9H6I image
Deposition Date 2024-10-24
Release Date 2026-02-04
Last Version Date 2026-02-04
Entry Detail
PDB ID:
9H6I
Keywords:
RIBOSOME
Title:
Structure of the Arabidopsis thaliana 80S ribosome in complex with P- and E-site tRNAs, mRNA, and thermospermine
Biological Source:
Source Organism(s):
Arabidopsis thaliana (Taxon ID: 3702)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
2.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9H6I validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:Transfer RNA Phe (GAA)
Chain IDs:A (auth: 2), YB (auth: W2)
Chain Length:76
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 5.8S
Chain IDs:B (auth: 3)
Chain Length:164
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 25S
Chain IDs:C (auth: A)
Chain Length:3385
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3z
Chain IDs:AB (auth: AA)
Chain Length:222
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4y
Chain IDs:YA (auth: AB)
Chain Length:197
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5y/uS5u/uS5v
Chain IDs:X (auth: AC)
Chain Length:284
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7y
Chain IDs:CA (auth: AD)
Chain Length:207
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8z/uS8w
Chain IDs:L (auth: AE)
Chain Length:130
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9z
Chain IDs:EB (auth: AF)
Chain Length:146
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL13z
Chain IDs:BB (auth: AG)
Chain Length:206
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL14y
Chain IDs:Z (auth: AH)
Chain Length:134
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS10z
Chain IDs:AC (auth: AI)
Chain Length:177
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL18x
Chain IDs:DA (auth: AJ)
Chain Length:187
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL19x
Chain IDs:WA (auth: AK)
Chain Length:214
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L18ae/LX family protein
Chain IDs:Q (auth: AL)
Chain Length:217
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL21z/eL21y
Chain IDs:W (auth: AM)
Chain Length:164
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL22z
Chain IDs:PB (auth: AN)
Chain Length:124
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL24z
Chain IDs:UA (auth: AO)
Chain Length:164
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL27x
Chain IDs:N (auth: AP)
Chain Length:135
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL28z
Chain IDs:KB (auth: AQ)
Chain Length:143
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Chain IDs:H (auth: AR)
Chain Length:83
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL30y
Chain IDs:IA (auth: AT)
Chain Length:112
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL31y
Chain IDs:I (auth: AU)
Chain Length:119
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL32z
Chain IDs:BA (auth: AV)
Chain Length:133
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL33y
Chain IDs:T (auth: AW)
Chain Length:112
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL36y
Chain IDs:M (auth: AX)
Chain Length:112
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL37z
Chain IDs:UB (auth: AY)
Chain Length:95
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL38z/eL38y
Chain IDs:HB (auth: AZ)
Chain Length:69
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS8z
Chain IDs:TB (auth: Aa)
Chain Length:222
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polyribonucleotide
Molecule:Messenger RNA (poly-U)
Chain IDs:XB (auth: B1)
Chain Length:12
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL39z/eL39x
Chain IDs:DB (auth: BA)
Chain Length:122
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS17w
Chain IDs:OB (auth: BB)
Chain Length:141
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS32 eS32z/eS32y/eS32x/eS32w/eS32v
Chain IDs:E (auth: BC)
Chain Length:25
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL42z/eL42y
Chain IDs:U (auth: BD)
Chain Length:105
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL43y
Chain IDs:IB (auth: BE)
Chain Length:92
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL6y
Chain IDs:ZA (auth: BF)
Chain Length:233
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL8y
Chain IDs:MA (auth: BG)
Chain Length:256
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL13y
Chain IDs:FA (auth: BH)
Chain Length:206
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL14x/uL14z/uL14y
Chain IDs:Y (auth: BI)
Chain Length:140
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL16y
Chain IDs:TA (auth: BJ)
Chain Length:221
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL18z
Chain IDs:HA (auth: BK)
Chain Length:301
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS19x
Chain IDs:RB (auth: BL)
Chain Length:143
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL22z
Chain IDs:F (auth: BM)
Chain Length:176
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL23y
Chain IDs:LA (auth: BN)
Chain Length:154
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL24z
Chain IDs:G (auth: BO)
Chain Length:146
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL29x
Chain IDs:KA (auth: BP)
Chain Length:123
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL2z
Chain IDs:EA (auth: BQ)
Chain Length:258
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Ribosomal protein L30/L7 family protein
Chain IDs:QA (auth: BR)
Chain Length:247
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3z
Chain IDs:V (auth: BS)
Chain Length:389
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL4z
Chain IDs:AA (auth: BT)
Chain Length:406
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL5z
Chain IDs:PA (auth: BU)
Chain Length:182
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS1y
Chain IDs:SA (auth: BV)
Chain Length:262
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS21y
Chain IDs:VA (auth: BW)
Chain Length:82
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10y
Chain IDs:ZB (auth: Ba)
Chain Length:122
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 5S
Chain IDs:D (auth: C3)
Chain Length:121
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14z/uS14y/uS14x
Chain IDs:VB (auth: Ca)
Chain Length:56
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15y
Chain IDs:GA (auth: Da)
Chain Length:151
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL15z
Chain IDs:P (auth: Ea)
Chain Length:204
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein eL34z
Chain IDs:NA (auth: Fa)
Chain Length:120
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-ribosomal protein eL40z fusion protein
Chain IDs:CB (auth: Ga)
Chain Length:128
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL15x
Chain IDs:OA (auth: Ha)
Chain Length:146
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL6z/uL6y
Chain IDs:K (auth: Ia)
Chain Length:194
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS4x
Chain IDs:O (auth: Ja)
Chain Length:262
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS24y
Chain IDs:S (auth: Ka)
Chain Length:133
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Nascent polypeptide
Chain IDs:BC (auth: L3)
Chain Length:23
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS25w
Chain IDs:SB (auth: La)
Chain Length:108
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS26y
Chain IDs:J (auth: Ma)
Chain Length:131
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS27y
Chain IDs:XA (auth: Na)
Chain Length:86
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS28x
Chain IDs:LB (auth: Oa)
Chain Length:64
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS30z/eS30y/eS30x
Chain IDs:JA (auth: Pa)
Chain Length:62
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS7x
Chain IDs:QB (auth: Ra)
Chain Length:190
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein eS6y
Chain IDs:GB (auth: Ta)
Chain Length:249
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11y
Chain IDs:MB (auth: Ua)
Chain Length:150
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12y
Chain IDs:R (auth: Va)
Chain Length:142
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13z/uS13y/uS13x
Chain IDs:FB (auth: Wa)
Chain Length:152
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17z
Chain IDs:RA (auth: Xa)
Chain Length:160
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS19y
Chain IDs:NB (auth: Ya)
Chain Length:150
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2z
Chain IDs:JB (auth: Za)
Chain Length:298
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Polymer Type:polyribonucleotide
Molecule:Ribosomal RNA 18S
Chain IDs:WB (auth: h1)
Chain Length:1805
Number of Molecules:1
Biological Source:Arabidopsis thaliana
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
A2M B A modified residue
HIC V HIS modified residue
MLY CB LYS modified residue
OMG B G modified residue
PSU B U modified residue
Ligand Molecules
EPE
K
MG
SPD
TER
ZN
Primary Citation
Structure of the Arabidopsis thaliana 80S ribosome in complex with P- and E-site tRNAs and mRNA
Science ? ? ? (2026)
DOI: 10.1126/science.adx2867
Primary Citation of related structures
9H3G
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