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- PDB-9iu5: Cryo-EM structure of the large serine recombinase Bxb1 in complex... -

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Basic information

Entry
Database: PDB / ID: 9iu5
TitleCryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA CDN) in the post-strand exchange state
Components
  • (attB-L) x 2
  • (attB-R) x 2
  • (attP-L) x 2
  • (attP-R) 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: 3.63 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: Mol Cell / Year: 2026
Title: Structure and engineering of the large serine recombinase Bxb1 for gene integration.
Authors: Teppei Soma / Masahiro Hiraizumi / Christopher W Fell / Dario Tagliaferri / Jason Lequyer / Sae Okazaki / Yukari Isayama / Kazuki Kato / Sworaj Sapkota / Harsh Ramani / Benjamin Arya / Cian ...Authors: Teppei Soma / Masahiro Hiraizumi / Christopher W Fell / Dario Tagliaferri / Jason Lequyer / Sae Okazaki / Yukari Isayama / Kazuki Kato / Sworaj Sapkota / Harsh Ramani / Benjamin Arya / Cian Schmitt-Ulms / Keitaro Yamashita / Jonathan S Gootenberg / Omar O Abudayyeh / Hiroshi Nishimasu /
Abstract: The large serine recombinase Bxb1 catalyzes recombination between DNA molecules containing compatible attP and attB sequences, offering broad applications in genome engineering and gene therapies. ...The large serine recombinase Bxb1 catalyzes recombination between DNA molecules containing compatible attP and attB sequences, offering broad applications in genome engineering and gene therapies. Here, we present cryo-electron microscopy structures of the Bxb1-attP-attB synaptic complex in four distinct functional states during its recombination cycle. Notably, the Bxb1 complex structures in the pre-, mid-, and post-strand-exchange states explain how the attP- and attB-bound Bxb1 dimers are assembled into a tetrameric synaptic complex and how an approximately 180° rotation occurs between the left and right dimers after DNA cleavage, thereby enabling DNA strand exchange and religation. Furthermore, we engineered Bxb1 variants with altered DNA preferences and enhanced recombination activity, which improved programmable gene integration in human cells. Overall, our findings advance the mechanistic understanding of large serine recombinases and provide a structural framework for future engineering of Bxb1-mediated genome integration technologies.
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
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Revision 1.1Jun 24, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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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
E1: attP-L
E2: attP-R
F1: attP-L
F2: attP-R
G1: attB-L
G2: attB-R
H1: attB-L
H2: attB-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,19616
Polymers285,93512
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 , 8 types, 8 molecules E1E2F1F2G1G2H1H2

#2: DNA chain attP-L


Mass: 8315.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium phage Bxb1 (virus) / References: GenBank: 12657854
#3: DNA chain attP-R


Mass: 7667.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium phage Bxb1 (virus) / References: GenBank: 12657854
#4: DNA chain attP-L


Mass: 7677.963 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium phage Bxb1 (virus) / References: GenBank: 12657854
#5: DNA chain attP-R


Mass: 8292.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium phage Bxb1 (virus) / References: GenBank: 12657854
#6: DNA chain attB-L


Mass: 7412.754 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycolicibacterium smegmatis (bacteria) / References: GenBank: LN831039.1
#7: 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
#8: 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
#9: DNA chain attB-R


