

Entry
Database: PDB / ID: 6pqn
TitleCrystal structure of HzTransib transposase
ComponentsPutative DNA-mediated transposase
KeywordsRECOMBINATION / RAG-like transposase / DDE family enzyme / Transib / Evolution of RAG
Function / homologyPHOSPHATE ION / Putative DNA-mediated transposase
Function and homology information
Biological speciesHelicoverpa zea (corn earworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.01 Å
AuthorsLiu, C. / Yang, Y. / Schatz, D.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI137079 United States
CitationJournal: Nature / Year: 2019
Title: Structures of a RAG-like transposase during cut-and-paste transposition.
Authors: Chang Liu / Yang Yang / David G Schatz /
Abstract: Transposons have had a pivotal role in genome evolution and are believed to be the evolutionary progenitors of the RAG1-RAG2 recombinase, an essential component of the adaptive immune system in jawed ...Transposons have had a pivotal role in genome evolution and are believed to be the evolutionary progenitors of the RAG1-RAG2 recombinase, an essential component of the adaptive immune system in jawed vertebrates. Here we report one crystal structure and five cryo-electron microscopy structures of Transib, a RAG1-like transposase from Helicoverpa zea, that capture the entire transposition process from the apo enzyme to the terminal strand transfer complex with transposon ends covalently joined to target DNA, at resolutions of 3.0-4.6 Å. These structures reveal a butterfly-shaped complex that undergoes two cycles of marked conformational changes in which the 'wings' of the transposase unfurl to bind substrate DNA, close to execute cleavage, open to release the flanking DNA and close again to capture and attack target DNA. Transib possesses unique structural elements that compensate for the absence of a RAG2 partner, including a loop that interacts with the transposition target site and an accordion-like C-terminal tail that elongates and contracts to help to control the opening and closing of the enzyme and assembly of the active site. Our findings reveal the detailed reaction pathway of a eukaryotic cut-and-paste transposase and illuminate some of the earliest steps in the evolution of the RAG recombinase.
History
DepositionJul 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative DNA-mediated transposase
B: Putative DNA-mediated transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,72920
Polymers113,1652
Non-polymers1,56418
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Size-exclusion chromatography followed by multiple angle light scattering showed the assembly has a molecular mass between 113-115 kDa, which is approximately double the ...Evidence: light scattering, Size-exclusion chromatography followed by multiple angle light scattering showed the assembly has a molecular mass between 113-115 kDa, which is approximately double the calculated molecular weight of HzTransib monomer (56.5 kDa)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-113 kcal/mol
Surface area40590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.292, 160.292, 235.858
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 22 through 75 or resid 77...A22 - 74
121(chain 'A' and (resid 22 through 75 or resid 77...A79 - 107
131(chain 'A' and (resid 22 through 75 or resid 77...A112 - 128
141(chain 'A' and (resid 22 through 75 or resid 77...A138 - 142
151(chain 'A' and (resid 22 through 75 or resid 77...A145 - 182
161(chain 'A' and (resid 22 through 75 or resid 77...A185 - 202
171(chain 'A' and (resid 22 through 75 or resid 77...A206
181(chain 'A' and (resid 22 through 75 or resid 77...A209 - 224
191(chain 'A' and (resid 22 through 75 or resid 77...A227 - 229
1101(chain 'A' and (resid 22 through 75 or resid 77...A232
1111(chain 'A' and (resid 22 through 75 or resid 77...A241 - 242
1121(chain 'A' and (resid 22 through 75 or resid 77...A268 - 274
1131(chain 'A' and (resid 22 through 75 or resid 77...A277 - 296
1141(chain 'A' and (resid 22 through 75 or resid 77...A301 - 316
1151(chain 'A' and (resid 22 through 75 or resid 77...A319 - 328
1161(chain 'A' and (resid 22 through 75 or resid 77...A333 - 386
1171(chain 'A' and (resid 22 through 75 or resid 77...A389 - 437
1181(chain 'A' and (resid 22 through 75 or resid 77...A440 - 462
1191(chain 'A' and (resid 22 through 75 or resid 77...A465 - 483
1201(chain 'A' and (resid 22 through 75 or resid 77...A486 - 488
1211(chain 'A' and (resid 22 through 75 or resid 77...A491 - 497
211(chain 'B' and (resid 22 through 75 or resid 77...B22 - 74
221(chain 'B' and (resid 22 through 75 or resid 77...B79 - 107
231(chain 'B' and (resid 22 through 75 or resid 77...B112 - 128
241(chain 'B' and (resid 22 through 75 or resid 77...B138 - 142
251(chain 'B' and (resid 22 through 75 or resid 77...B145 - 182
261(chain 'B' and (resid 22 through 75 or resid 77...B185 - 202
271(chain 'B' and (resid 22 through 75 or resid 77...B206
281(chain 'B' and (resid 22 through 75 or resid 77...B209 - 224
291(chain 'B' and (resid 22 through 75 or resid 77...B227 - 229
2101(chain 'B' and (resid 22 through 75 or resid 77...B232
2111(chain 'B' and (resid 22 through 75 or resid 77...B241 - 242
2121(chain 'B' and (resid 22 through 75 or resid 77...B268 - 274
2131(chain 'B' and (resid 22 through 75 or resid 77...B277 - 296
2141(chain 'B' and (resid 22 through 75 or resid 77...B301 - 316
2151(chain 'B' and (resid 22 through 75 or resid 77...B319 - 328
2161(chain 'B' and (resid 22 through 75 or resid 77...B333 - 386
2171(chain 'B' and (resid 22 through 75 or resid 77...B389 - 437
2181(chain 'B' and (resid 22 through 75 or resid 77...B440 - 462
2191(chain 'B' and (resid 22 through 75 or resid 77...B465 - 483
2201(chain 'B' and (resid 22 through 75 or resid 77...B486 - 488
2211(chain 'B' and (resid 22 through 75 or resid 77...B491 - 497

