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- PDB-9iu6: Cryo-EM structure of the large serine recombinase Bxb1 in complex... -

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Basic information

Entry
Database: PDB / ID: 9iu6
TitleCryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA CDN) in the intermediate-strand exchange state 1
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 (CA/CA CDN) in the intermediate-strand exchange state 1
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

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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 intermediate-strand exchange state 1COMPLEX#1-#2, #4, #3, #5-#6, #8, #7, #90MULTIPLE SOURCES
2large serine recombinaseCOMPLEX#11RECOMBINANT
3attPCOMPLEX#2, #4, #3, #51SYNTHETIC
4attBCOMPLEX#6, #8, #7, #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: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183795 / Symmetry type: POINT
RefinementResolution: 3.97→3.97 Å / Num. reflection obs: 735340 / Average fsc work: 0.6571
Displacement parametersBiso mean: 221.25 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0064203060.0116
ELECTRON MICROSCOPYs_angle_nonh_deg1.6304283941.8347
ELECTRON MICROSCOPYs_dihedral_angle_1_deg3.479119402
ELECTRON MICROSCOPYs_dihedral_angle_2_deg1.52038804.3182
ELECTRON MICROSCOPYs_dihedral_angle_3_deg12.808385610
ELECTRON MICROSCOPYs_dihedral_angle_6_deg12.982892010
ELECTRON MICROSCOPYs_chiral_restr0.062831040.126
ELECTRON MICROSCOPYs_planes0.0041265520.02
ELECTRON MICROSCOPYs_nbd0.1811232930.2
ELECTRON MICROSCOPYs_nbtor0.2047298480.2
ELECTRON MICROSCOPYs_hbond_nbd0.14145120.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
4-4.06ELECTRON MICROSCOPY317430.3939
4.061-4.119ELECTRON MICROSCOPY303130.4496
4.12-4.18ELECTRON MICROSCOPY287410.4932
4.181-4.243ELECTRON MICROSCOPY284550.5197
4.244-4.308ELECTRON MICROSCOPY271570.5578
4.309-4.375ELECTRON MICROSCOPY270450.6052
4.375-4.444ELECTRON MICROSCOPY257770.6286
4.445-4.515ELECTRON MICROSCOPY244350.6388
4.515-4.588ELECTRON MICROSCOPY242770.6434
4.589-4.664ELECTRON MICROSCOPY233170.6461
4.665-4.742ELECTRON MICROSCOPY228510.6501
4.743-4.823ELECTRON MICROSCOPY217450.6545
4.824-4.907ELECTRON MICROSCOPY210330.6702
4.908-4.994ELECTRON MICROSCOPY207130.6925
4.995-5.084ELECTRON MICROSCOPY196470.7104
5.085-5.177ELECTRON MICROSCOPY188410.717
5.178-5.273ELECTRON MICROSCOPY182170.7161
5.275-5.375ELECTRON MICROSCOPY177270.7108
5.375-5.479ELECTRON MICROSCOPY171250.6994
5.481-5.586ELECTRON MICROSCOPY161250.6864
5.588-5.7ELECTRON MICROSCOPY158710.6783
5.701-5.818ELECTRON MICROSCOPY152250.6705
5.819-5.94ELECTRON MICROSCOPY145330.6669
5.941-6.068ELECTRON MICROSCOPY137530.6697
6.069-6.2ELECTRON MICROSCOPY130590.6765
6.203-6.34ELECTRON MICROSCOPY129730.6758
6.344-6.486ELECTRON MICROSCOPY120210.6793
6.488-6.637ELECTRON MICROSCOPY117310.6903
6.64-6.799ELECTRON MICROSCOPY109810.7018
6.8-6.966ELECTRON MICROSCOPY107250.7183
6.968-7.143ELECTRON MICROSCOPY101170.7266
7.145-7.328ELECTRON MICROSCOPY93750.7282
7.33-7.521ELECTRON MICROSCOPY91330.7412
7.526-7.729ELECTRON MICROSCOPY85770.7545
7.732-7.947ELECTRON MICROSCOPY82270.7727
7.95-8.174ELECTRON MICROSCOPY75970.7832
8.181-8.421ELECTRON MICROSCOPY73770.7773
8.425-8.68ELECTRON MICROSCOPY69010.7801
8.684-8.955ELECTRON MICROSCOPY63030.7784
8.96-9.249ELECTRON MICROSCOPY60730.7858
9.254-9.556ELECTRON MICROSCOPY56130.7912
9.567-9.897ELECTRON MICROSCOPY52750.7952
9.903-10.257ELECTRON MICROSCOPY49810.8154
10.264-10.636ELECTRON MICROSCOPY45330.8386
10.651-11.06ELECTRON MICROSCOPY43030.8504
11.069-11.511ELECTRON MICROSCOPY40170.8583
11.521-12ELECTRON MICROSCOPY35650.8591
12.011-12.533ELECTRON MICROSCOPY33010.8606
12.545-13.101ELECTRON MICROSCOPY29910.8624
13.129-13.754ELECTRON MICROSCOPY28570.8764
13.77-14.458ELECTRON MICROSCOPY25170.8913
14.496-15.215ELECTRON MICROSCOPY21790.8865
15.26-16.106ELECTRON MICROSCOPY20850.882
16.132-17.08ELECTRON MICROSCOPY18610.8855
17.111-18.178ELECTRON MICROSCOPY16690.9081
18.292-19.427ELECTRON MICROSCOPY13110.9135
19.474-20.804ELECTRON MICROSCOPY12490.8835
20.918-22.522ELECTRON MICROSCOPY10890.8693
22.667-24.47ELECTRON MICROSCOPY9070.8853
24.562-26.547ELECTRON MICROSCOPY7290.8848
26.907-29.583ELECTRON MICROSCOPY6250.9059
29.746-33.029ELECTRON MICROSCOPY5710.9281
33.258-37.378ELECTRON MICROSCOPY3810.9419
37.711-43.035ELECTRON MICROSCOPY3010.9457
43.544-49.886ELECTRON MICROSCOPY2250.9337
51.522-61.581ELECTRON MICROSCOPY1750.9317
63.102-78.268ELECTRON MICROSCOPY1050.9403
81.464-99.773ELECTRON MICROSCOPY490.9092
115.208-282.2ELECTRON MICROSCOPY400.8469

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