Mass: 7404.782 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

#10: Chemical
ChemComp-ZN / ZINC ION


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

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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 (CA/CA CDN) in the post-strand exchange stateCOMPLEX#1-#90MULTIPLE SOURCES
2large serine recombinaseCOMPLEX#11RECOMBINANT
3attPCOMPLEX#2-#51SYNTHETIC
4attBCOMPLEX#6-#91SYNTHETIC
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Mycobacterium phage Bxb1 (virus)2902907
33Mycobacterium phage Bxb1 (virus)2902907
44Mycolicibacterium 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: 49.5 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
9Servalcatmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149931 / Symmetry type: POINT
RefinementResolution: 3.63→3.63 Å / Num. reflection obs: 1097626 / Average fsc work: 0.726
Displacement parametersBiso mean: 224.58 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0069203060.0116
ELECTRON MICROSCOPYs_angle_nonh_deg1.6985283941.8347
ELECTRON MICROSCOPYs_dihedral_angle_1_deg3.625119402
ELECTRON MICROSCOPYs_dihedral_angle_2_deg1.68048804.3182
ELECTRON MICROSCOPYs_dihedral_angle_3_deg13.1236385610
ELECTRON MICROSCOPYs_dihedral_angle_6_deg13.290292010
ELECTRON MICROSCOPYs_chiral_restr0.067831040.126
ELECTRON MICROSCOPYs_planes0.0048265520.02
ELECTRON MICROSCOPYs_nbd0.1854236950.2
ELECTRON MICROSCOPYs_nbtor0.2071299470.2
ELECTRON MICROSCOPYs_hbond_nbd0.14145020.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
3.5-3.549ELECTRON MICROSCOPY451930.3602
3.55-3.595ELECTRON MICROSCOPY391890.3811
3.595-3.641ELECTRON MICROSCOPY378610.4028
3.641-3.689ELECTRON MICROSCOPY374550.4401
3.689-3.738ELECTRON MICROSCOPY363730.5055
3.738-3.787ELECTRON MICROSCOPY350130.564
3.788-3.839ELECTRON MICROSCOPY348490.6031
3.84-3.892ELECTRON MICROSCOPY333430.6336
3.893-3.947ELECTRON MICROSCOPY328650.6644
3.947-4.003ELECTRON MICROSCOPY312850.6959
4.003-4.06ELECTRON MICROSCOPY306030.73
4.061-4.119ELECTRON MICROSCOPY303130.7615
4.12-4.18ELECTRON MICROSCOPY287410.7899
4.181-4.243ELECTRON MICROSCOPY284550.8105
4.244-4.308ELECTRON MICROSCOPY271570.8236
4.309-4.375ELECTRON MICROSCOPY270450.8341
4.375-4.444ELECTRON MICROSCOPY257770.8404
4.445-4.515ELECTRON MICROSCOPY244350.8397
4.515-4.588ELECTRON MICROSCOPY242770.8371
4.589-4.664ELECTRON MICROSCOPY233170.8394
4.665-4.742ELECTRON MICROSCOPY228510.8412
4.743-4.823ELECTRON MICROSCOPY217450.8421
4.824-4.907ELECTRON MICROSCOPY210330.8494
4.908-4.994ELECTRON MICROSCOPY207130.8547
4.995-5.084ELECTRON MICROSCOPY196470.8502
5.085-5.177ELECTRON MICROSCOPY188410.8464
5.178-5.273ELECTRON MICROSCOPY182170.8355
5.275-5.375ELECTRON MICROSCOPY177270.8321
5.375-5.479ELECTRON MICROSCOPY171250.8307
5.481-5.586ELECTRON MICROSCOPY161250.8293
5.588-5.7ELECTRON MICROSCOPY158710.8221
5.701-5.818ELECTRON MICROSCOPY152250.814
5.819-5.94ELECTRON MICROSCOPY145330.808
5.941-6.068ELECTRON MICROSCOPY137530.8058
6.069-6.2ELECTRON MICROSCOPY130590.812
6.203-6.34ELECTRON MICROSCOPY129730.8134
6.344-6.486ELECTRON MICROSCOPY120210.8099
6.488-6.637ELECTRON MICROSCOPY117310.8174
6.64-6.799ELECTRON MICROSCOPY109810.8232
6.8-6.966ELECTRON MICROSCOPY107250.8182
6.968-7.143ELECTRON MICROSCOPY101170.8235
7.145-7.328ELECTRON MICROSCOPY93750.8359
7.33-7.521ELECTRON MICROSCOPY91330.8422
7.526-7.729ELECTRON MICROSCOPY85770.8473
7.732-7.947ELECTRON MICROSCOPY82270.8544
7.95-8.174ELECTRON MICROSCOPY75970.8588
8.181-8.421ELECTRON MICROSCOPY73770.8589
8.425-8.68ELECTRON MICROSCOPY69010.869
8.684-8.955ELECTRON MICROSCOPY63030.8742
8.96-9.249ELECTRON MICROSCOPY60730.879
9.254-9.556ELECTRON MICROSCOPY56130.879
9.567-9.897ELECTRON MICROSCOPY52750.8749
9.903-10.257ELECTRON MICROSCOPY49810.8809
10.264-10.636ELECTRON MICROSCOPY45330.9004
10.651-11.06ELECTRON MICROSCOPY43030.9119
11.069-11.511ELECTRON MICROSCOPY40170.9166
11.521-12ELECTRON MICROSCOPY35650.9105
12.011-12.533ELECTRON MICROSCOPY33010.911
12.545-13.101ELECTRON MICROSCOPY29910.9202
13.129-13.754ELECTRON MICROSCOPY28570.9237
13.77-14.458ELECTRON MICROSCOPY25170.9252
14.496-15.215ELECTRON MICROSCOPY21790.9294
15.26-16.106ELECTRON MICROSCOPY20850.9324
16.132-17.08ELECTRON MICROSCOPY18610.9356
17.111-18.178ELECTRON MICROSCOPY16690.9391
18.292-19.427ELECTRON MICROSCOPY13110.9384
19.474-20.804ELECTRON MICROSCOPY12490.929
20.918-22.522ELECTRON MICROSCOPY10890.9181
22.667-24.47ELECTRON MICROSCOPY9070.9085
24.562-26.547ELECTRON MICROSCOPY7290.9278
26.907-29.583ELECTRON MICROSCOPY6250.9487
29.746-33.029ELECTRON MICROSCOPY5710.963
33.258-37.378ELECTRON MICROSCOPY3810.9721
37.711-43.035ELECTRON MICROSCOPY3010.9767
43.544-49.886ELECTRON MICROSCOPY2250.9738
51.522-61.581ELECTRON MICROSCOPY1750.9574
63.102-78.268ELECTRON MICROSCOPY1050.955
81.464-99.773ELECTRON MICROSCOPY490.9156
115.208-282.2ELECTRON MICROSCOPY400.8451

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