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- PDB-9iu2: Cryo-EM structure of the large serine recombinase Bxb1 in complex... -

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Basic information

Entry
Database: PDB / ID: 9iu2
TitleCryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state
Components
  • (attB-L) x 2
  • (attB-R) x 2
  • (attP) x 2
  • Integrase
KeywordsDNA BINDING PROTEIN / large serine recombinase
Function / homology
Function and homology information


DNA strand exchange activity / DNA binding
Similarity search - Function
Recombinase / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Resolvase/invertase-type recombinase catalytic domain profile. / : / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain
Similarity search - Domain/homology
: / : / DNA / DNA (> 10) / Integrase
Similarity search - Component
Biological speciesMycobacterium phage Bxb1 (virus)
Mycolicibacterium smegmatis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsSoma, T. / Hiraizumi, M. / Yamashita, K. / Nishimasu, H.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX232F Japan
Japan Science and TechnologyJPMJCR23B6 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state
Authors: Soma, T.
History
DepositionJul 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrase
B: Integrase
C: Integrase
D: Integrase
E: attP
F: attP
G1: attB-L
G2: attB-R
H1: attB-L
H2: attB-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,32314
Polymers286,06110
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA chain , 6 types, 6 molecules EFG1G2H1H2

#2: DNA chain attP


Mass: 16028.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium phage Bxb1 (virus) / References: GenBank: 12657854
#3: DNA chain attP


Mass: 16015.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium phage Bxb1 (virus) / References: GenBank: 12657854
#4: DNA chain attB-L


Mass: 7443.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycolicibacterium smegmatis (bacteria) / References: GenBank: LN831039.1
#5: DNA chain attB-R


Mass: 6704.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycolicibacterium smegmatis (bacteria) / References: GenBank: LN831039.1
#6: DNA chain attB-L


Mass: 6699.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycolicibacterium smegmatis (bacteria) / References: GenBank: LN831039.1
#7: DNA chain attB-R


Mass: 7410.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycolicibacterium smegmatis (bacteria) / References: GenBank: LN831039.1

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Protein / Non-polymers , 2 types, 8 molecules ABCD

