ISDA

Deposition Date 2016-08-23

Release Date 2017-01-25

Last Version Date 2024-11-13

Entry Detail

PDB ID:

5T2A

Keywords:

RIBOSOME

Title:

CryoEM structure of the Leishmania donovani 80S ribosome at 2.9 Angstrom resolution

Biological Source:

Source Organism:

Leishmania donovani (Taxon ID: 5661)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS1
Gene (Uniprot):CGC20_0740, CGC20_0745, CGC21_5810, CGC21_5815, LDBPK_350400, LDBPK_350410, LdCL_350009100, LdCL_350009200, LDHU3_35.0560, LDHU3_35.0570
Chain IDs:XA (auth: 0)
Chain Length:264
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BRS2 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS4
Chain IDs:YA (auth: 1)
Chain Length:273
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8I8K3 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121

Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:ZA (auth: 2)
Chain Length:2205
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:eS6
Chain IDs:AB (auth: 3)
Chain Length:249
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:eS7
Chain IDs:BB (auth: 4)
Chain Length:200
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS8
Chain IDs:CB (auth: 5)
Chain Length:220
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8ID68 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS4
Chain IDs:DB (auth: 6)
Chain Length:190
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S5H5Z2 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:RACK1
Chain IDs:EB (auth: 7)
Chain Length:312
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:Q9BIJ5 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS14
Gene (Uniprot):LDBPK_282360, LDBPK_282650, LdCL_280028700, LdCL_280031600, LDHU3_28.3200, LDHU3_28.3580
Chain IDs:FB (auth: 8)
Chain Length:57
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BJV7 Pfam ID:PF00253

Polymer Type:polyribonucleotide
Molecule:LSU-alpha
Chain IDs:A
Chain Length:1781
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uS2
Chain IDs:GB (auth: AC)
Chain Length:246
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS10
Gene (Uniprot):LDBPK_361040
Chain IDs:HB (auth: AD)
Chain Length:153
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BTG4 Pfam ID:PF03501

Polymer Type:polypeptide(L)
Molecule:uS17
Chain IDs:IB (auth: AE)
Chain Length:173
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uS15
Chain IDs:JB (auth: AG)
Chain Length:151
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uS11
Chain IDs:KB (auth: AH)
Chain Length:144
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uS19
Chain IDs:LB (auth: AI)
Chain Length:152
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS8
Gene (Uniprot):CGC20_25145, CGC20_31130, CGC21_28485, LDBPK_111180, LDBPK_291920, LdCL_110017700, LdCL_290024900, LDHU3_11.1430, LDHU3_29.2740
Chain IDs:MB (auth: AJ)
Chain Length:130
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BAV6 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS9
Gene (Uniprot):CGC20_4945, CGC21_31780, CGC21_31785, LDBPK_260840, LDBPK_260850, LdCL_260014100, LdCL_260014200, LDHU3_26.1100
Chain IDs:NB (auth: AK)
Chain Length:149
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BI96 Pfam ID:PF00380

Polymer Type:polypeptide(L)
Molecule:eS17
Chain IDs:OB (auth: AL)
Chain Length:143
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS13
Gene (Uniprot):LDBPK_360990, LDBPK_361000, LdCL_360015000
Chain IDs:PB (auth: AM)
Chain Length:153
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BTF9 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS7
Gene (Uniprot):LMJF_11_0960, LMJF_11_0970
Chain IDs:QB (auth: AN)
Chain Length:190
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:Q868B1 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS19
Gene (Uniprot):LDBPK_342620
Chain IDs:RB (auth: AO)
Chain Length:179
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BR60 Pfam ID:PF01090

Polymer Type:polypeptide(L)
Molecule:uS5
Chain IDs:SB (auth: AP)
Chain Length:265
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uS10
Gene (Uniprot):CGC20_13545, CGC20_13555, CGC21_22050, LDBPK_281100, LDBPK_281120, LdCL_280015600, LdCL_280015800, LDHU3_28.1350, LDHU3_28.1370
Chain IDs:TB (auth: AQ)
Chain Length:116
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BJI2 Pfam ID:PF00338