NCS ensembles : (Details: 1 )

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative DNA-mediated transposase


Mass: 56582.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicoverpa zea (corn earworm) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B0F0C5

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Non-polymers , 5 types, 46 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.86 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 0.7-0.8 M NaH2PO4, 0.75 M KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792, 0.9197, 1.4586, 1.1398, 1.0718, 1.0087
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.91971
31.45861
41.13981
51.07181
61.00871
ReflectionResolution: 3.01→200 Å / Num. obs: 35894 / % possible obs: 99.19 % / Redundancy: 7.7 % / Biso Wilson estimate: 120.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08633 / Rpim(I) all: 0.03321 / Rrim(I) all: 0.09273 / Net I/σ(I): 14.47
Reflection shellResolution: 3.01→3.1173 Å / Redundancy: 7.6 % / Rmerge(I) obs: 2.012 / Mean I/σ(I) obs: 0.66 / Num. unique obs: 3455 / CC1/2: 0.51 / Rpim(I) all: 0.7716 / Rrim(I) all: 2.16 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
Coot0.8.8model building
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.01→80.15 Å / SU ML: 0.5243 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9796
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1792 5 %Random selection
Rwork0.2193 ---
obs0.2222 35840 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 148.17 Å2
Refinement stepCycle: LAST / Resolution: 3.01→80.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7247 0 83 28 7358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047492
X-RAY DIFFRACTIONf_angle_d0.750110106
X-RAY DIFFRACTIONf_chiral_restr0.04591133
X-RAY DIFFRACTIONf_plane_restr0.00471270
X-RAY DIFFRACTIONf_dihedral_angle_d4.41745443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.090.3951310.35562534X-RAY DIFFRACTION97.76
3.09-3.180.4381350.38172552X-RAY DIFFRACTION99.81
3.18-3.280.45181370.36792602X-RAY DIFFRACTION99.64
3.28-3.40.39011360.30942569X-RAY DIFFRACTION99.63
3.4-3.540.28551360.26532579X-RAY DIFFRACTION99.56
3.54-3.70.30381370.22762610X-RAY DIFFRACTION99.53
3.7-3.890.29271370.2182595X-RAY DIFFRACTION99.64
3.89-4.140.25841370.1932606X-RAY DIFFRACTION99.46
4.14-4.460.2451380.17112629X-RAY DIFFRACTION99.25
4.46-4.910.2351380.1662615X-RAY DIFFRACTION99.39
4.91-5.620.25471390.20122649X-RAY DIFFRACTION99.15
5.62-7.080.30511420.25822683X-RAY DIFFRACTION99.12
7.08-80.150.25591490.20982825X-RAY DIFFRACTION97.67
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)
15.29316370447-0.40411007663-0.233999113931.986876764-0.6949116712151.63316593912-0.152952486359-0.8201051378591.090797128750.07558975634810.0779182307293-0.243478827168-0.48156122483-0.04631095272510.1142700459891.074027678930.117802357811-0.04787396439731.13352826668-0.5975029789991.4543284155841.138092016986.1051929835132.081968095
22.697259700660.6044453983151.454826674983.65236070245-2.350047628742.817847433740.186236039194-0.7024090198880.7641370599280.460060327164-0.20359134236-0.3003454170680.9047862761273.02586176449-0.1803112558241.068785610290.408195406873-0.223160234031.98873195243-0.2958957642561.3620241811262.682304876877.9295113134122.714610402
35.76579932257-2.18303448589-0.5541415580713.932706545545.070626400737.86569395826-0.3033242618850.2763044824790.278656128771-0.843278899748-0.09433432676630.185730941211-0.222876244577-0.01201718826880.4782220526131.086357833490.05704344745710.1004723186851.11422698932-0.1213922412350.90067336663347.127784165955.971826967112.702443085