#1: Protein
Integrase


Mass: 56439.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium phage Bxb1 (virus) / Gene: 35, PBI_BXB1_35 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9B086
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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
1The large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange stateCOMPLEX#4, #7, #1-#3, #5-#60MULTIPLE SOURCES
2attBCOMPLEX#4, #7, #5-#61SYNTHETIC
3large serine recombinaseCOMPLEX#11RECOMBINANT
4attPCOMPLEX#2-#31SYNTHETIC
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Mycobacterium phage Bxb1 (virus)2902907
34Mycobacterium phage Bxb1 (virus)2902907
42Mycolicibacterium smegmatis (bacteria)1772
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7Cootmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 266035 / Symmetry type: POINT
RefinementResolution: 3.22→3.22 Å / Num. reflection obs: 1579765 / Average fsc work: 0.750827587
Displacement parametersBiso mean: 187.443405 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.00911188253203160.0117062808
ELECTRON MICROSCOPYs_angle_nonh_deg1.82605928284101.83474164
ELECTRON MICROSCOPYs_dihedral_angle_1_deg6.4783592620385.47105005
ELECTRON MICROSCOPYs_dihedral_angle_2_deg3.205797218804.31477273
ELECTRON MICROSCOPYs_dihedral_angle_3_deg13.4034173386110
ELECTRON MICROSCOPYs_dihedral_angle_6_deg13.318140892110
ELECTRON MICROSCOPYs_chiral_restr0.14962924332970.14777505
ELECTRON MICROSCOPYs_planes0.00668812363265660.02
ELECTRON MICROSCOPYs_nbd0.168129186235320.2
ELECTRON MICROSCOPYs_nbtor0.198100526298050.2
ELECTRON MICROSCOPYs_hbond_nbd0.1391815475320.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
3.10016323-3.11789907ELECTRON MICROSCOPY266970.233364646
3.11827975-3.15292514ELECTRON MICROSCOPY512950.267272513
3.15312194-3.18854802ELECTRON MICROSCOPY498450.315119427
3.18875157-3.22498502ELECTRON MICROSCOPY486370.384097365
3.22519563-3.26226437ELECTRON MICROSCOPY472390.477599059
3.26248237-3.30018992ELECTRON MICROSCOPY465690.580449476
3.30064135-3.33946971ELECTRON MICROSCOPY457690.65798427
3.33970356-3.37945908ELECTRON MICROSCOPY440670.717406901
3.37994383-3.42016652ELECTRON MICROSCOPY432730.757695192
3.420669-3.46238134ELECTRON MICROSCOPY423330.777993756
3.46264197-3.50538734ELECTRON MICROSCOPY415930.781043335
3.50565781-3.54947507ELECTRON MICROSCOPY400150.776517947
3.54975587-3.59468584ELECTRON MICROSCOPY391890.776617799
3.59497751-3.6407601ELECTRON MICROSCOPY378610.787966881
3.64136624-3.68865267ELECTRON MICROSCOPY374550.799269984
3.68928304-3.73750261ELECTRON MICROSCOPY363730.804216469
3.73783044-3.78732257ELECTRON MICROSCOPY350130.808177149
3.78800491-3.83918943ELECTRON MICROSCOPY348490.810789922
3.83954476-3.89213626ELECTRON MICROSCOPY333430.808777683
3.8925065-3.9465638ELECTRON MICROSCOPY328650.811782908
3.9469498-4.00253505ELECTRON MICROSCOPY312850.827109181
4.00293769-4.05969645ELECTRON MICROSCOPY306030.844940741
4.06053688-4.11937897ELECTRON MICROSCOPY303130.850501371
4.11981793-4.18039684ELECTRON MICROSCOPY287410.85879555
4.18085559-4.24276977ELECTRON MICROSCOPY284550.870490304
4.24372913-4.30802056ELECTRON MICROSCOPY271570.877609804
4.30852263-4.37479963ELECTRON MICROSCOPY270450.878407964
4.37532542-4.4436814ELECTRON MICROSCOPY257770.875306506
4.44533507-4.51476676ELECTRON MICROSCOPY244350.87354545
4.51534465-4.58755687ELECTRON MICROSCOPY242770.870102664
4.58876971-4.66398516ELECTRON MICROSCOPY233170.868365195
4.66462228-4.742355ELECTRON MICROSCOPY228510.863111733
4.74302478-4.82269889ELECTRON MICROSCOPY217450.857827612
4.824108-4.9072697ELECTRON MICROSCOPY210330.857586733
4.90801182-4.99410381ELECTRON MICROSCOPY207130.860415562
4.99488603-5.08406595ELECTRON MICROSCOPY196470.859341687
5.08489122-5.17732823ELECTRON MICROSCOPY188410.853893193
5.17819976-5.27315477ELECTRON MICROSCOPY182170.851504558
5.27499692-5.37450711ELECTRON MICROSCOPY177270.85204316
5.37548208-5.47883725ELECTRON MICROSCOPY171250.849672867
5.48090357-5.58620269ELECTRON MICROSCOPY161250.84738292
5.58839293-5.70013799ELECTRON MICROSCOPY158710.84834165
5.70130116-5.81762952ELECTRON MICROSCOPY152250.845871453
5.81886613-5.94006566ELECTRON MICROSCOPY145330.841860156
5.94138201-6.06776518ELECTRON MICROSCOPY137530.836368442
6.06916829-6.1995783ELECTRON MICROSCOPY130590.836954205
6.20257254-6.3403727ELECTRON MICROSCOPY129730.840399555
6.34357571-6.48607129ELECTRON MICROSCOPY120210.839849186
6.48778514-6.63678596ELECTRON MICROSCOPY117310.841493746
6.6404598-6.7985201ELECTRON MICROSCOPY109810.848978922
6.80049384-6.966309ELECTRON MICROSCOPY107250.856725789
6.96843255-7.14258756ELECTRON MICROSCOPY101170.859566382
7.14487649-7.32801668ELECTRON MICROSCOPY93750.860959141
7.3304886-7.52065554ELECTRON MICROSCOPY91330.873664787
7.52600261-7.72933179ELECTRON MICROSCOPY85770.879418977
7.73223264-7.94693172ELECTRON MICROSCOPY82270.878846462
7.95008464-8.17370383ELECTRON MICROSCOPY75970.87973878
8.1805696-8.42106746ELECTRON MICROSCOPY73770.884182909
8.42481933-8.67999612ELECTRON MICROSCOPY69010.891925729
8.684105-8.95534663ELECTRON MICROSCOPY63030.895134762
8.95985928-9.24873177ELECTRON MICROSCOPY60730.899135441
9.25370287-9.5564982ELECTRON MICROSCOPY56130.903867593
9.56747638-9.89718645ELECTRON MICROSCOPY52750.905145776
9.9032789-10.2567338ELECTRON MICROSCOPY49810.904123138
10.2635151-10.6358131ELECTRON MICROSCOPY45330.918225668
10.650953-11.0602904ELECTRON MICROSCOPY43030.933814962
11.0687951-11.5111785ELECTRON MICROSCOPY40170.93424824
11.5207672-12.0003651ELECTRON MICROSCOPY35650.928811463
12.0112301-12.5329424ELECTRON MICROSCOPY33010.933239572
12.5453207-13.1008066ELECTRON MICROSCOPY29910.941074803
13.1291327-13.7535869ELECTRON MICROSCOPY28570.941884582
13.7699505-14.4575445ELECTRON MICROSCOPY25170.93811142
14.4956408-15.2152048ELECTRON MICROSCOPY21790.938094012
15.2596289-16.1060053ELECTRON MICROSCOPY20850.94141349
16.1323008-17.0795216ELECTRON MICROSCOPY18610.946687556
17.110889-18.1781006ELECTRON MICROSCOPY16690.953934719
18.2923097-19.4274499ELECTRON MICROSCOPY13110.952019415
19.4736508-20.8040608ELECTRON MICROSCOPY12490.947993366
20.9180565-22.5220127ELECTRON MICROSCOPY10890.933450035
22.6668503-24.4698442ELECTRON MICROSCOPY9070.934581889
24.5623581-26.5471438ELECTRON MICROSCOPY7290.95134439
26.9067152-29.5825991ELECTRON MICROSCOPY6250.9641506
29.7464929-33.0290129ELECTRON MICROSCOPY5710.975812955
33.2575901-37.3783044ELECTRON MICROSCOPY3810.980312068
37.7105626-43.0350981ELECTRON MICROSCOPY3010.982876226
43.5444069-49.8863852ELECTRON MICROSCOPY2250.979954854
51.5224371-61.5810908ELECTRON MICROSCOPY1750.968185206
63.1018406-78.2682005ELECTRON MICROSCOPY1050.968126361
81.4641259-99.7727704ELECTRON MICROSCOPY490.958783027
115.207672-282.20001ELECTRON MICROSCOPY400.874007998

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