Polymer Type:polypeptide(L)
Molecule:eS21
Chain IDs:UB (auth: AR)
Chain Length:164
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uS12
Chain IDs:VB (auth: AS)
Chain Length:143
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:eS24
Chain IDs:WB (auth: AT)
Chain Length:137
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:eS26
Chain IDs:XB (auth: AV)
Chain Length:112
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:eS27
Chain IDs:YB (auth: AW)
Chain Length:86
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uS3
Chain IDs:ZB (auth: AX)
Chain Length:219
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eS30
Gene (Uniprot):LDBPK_300690, LDBPK_300710, LdCL_300012000, LdCL_300012100, LdCL_300012200, LDHU3_30.0880, LDHU3_30.0890, LDHU3_30.0900
Chain IDs:AC (auth: AY)
Chain Length:66
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BLG3 Pfam ID:PF04758

Polymer Type:polypeptide(L)
Molecule:eS28
Chain IDs:BC (auth: AZ)
Chain Length:87
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polyribonucleotide
Molecule:LSU-beta
Chain IDs:B
Chain Length:70
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:C
Chain Length:260
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:D
Chain Length:120
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polyribonucleotide
Molecule:srRNA1
Chain IDs:E
Chain Length:213
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polyribonucleotide
Molecule:srRNA3
Chain IDs:F
Chain Length:73
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polyribonucleotide
Molecule:srRNA2
Chain IDs:G
Chain Length:133
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polyribonucleotide
Molecule:srRNA4
Chain IDs:H
Chain Length:127
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL18
Chain IDs:I
Chain Length:198
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S7XBN1 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL16
Chain IDs:J
Chain Length:213
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S5H5C4 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL5
Chain IDs:K
Chain Length:188
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S5H5A8 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:eL13
Chain IDs:L
Chain Length:220
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uL13
Chain IDs:M
Chain Length:222
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL14
Gene (Uniprot):RPL14
Chain IDs:N
Chain Length:83
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:Q25278 Pfam ID:PF00467, PF01929

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL15
Gene (Uniprot):CGC20_0090, CGC20_6005, CGC21_36545, CGC21_6465, LDBPK_303710, LDBPK_351890, LdCL_300042500, LdCL_350024100, LDHU3_30.4940
Chain IDs:O
Chain Length:204
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BMB4 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL22
Chain IDs:P
Chain Length:166
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S7WY02 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL20
Chain IDs:Q
Chain Length:179
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8II03 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL19
Gene (Uniprot):CGC21_24350, LDBPK_060410
Chain IDs:R
Chain Length:106
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9B8Q2 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL21
Chain IDs:S
Chain Length:159
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8ICH0 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL22
Chain IDs:T
Chain Length:129
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8IJA8 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL14
Chain IDs:U
Chain Length:252
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8IIA7 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL23
Chain IDs:V
Chain Length:348
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:D1M863 Pfam ID:PF00276

Polymer Type:polypeptide(L)
Molecule:eL24
Chain IDs:W
Chain Length:124
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uL24
Chain IDs:X
Chain Length:143
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL27
Gene (Uniprot):CGC20_34735, CGC21_20965, LDBPK_322830, LDBPK_322850, LdCL_320034200, LdCL_320034400, LDHU3_32.3590, LDHU3_32.3610
Chain IDs:Y
Chain Length:134
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BP34 Pfam ID:PF00467, PF01777

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL15
Chain IDs:Z
Chain Length:145
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8IGI9 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL28
Chain IDs:AA (auth: a)
Chain Length:1781
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8I959 Pfam ID:PF01778

Polymer Type:polypeptide(L)
Molecule:eL29
Chain IDs:BA (auth: b)
Chain Length:70
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uL2
Chain IDs:CA (auth: c)
Chain Length:260
Number of Molecules:1
Biological Source:Leishmania donovani

