ISDA

Deposition Date 2014-04-05

Release Date 2014-07-16

Last Version Date 2024-11-13

Entry Detail

PDB ID:

4UJE

Keywords:

RIBOSOME

Title:

Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement

Biological Source:

Source Organism:

ESCHERICHIA COLI (Taxon ID: 562)
ORYCTOLAGUS CUNICULUS (Taxon ID: 9986)
BOS TAURUS (Taxon ID: 9913)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

6.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:28S Ribosomal RNA
Chain IDs:CC (auth: A2)
Chain Length:5025
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polyribonucleotide
Molecule:5.8S Ribosomal RNA
Chain IDs:DC (auth: A3)
Chain Length:194
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:EC (auth: A4)
Chain Length:121
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polyribonucleotide
Molecule:TRNA-LYS
Chain IDs:A (auth: AV)
Chain Length:76
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polyribonucleotide
Molecule:TRNA-PHE
Chain IDs:B (auth: AW)
Chain Length:76
Number of Molecules:1
Biological Source:BOS TAURUS

Polymer Type:polyribonucleotide
Molecule:Messenger RNA
Chain IDs:C (auth: AX)
Chain Length:28
Number of Molecules:1
Biological Source:ESCHERICHIA COLI

Polymer Type:polyribonucleotide
Molecule:18S Ribosomal RNA
Chain IDs:D (auth: B1)
Chain Length:1869
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN SA
Chain IDs:E (auth: BA)
Chain Length:115
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S3A
Chain IDs:F (auth: BB)
Chain Length:84
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S2
Chain IDs:G (auth: BC)
Chain Length:69
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S3
Chain IDs:H (auth: BD)
Chain Length:243
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S4, Y ISOFORM 1
Chain IDs:I (auth: BE)
Chain Length:263
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S5
Chain IDs:J (auth: BF)
Chain Length:156
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S6
Chain IDs:K (auth: BG)
Chain Length:317
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S7
Chain IDs:L (auth: BH)
Chain Length:194
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S8
Chain IDs:M (auth: BI)
Chain Length:208
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S9
Chain IDs:N (auth: BJ)
Chain Length:194
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S10
Chain IDs:O (auth: BK)
Chain Length:165
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S11
Chain IDs:P (auth: BL)
Chain Length:158
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S12
Chain IDs:Q (auth: BM)
Chain Length:132
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S13
Chain IDs:R (auth: BN)
Chain Length:151
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S14
Chain IDs:S (auth: BO)
Chain Length:151
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S15
Chain IDs:T (auth: BP)
Chain Length:145
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S16
Chain IDs:U (auth: BQ)
Chain Length:146
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S17
Chain IDs:V (auth: BR)
Chain Length:135
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S18
Chain IDs:W (auth: BS)
Chain Length:152
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S19
Chain IDs:X (auth: BT)
Chain Length:145
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S20
Chain IDs:Y (auth: BU)
Chain Length:119
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S21
Chain IDs:Z (auth: BV)
Chain Length:83
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S15A
Chain IDs:AA (auth: BW)
Chain Length:130
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S23
Chain IDs:BA (auth: BX)
Chain Length:143
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S24
Chain IDs:CA (auth: BY)
Chain Length:133
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S25
Chain IDs:DA (auth: BZ)
Chain Length:125
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S26
Chain IDs:EA (auth: Ba)
Chain Length:115
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S27
Chain IDs:FA (auth: Bb)
Chain Length:84
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S28
Chain IDs:GA (auth: Bc)
Chain Length:69
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S29
Chain IDs:HA (auth: Bd)
Chain Length:243
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN S30
Chain IDs:IA (auth: Be)
Chain Length:263
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:UBIQUITIN-40S RIBOSOMAL PROTEIN S27A
Chain IDs:JA (auth: Bf)
Chain Length:156
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1
Chain IDs:KA (auth: Bg)
Chain Length:317
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L8
Chain IDs:LA (auth: CA)
Chain Length:148
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L3
Chain IDs:MA (auth: CB)
Chain Length:403
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L4
Chain IDs:NA (auth: CC)
Chain Length:427
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L5
Chain IDs:OA (auth: CD)
Chain Length:297
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L6
Chain IDs:PA (auth: CE)
Chain Length:135
