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- PDB-9iu4: Cryo-EM structure of the large serine recombinase Bxb1 in complex... -

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Basic information

Entry
Database: PDB / ID: 9iu4
TitleCryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (CA/CA 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: 3.58 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 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)286,28614
Polymers286,02410
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: 7412.754 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: 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

#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 (CA/CA CDN) in the pre-strand exchange stateCOMPLEX#1-#4, #6-#7, #50MULTIPLE SOURCES
2large serine recombinaseCOMPLEX#11RECOMBINANT
3attPCOMPLEX#2-#31SYNTHETIC
4attBCOMPLEX#4, #6-#7, #51SYNTHETIC
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: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 412864 / Symmetry type: POINT
RefinementResolution: 3.58→3.58 Å / Num. reflection obs: 1097626 / Average fsc work: 0.7186
Displacement parametersBiso mean: 240.31 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0071203150.0116
ELECTRON MICROSCOPYs_angle_nonh_deg1.727284071.8349
ELECTRON MICROSCOPYs_dihedral_angle_1_deg3.966219422
ELECTRON MICROSCOPYs_dihedral_angle_2_deg1.64728834.3171
ELECTRON MICROSCOPYs_dihedral_angle_3_deg13.1819386110
ELECTRON MICROSCOPYs_dihedral_angle_6_deg13.044292110
ELECTRON MICROSCOPYs_chiral_restr0.069631050.126
ELECTRON MICROSCOPYs_planes0.0045265760.02
ELECTRON MICROSCOPYs_nbd0.1835236240.2
ELECTRON MICROSCOPYs_nbtor0.2067298880.2
ELECTRON MICROSCOPYs_hbond_nbd0.14325150.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
3.5-3.549ELECTRON MICROSCOPY451930.3549
3.55-3.595ELECTRON MICROSCOPY391890.3862
3.595-3.641ELECTRON MICROSCOPY378610.4347
3.641-3.689ELECTRON MICROSCOPY374550.4935
3.689-3.738ELECTRON MICROSCOPY363730.5402
3.738-3.787ELECTRON MICROSCOPY350130.566
3.788-3.839ELECTRON MICROSCOPY348490.5965
3.84-3.892ELECTRON MICROSCOPY333430.6231
3.893-3.947ELECTRON MICROSCOPY328650.6465
3.947-4.003ELECTRON MICROSCOPY312850.6781
4.003-4.06ELECTRON MICROSCOPY306030.7161
4.061-4.119ELECTRON MICROSCOPY303130.7429
4.12-4.18ELECTRON MICROSCOPY287410.7649
4.181-4.243ELECTRON MICROSCOPY284550.7852
4.244-4.308ELECTRON MICROSCOPY271570.7975
4.309-4.375ELECTRON MICROSCOPY270450.8114
4.375-4.444ELECTRON MICROSCOPY257770.8193
4.445-4.515ELECTRON MICROSCOPY244350.8235
4.515-4.588ELECTRON MICROSCOPY242770.8199
4.589-4.664ELECTRON MICROSCOPY233170.818
4.665-4.742ELECTRON MICROSCOPY228510.8172
4.743-4.823ELECTRON MICROSCOPY217450.8179
4.824-4.907ELECTRON MICROSCOPY210330.8187
4.908-4.994ELECTRON MICROSCOPY207130.8231
4.995-5.084ELECTRON MICROSCOPY196470.8265
5.085-5.177ELECTRON MICROSCOPY188410.8257
5.178-5.273ELECTRON MICROSCOPY182170.8214
5.275-5.375ELECTRON MICROSCOPY177270.8156
5.375-5.479ELECTRON MICROSCOPY171250.8096
5.481-5.586ELECTRON MICROSCOPY161250.8031
5.588-5.7ELECTRON MICROSCOPY158710.7994
5.701-5.818ELECTRON MICROSCOPY152250.8031
5.819-5.94ELECTRON MICROSCOPY145330.7993
5.941-6.068ELECTRON MICROSCOPY137530.79
6.069-6.2ELECTRON MICROSCOPY130590.7883
6.203-6.34ELECTRON MICROSCOPY129730.7977
6.344-6.486ELECTRON MICROSCOPY120210.7997
6.488-6.637ELECTRON MICROSCOPY117310.804
6.64-6.799ELECTRON MICROSCOPY109810.8125
6.8-6.966ELECTRON MICROSCOPY107250.8288
6.968-7.143ELECTRON MICROSCOPY101170.8345
7.145-7.328ELECTRON MICROSCOPY93750.8416
7.33-7.521ELECTRON MICROSCOPY91330.8521
7.526-7.729ELECTRON MICROSCOPY85770.857
7.732-7.947ELECTRON MICROSCOPY82270.855
7.95-8.174ELECTRON MICROSCOPY75970.8583
8.181-8.421ELECTRON MICROSCOPY73770.8636
8.425-8.68ELECTRON MICROSCOPY69010.8684
8.684-8.955ELECTRON MICROSCOPY63030.8745
8.96-9.249ELECTRON MICROSCOPY60730.8816
9.254-9.556ELECTRON MICROSCOPY56130.8833
9.567-9.897ELECTRON MICROSCOPY52750.8891
9.903-10.257ELECTRON MICROSCOPY49810.8901
10.264-10.636ELECTRON MICROSCOPY45330.9061
10.651-11.06ELECTRON MICROSCOPY43030.9246
11.069-11.511ELECTRON MICROSCOPY40170.9279
11.521-12ELECTRON MICROSCOPY35650.9208
12.011-12.533ELECTRON MICROSCOPY33010.921
12.545-13.101ELECTRON MICROSCOPY29910.9305
13.129-13.754ELECTRON MICROSCOPY28570.9336
13.77-14.458ELECTRON MICROSCOPY25170.9298
14.496-15.215ELECTRON MICROSCOPY21790.9301
15.26-16.106ELECTRON MICROSCOPY20850.9336
16.132-17.08ELECTRON MICROSCOPY18610.9375
17.111-18.178ELECTRON MICROSCOPY16690.9454
18.292-19.427ELECTRON MICROSCOPY13110.9438
19.474-20.804ELECTRON MICROSCOPY12490.9419
20.918-22.522ELECTRON MICROSCOPY10890.9282
22.667-24.47ELECTRON MICROSCOPY9070.9271
24.562-26.547ELECTRON MICROSCOPY7290.9444
26.907-29.583ELECTRON MICROSCOPY6250.9577
29.746-33.029ELECTRON MICROSCOPY5710.9747
33.258-37.378ELECTRON MICROSCOPY3810.9811
37.711-43.035ELECTRON MICROSCOPY3010.9827
43.544-49.886ELECTRON MICROSCOPY2250.979
51.522-61.581ELECTRON MICROSCOPY1750.9722
63.102-78.268ELECTRON MICROSCOPY1050.9658
81.464-99.773ELECTRON MICROSCOPY490.9444
115.208-282.2ELECTRON MICROSCOPY400.869

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