Polymer Type:polypeptide(L)
Molecule:uL3
Chain IDs:DA (auth: d)
Chain Length:120
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL30
Chain IDs:EA (auth: e)
Chain Length:213
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8IET6 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL31
Gene (Uniprot):LDBPK_353330, LDBPK_353340
Chain IDs:FA (auth: f)
Chain Length:73
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BSK4 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL32
Chain IDs:GA (auth: g)
Chain Length:133
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S7X954 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL34
Chain IDs:HA (auth: h)
Chain Length:127
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8IHK2 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL29
Gene (Uniprot):CGC20_5605, CGC20_5610, CGC21_32450, CGC21_32455, LDBPK_262350, LDBPK_262360, LDHU3_26.3070, LDHU3_26.3080
Chain IDs:IA (auth: i)
Chain Length:198
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BIP6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL33
Chain IDs:JA (auth: j)
Chain Length:213
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8II82 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL36
Chain IDs:KA (auth: k)
Chain Length:188
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S7X961 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL37
Gene (Uniprot):RPL37
Chain IDs:LA (auth: l)
Chain Length:220
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:P62885 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL43
Gene (Uniprot):LDBPK_212190, LDBPK_362020, LdCL_210027600, LdCL_360025700, LDHU3_21.2600, LDHU3_36.2630
Chain IDs:MA (auth: m)
Chain Length:222
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BFK4 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL38
Gene (Uniprot):LDBPK_030240, LDBPK_262230, LdCL_030007400, LdCL_260028000, LDHU3_03.0250, LDHU3_26.2920
Chain IDs:NA (auth: n)
Chain Length:83
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9B7P2 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL39
Gene (Uniprot):LDBPK_161220, LDBPK_292480, LdCL_160017400, LdCL_290030800, LDHU3_16.1490, LDHU3_29.3680
Chain IDs:OA (auth: o)
Chain Length:204
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BCX6 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL4
Chain IDs:PA (auth: p)
Chain Length:166
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S5H7L0 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL40
Chain IDs:QA (auth: q)
Chain Length:179
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8ISR1 Pfam ID:PF00240, PF01020

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL42
Gene (Uniprot):CGC20_16835, CGC20_9735, CGC21_33710, CGC21_5530, LDBPK_131410, LDBPK_333380, LdCL_130021400, LdCL_330041500, LDHU3_13.1930, LDHU3_33.4890
Chain IDs:RA (auth: r)
Chain Length:106
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BBL5 Pfam ID:PF00935

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL18
Chain IDs:SA (auth: s)
Chain Length:159
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3Q8IJC5 Pfam ID:PF17144, PF14204

Polymer Type:polypeptide(L)
Molecule:eL6
Chain IDs:TA (auth: t)
Chain Length:129
Number of Molecules:1
Biological Source:Leishmania donovani

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL30
Gene (Uniprot):LDBPK_260160
Chain IDs:UA (auth: u)
Chain Length:252
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9BI29 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:eL8
Gene (Uniprot):LDBPK_070550
Chain IDs:VA (auth: v)
Chain Length:348
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:E9B949 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Molecule:uL6
Chain IDs:WA (auth: w)
Chain Length:124
Number of Molecules:1
Biological Source:Leishmania donovani

UniProt ID:A0A3S7WWL2 Pfam ID:PF00347

Ligand Molecules

Primary Citation

Structures and stabilization of kinetoplastid-specific split rRNAs revealed by comparing leishmanial and human ribosomes.

Zhang, X, Lai, M, Chang, W, Yu, I, Ding, K, Mrazek, J, Ng, H.L, Yang, O.O, Maslov, D.A, Zhou, Z.H.Show

Nat Commun 7 13223 13223 (2016)

PMID: 27752045 DOI: 10.1038/ncomms13223

Abstact

The recent success in ribosome structure determination by cryoEM has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. Here, by direct electron-counting cryoEM, we have determined the structures of the Leishmania donovani and human ribosomes at 2.9 Å and 3.6 Å, respectively. Our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rRNA (as opposed to a single 28S rRNA in most eukaryotes, including humans) and reveals atomic details of a unique 20 amino acid extension of the uL13 protein that pins down the ends of three of the rRNA fragments. The structure also fashions many large rRNA expansion segments. Direct comparison of our human and leishmanial ribosome structures at the decoding A-site sheds light on how the bacterial ribosome-targeting drug paromomycin selectively inhibits the eukaryotic L. donovani, but not human, ribosome.

Legend

Protein

Chemical

Disease

Primary Citation of related structures