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L7
Chain IDs:QA (auth: CF)
Chain Length:110
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L7A
Chain IDs:RA (auth: CG)
Chain Length:266
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L9
Chain IDs:SA (auth: CH)
Chain Length:192
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L10
Chain IDs:TA (auth: CI)
Chain Length:105
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L11
Chain IDs:UA (auth: CJ)
Chain Length:97
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L13
Chain IDs:VA (auth: CL)
Chain Length:211
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L14
Chain IDs:WA (auth: CM)
Chain Length:128
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L15
Chain IDs:XA (auth: CN)
Chain Length:204
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L13A
Chain IDs:YA (auth: CO)
Chain Length:106
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L17
Chain IDs:ZA (auth: CP)
Chain Length:184
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L18
Chain IDs:AB (auth: CQ)
Chain Length:188
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L19
Chain IDs:BB (auth: CR)
Chain Length:196
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L18A
Chain IDs:CB (auth: CS)
Chain Length:176
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L21
Chain IDs:DB (auth: CT)
Chain Length:137
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L22
Chain IDs:EB (auth: CU)
Chain Length:210
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L23
Chain IDs:FB (auth: CV)
Chain Length:140
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L24
Chain IDs:GB (auth: CW)
Chain Length:157
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L23A
Chain IDs:HB (auth: CX)
Chain Length:156
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L26
Chain IDs:IB (auth: CY)
Chain Length:145
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L27
Chain IDs:JB (auth: CZ)
Chain Length:136
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L27A
Chain IDs:KB (auth: Ca)
Chain Length:148
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L29
Chain IDs:LB (auth: Cb)
Chain Length:403
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L30
Chain IDs:MB (auth: Cc)
Chain Length:427
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L31
Chain IDs:NB (auth: Cd)
Chain Length:297
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L32
Chain IDs:OB (auth: Ce)
Chain Length:135
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L35A
Chain IDs:PB (auth: Cf)
Chain Length:110
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L34
Chain IDs:QB (auth: Cg)
Chain Length:266
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L35
Chain IDs:RB (auth: Ch)
Chain Length:192
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L36
Chain IDs:SB (auth: Ci)
Chain Length:105
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L37
Chain IDs:TB (auth: Cj)
Chain Length:97
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L38
Chain IDs:UB (auth: Ck)
Chain Length:70
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L39
Chain IDs:VB (auth: Cl)
Chain Length:211
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:UBIQUITIN-60S RIBOSOMAL PROTEIN L40
Chain IDs:WB (auth: Cm)
Chain Length:128
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L41
Chain IDs:XB (auth: Cn)
Chain Length:204
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L36A
Chain IDs:YB (auth: Co)
Chain Length:106
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L37A
Chain IDs:ZB (auth: Cp)
Chain Length:184
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L28
Chain IDs:AC (auth: Ct)
Chain Length:137
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L10A
Chain IDs:BC (auth: Cu)
Chain Length:210
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
MIA	B	A	?

Ligand Molecules

Primary Citation

Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement.

Budkevich, T.V, Giesebrecht, J, Behrmann, E, Loerke, J, Ramrath, D.J, Mielke, T, Ismer, J, Hildebrand, P.W, Tung, C.S, Nierhaus, K.H, Sanbonmatsu, K.Y, Spahn, C.M.Show

Cell(Cambridge,Mass.) 158 121 ? (2014)

PMID: 24995983 DOI: 10.1016/J.CELL.2014.04.044

Abstact

The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅Val-tRNA⋅GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ribosomes, a rotation of the small subunit around its long axis and orthogonal to the well-known intersubunit rotation distinguishes the posttranslocational state from the classical pretranslocational state ribosome. We term this motion "subunit rolling." Correspondingly, a mammalian decoding complex visualized in substates before and after codon recognition reveals structural distinctions from the bacterial system. These findings suggest how codon recognition leads to GTPase activation in the mammalian system and demonstrate that in mammalia subunit rolling occurs during tRNA selection.

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Protein

Chemical

Disease

Primary Citation of related structures