44.64853947914-2.19960466551-1.732493809294.436958996031.054790676542.51741871801-0.77847929294-0.7266803278720.3307743562220.5551093167110.5222846480380.5237830206070.4368655655640.1172955281390.1633812037420.8286071143540.1162644163960.06177687175381.40005707863-0.2580259484581.0022875992745.434863998167.6211418055128.923225395
58.773431653612.579576330911.513507517434.86941612659-1.401186121531.53206999308-0.809344141065-1.99591199805-1.342053821540.3397658963120.4040605530940.06430117980820.6285203914570.2625192781940.5874769221051.143180124070.523395472820.257545179261.910949732070.1744925422581.2475643792623.773080991864.602031671145.372783503
66.135916681590.4493276851580.6138457021254.10080279674-3.014209511252.57338488607-0.17425933844-0.242625598387-1.14159828943-0.5485090920930.386593000348-0.003524767040120.8076109357510.421642053604-0.1244178830061.069374354980.1537375197990.3880138169960.875651500730.01835861870881.319951284350.35897640758453.5216512109134.261239511
70.764581456751-0.7699703868232.19977887773.77872149615-1.90057594515.22193343077-0.677084699978-1.19592206316-0.705400422356-0.04581699306461.08860763520.438221673081.792713818030.05901585426850.2359013348941.24820496474-0.2866416478770.2497930333441.51294439546-0.03304590410071.09058081831-14.315969298965.7925944745121.697793633
82.951054636910.413539527176-0.01001149890524.58639629125-0.5233468137394.86850696295-1.463712520152.20440414395-0.307587083333-0.997705227360.813079221914-0.5695479069760.3348494655851.24305188153-0.05480684662930.973945600847-0.876794607890.040944115172.24051303883-0.08426829826110.8449294532463.2129161469980.8921439521113.198544478
94.27794168871-0.155347801482-1.222775114694.40681043017-2.289554064856.67615302411-0.8042959806740.6917361890920.0312608737153-0.2681799949420.9012980066390.846838480123-0.277063084896-0.1672785303720.1231634557440.824949068696-0.386556473231-0.06549057450411.005893266950.09603536853720.759784354817-9.1723045755680.7479076884124.226918943
106.35240705079-2.211290133450.02038315446222.059493247630.2033566875780.3828348279040.449893876190.488515919098-0.406354257329-0.730042629184-0.261053369787-0.540122461495-0.7644420040591.528217157470.0647442070771.367324278050.3462621320760.626615788062.434415415410.02631290567581.8387022863718.792892749657.3062088919124.564772882
115.02808077083-1.678865721985.9058355916.58279496681-3.041983292267.29799320816-1.92702346908-1.0558753938-0.06286901949880.6617011682890.526680617022-1.30201066951-0.8859670329471.317359248010.04400961372510.7779951707530.3246872170490.3205584984291.978731249790.1665688839440.9710897012597.4330647503775.6523476985138.478658075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 213 )
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 271 )
3X-RAY DIFFRACTION3chain 'A' and (resid 272 through 345 )
4X-RAY DIFFRACTION4chain 'A' and (resid 346 through 501 )
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 72 )
6X-RAY DIFFRACTION6chain 'B' and (resid 73 through 222 )
7X-RAY DIFFRACTION7chain 'B' and (resid 223 through 271 )
8X-RAY DIFFRACTION8chain 'B' and (resid 272 through 379 )
9X-RAY DIFFRACTION9chain 'B' and (resid 380 through 427 )
10X-RAY DIFFRACTION10chain 'B' and (resid 428 through 468 )
11X-RAY DIFFRACTION11chain 'B' and (resid 469 through 501 )

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