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- PDB-9iu3: Cryo-EM structure of the large serine recombinase Bxb1 in complex... -

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Basic information

Entry
Database: PDB / ID: 9iu3
TitleCryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT 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: 3.97 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 post-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
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)286,23316
Polymers285,97212
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: 7443.764 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: 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

#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 (GT/TT CDN) in the post-strand exchange stateCOMPLEX#1-#90MULTIPLE SOURCES
2large serine recobinaseCOMPLEX#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: 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
9Servalcatmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119042 / Symmetry type: POINT
RefinementResolution: 3.97→3.97 Å / Num. reflection obs: 857802 / Average fsc work: 0.5193
Displacement parametersBiso mean: 229.97 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0084203160.0116
ELECTRON MICROSCOPYs_angle_nonh_deg1.8084284101.8348
ELECTRON MICROSCOPYs_dihedral_angle_1_deg6.104219425
ELECTRON MICROSCOPYs_dihedral_angle_2_deg2.74658804.3148
ELECTRON MICROSCOPYs_dihedral_angle_3_deg12.9897385910
ELECTRON MICROSCOPYs_dihedral_angle_6_deg13.193692110
ELECTRON MICROSCOPYs_chiral_restr0.066831050.126
ELECTRON MICROSCOPYs_planes0.0048265660.02
ELECTRON MICROSCOPYs_nbd0.171225600.2
ELECTRON MICROSCOPYs_nbtor0.197295480.2
ELECTRON MICROSCOPYs_hbond_nbd0.13234880.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
3.8-3.839ELECTRON MICROSCOPY261090.205
3.84-3.892ELECTRON MICROSCOPY333430.215
3.893-3.947ELECTRON MICROSCOPY328650.2233
3.947-4.003ELECTRON MICROSCOPY312850.2359
4.003-4.06ELECTRON MICROSCOPY306030.2774
4.061-4.119ELECTRON MICROSCOPY303130.3175
4.12-4.18ELECTRON MICROSCOPY287410.3541
4.181-4.243ELECTRON MICROSCOPY284550.3684
4.244-4.308ELECTRON MICROSCOPY271570.3959
4.309-4.375ELECTRON MICROSCOPY270450.4357
4.375-4.444ELECTRON MICROSCOPY257770.4508
4.445-4.515ELECTRON MICROSCOPY244350.4618
4.515-4.588ELECTRON MICROSCOPY242770.4825
4.589-4.664ELECTRON MICROSCOPY233170.4995
4.665-4.742ELECTRON MICROSCOPY228510.5186
4.743-4.823ELECTRON MICROSCOPY217450.5437
4.824-4.907ELECTRON MICROSCOPY210330.563
4.908-4.994ELECTRON MICROSCOPY207130.5757
4.995-5.084ELECTRON MICROSCOPY196470.5779
5.085-5.177ELECTRON MICROSCOPY188410.5849
5.178-5.273ELECTRON MICROSCOPY182170.6024
5.275-5.375ELECTRON MICROSCOPY177270.6139
5.375-5.479ELECTRON MICROSCOPY171250.6247
5.481-5.586ELECTRON MICROSCOPY161250.6265
5.588-5.7ELECTRON MICROSCOPY158710.632
5.701-5.818ELECTRON MICROSCOPY152250.6268
5.819-5.94ELECTRON MICROSCOPY145330.6331
5.941-6.068ELECTRON MICROSCOPY137530.6453
6.069-6.2ELECTRON MICROSCOPY130590.6402
6.203-6.34ELECTRON MICROSCOPY129730.6324
6.344-6.486ELECTRON MICROSCOPY120210.6596
6.488-6.637ELECTRON MICROSCOPY117310.6818
6.64-6.799ELECTRON MICROSCOPY109810.6929
6.8-6.966ELECTRON MICROSCOPY107250.7004
6.968-7.143ELECTRON MICROSCOPY101170.7184
7.145-7.328ELECTRON MICROSCOPY93750.7295
7.33-7.521ELECTRON MICROSCOPY91330.7392
7.526-7.729ELECTRON MICROSCOPY85770.7603
7.732-7.947ELECTRON MICROSCOPY82270.7817
7.95-8.174ELECTRON MICROSCOPY75970.7886
8.181-8.421ELECTRON MICROSCOPY73770.791
8.425-8.68ELECTRON MICROSCOPY69010.8084
8.684-8.955ELECTRON MICROSCOPY63030.822
8.96-9.249ELECTRON MICROSCOPY60730.8287
9.254-9.556ELECTRON MICROSCOPY56130.8187
9.567-9.897ELECTRON MICROSCOPY52750.8213
9.903-10.257ELECTRON MICROSCOPY49810.8293
10.264-10.636ELECTRON MICROSCOPY45330.8452
10.651-11.06ELECTRON MICROSCOPY43030.8675
11.069-11.511ELECTRON MICROSCOPY40170.8741
11.521-12ELECTRON MICROSCOPY35650.8667
12.011-12.533ELECTRON MICROSCOPY33010.8705
12.545-13.101ELECTRON MICROSCOPY29910.8749
13.129-13.754ELECTRON MICROSCOPY28570.8841
13.77-14.458ELECTRON MICROSCOPY25170.8856
14.496-15.215ELECTRON MICROSCOPY21790.8829
15.26-16.106ELECTRON MICROSCOPY20850.8921
16.132-17.08ELECTRON MICROSCOPY18610.9032
17.111-18.178ELECTRON MICROSCOPY16690.9136
18.292-19.427ELECTRON MICROSCOPY13110.9159
19.474-20.804ELECTRON MICROSCOPY12490.9026
20.918-22.522ELECTRON MICROSCOPY10890.885
22.667-24.47ELECTRON MICROSCOPY9070.8748
24.562-26.547ELECTRON MICROSCOPY7290.8977
26.907-29.583ELECTRON MICROSCOPY6250.9229
29.746-33.029ELECTRON MICROSCOPY5710.9373
33.258-37.378ELECTRON MICROSCOPY3810.9517
37.711-43.035ELECTRON MICROSCOPY3010.9549
43.544-49.886ELECTRON MICROSCOPY2250.9474
51.522-61.581ELECTRON MICROSCOPY1750.9228
63.102-78.268ELECTRON MICROSCOPY1050.9221
81.464-99.773ELECTRON MICROSCOPY490.872
115.208-282.2ELECTRON MICROSCOPY400.8014

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