9YXB image
Deposition Date 2025-10-27
Release Date 2026-06-24
Last Version Date 2026-09-16
Entry Detail
PDB ID:
9YXB
Keywords:
Title:
Babesia divergens ribosome structure by single-particle cryo-EM (3D class1, A-, P-, and E-site tRNAs and mRNA)
Biological Source:
Source Organism(s):
Method Details:
Experimental Method:
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:SB (auth: L3)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:TB (auth: L4)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polyribonucleotide
Molecule:28S ribosomal RNA
Chain IDs:UB (auth: L5)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL2
Gene (Uniprot):X943_002221
Chain IDs:LA (auth: LB)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL3
Gene (Uniprot):X943_001269
Chain IDs:VA (auth: LC)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL4
Gene (Uniprot):X943_001467
Chain IDs:QA (auth: LD)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL5
Gene (Uniprot):X943_001566
Chain IDs:FB (auth: LE)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL6
Gene (Uniprot):X943_002102
Chain IDs:CC (auth: LF)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL6
Gene (Uniprot):X943_003029
Chain IDs:QB (auth: LG)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL8
Gene (Uniprot):X943_002884
Chain IDs:UA (auth: LH)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL13
Gene (Uniprot):X943_001396
Chain IDs:MA (auth: LI)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL13
Gene (Uniprot):X943_002211
Chain IDs:NA (auth: LJ)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL14
Gene (Uniprot):X943_001012
Chain IDs:XA (auth: LK)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL14
Gene (Uniprot):X943_000349
Chain IDs:WA (auth: LL)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL15
Gene (Uniprot):X943_000630
Chain IDs:FA (auth: LM)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL15
Gene (Uniprot):X943_000477
Chain IDs:HB (auth: LN)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL16
Gene (Uniprot):X943_001191
Chain IDs:GB (auth: LO)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL18
Gene (Uniprot):X943_000574
Chain IDs:RA (auth: LP)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL18
Gene (Uniprot):X943_003255
Chain IDs:KA (auth: LQ)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL19
Gene (Uniprot):X943_001451
Chain IDs:EB (auth: LR)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL20
Gene (Uniprot):X943_002821
Chain IDs:GA (auth: LS)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL21
Gene (Uniprot):X943_003482
Chain IDs:BB (auth: LT)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL22
Gene (Uniprot):X943_000090
Chain IDs:TA (auth: LU)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL22
Gene (Uniprot):X943_002281
Chain IDs:KB (auth: LV)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL23
Gene (Uniprot):X943_000531
Chain IDs:YA (auth: LW)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL24
Gene (Uniprot):X943_000193
Chain IDs:OA (auth: LX)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL24
Gene (Uniprot):X943_001327
Chain IDs:PB (auth: LY)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL27
Gene (Uniprot):X943_001952
Chain IDs:SA (auth: LZ)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL29
Gene (Uniprot):X943_004019
Chain IDs:PA (auth: La)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL29
Gene (Uniprot):X943_000841
Chain IDs:NB (auth: Lb)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein uL30
Gene (Uniprot):X943_003138
Chain IDs:JB (auth: Lc)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL30
Gene (Uniprot):X943_003932
Chain IDs:LB (auth: Ld)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL31
Gene (Uniprot):X943_003746
Chain IDs:HA (auth: Le)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL32
Gene (Uniprot):X943_000313
Chain IDs:IA (auth: Lf)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL33
Gene (Uniprot):X943_001196
Chain IDs:IB (auth: Lg)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL34
Gene (Uniprot):X943_000614
Chain IDs:OB (auth: Lh)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL36
Gene (Uniprot):X943_000927
Chain IDs:ZA (auth: Li)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL37
Gene (Uniprot):X943_004077
Chain IDs:JA (auth: Lj)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL38
Gene (Uniprot):X943_000458
Chain IDs:DC (auth: Lk)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL39
Gene (Uniprot):X943_002308
Chain IDs:DB (auth: Ll)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL40
Gene (Uniprot):X943_001479
Chain IDs:AB (auth: Lm)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL41
Chain IDs:RB (auth: Ln)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL42
Gene (Uniprot):X943_002338
Chain IDs:CB (auth: Lo)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein eL43
Gene (Uniprot):X943_003470
Chain IDs:MB (auth: Lp)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polyribonucleotide
Molecule:18S ribosomal RNA
Chain IDs:EA (auth: S1)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polyribonucleotide
Molecule:mRNA fragment
Chain IDs:YB (auth: S6)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:VB (auth: S7)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:WB (auth: S8)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polyribonucleotide
Molecule:A-site tRNA
Chain IDs:XB (auth: S9)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS1
Gene (Uniprot):X943_000220
Chain IDs:H (auth: SA)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS2
Gene (Uniprot):X943_003994
Chain IDs:T (auth: SB)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS3
Gene (Uniprot):X943_001660
Chain IDs:R (auth: SC)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS4
Gene (Uniprot):X943_001267
Chain IDs:BA (auth: SD)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS4
Gene (Uniprot):X943_000864
Chain IDs:AC (auth: SE)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS5
Gene (Uniprot):X943_002900
Chain IDs:U (auth: SF)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS6
Gene (Uniprot):X943_003522
Chain IDs:M (auth: SG)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS7
Gene (Uniprot):X943_003661
Chain IDs:F (auth: SH)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS7
Gene (Uniprot):X943_002839
Chain IDs:K (auth: SI)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS8
Gene (Uniprot):X943_001911
Chain IDs:J (auth: SJ)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS8
Gene (Uniprot):X943_000129
Chain IDs:L (auth: SK)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS9
Gene (Uniprot):X943_002238
Chain IDs:D (auth: SL)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS10
Gene (Uniprot):X943_003414
Chain IDs:N (auth: SM)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS10
Gene (Uniprot):X943_000376
Chain IDs:I (auth: SN)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS11
Gene (Uniprot):X943_003870
Chain IDs:X (auth: SO)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS12
Chain IDs:A (auth: SP)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS12
Gene (Uniprot):X943_000457
Chain IDs:AA (auth: SQ)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS13
Gene (Uniprot):X943_003294
Chain IDs:E (auth: SR)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS14
Gene (Uniprot):X943_000046
Chain IDs:P (auth: SS)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS15
Gene (Uniprot):X943_002774
Chain IDs:G (auth: ST)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS17
Gene (Uniprot):X943_003663
Chain IDs:C (auth: SU)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS17
Chain IDs:W (auth: SV)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein uS19
Gene (Uniprot):X943_000553
Chain IDs:S (auth: SW)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS19
Gene (Uniprot):X943_003646
Chain IDs:B (auth: SX)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS21
Gene (Uniprot):X943_003139
Chain IDs:ZB (auth: SY)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS24
Gene (Uniprot):X943_003503
Chain IDs:Y (auth: SZ)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS25
Gene (Uniprot):X943_001183
Chain IDs:Z (auth: Sa)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS26
Gene (Uniprot):X943_001190
Chain IDs:V (auth: Sb)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS27
Gene (Uniprot):X943_002594
Chain IDs:DA (auth: Sc)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS28
Gene (Uniprot):X943_003201
Chain IDs:Q (auth: Sd)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS30
Gene (Uniprot):X943_003810
Chain IDs:O (auth: Se)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein eS31
Gene (Uniprot):X943_000166
Chain IDs:CA (auth: Sf)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Polymer Type:polypeptide(L)
Molecule:Receptor for activated C kina
Gene (Uniprot):X943_001939
Chain IDs:BC (auth: Sg)
Chain Length:0
Number of Molecules:1
Biological Source:Babesia divergens
Primary Citation
Ribosomal architecture and rRNA modification landscape in the tick-borne parasite Babesia divergens.
Nat Commun 17 ? ? (2026)
PMID: 42693083 DOI: 10.1038/s41467-026-75282-4
Primary Citation of related structures
Feedback Form
Name
Email
Institute
Feedback