5UQ8 image
Deposition Date 2017-02-07
Release Date 2018-03-07
Last Version Date 2025-03-19
Entry Detail
PDB ID:
5UQ8
Keywords:
RIBOSOME
Title:
70S ribosome complex with dnaX mRNA stem-loop and E-site tRNA ("out" conformation)
Biological Source:
Source Organism:
synthetic construct (Taxon ID: 32630)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (Taxon ID: 300852)
Escherichia coli K-12 (Taxon ID: 83333)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5UQ8 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: 0)
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60493 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: 1)
Chain Length:97
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60494 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: 2)
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHP6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: 3)
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:Z (auth: 4)
Chain Length:69
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SJE1 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: 5)
Chain Length:59
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80339 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: 6)
Chain Length:53
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P35871 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 7)
Chain Length:48
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80340 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: 8)
Chain Length:64
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SKU1 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: 9)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHR2 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:A
Chain Length:1521
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:B
Chain Length:120
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:BB (auth: C)
Chain Length:226
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SLP7 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: D)
Chain Length:275
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: E)
Chain Length:148
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHN8 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: F)
Chain Length:203
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHN9 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: G)
Chain Length:155
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:G (auth: H)
Chain Length:173
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: I)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I (auth: N)
Chain Length:140
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60488 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J (auth: O)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHP8 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K (auth: P)
Chain Length:82
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: Q)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60489 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:M (auth: R)
Chain Length:68
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:N (auth: S)
Chain Length:110
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O (auth: T)
Chain Length:131
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60490 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:P (auth: U)
Chain Length:116
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60491 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: V)
Chain Length:101
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P60492 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: W)
Chain Length:112
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHP3 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:S (auth: X)
Chain Length:55
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHP0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T (auth: Y)
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: Z)
Chain Length:76
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:FA (auth: a)
Chain Length:1521
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:GA (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80371 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:HA (auth: c)
Chain Length:226
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:IA (auth: d)
Chain Length:275
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:JA (auth: e)
Chain Length:148
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:KA (auth: f)
Chain Length:203
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SLP8 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:LA (auth: g)
Chain Length:155
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P17291 Pfam ID:PF00177
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:MA (auth: h)
Chain Length:173
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:NA (auth: i)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80374 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:OA (auth: j)
Chain Length:96
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHN7 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:PA (auth: k)
Chain Length:114
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80376 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:QA (auth: l)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHN3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:RA (auth: m)
Chain Length:114
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80377 Pfam ID:PF00416
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:SA (auth: n)
Chain Length:140
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:TA (auth: o)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SJ76 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:UA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SJH3 Pfam ID:PF00886
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:VA (auth: q)
Chain Length:99
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:WA (auth: r)
Chain Length:68
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:XA (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SHP2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:YA (auth: t)
Chain Length:131
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:P80380 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:ZA (auth: u)
Chain Length:116
Number of Molecules:1
Biological Source:Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:messenger RNA
Chain IDs:DB (auth: x)
Chain Length:55
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:P-site tRNA fMet
Chain IDs:AB (auth: y)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:E-site tRNA Phe
Chain IDs:CB (auth: z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli K-12
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
0TD QA ASP modified residue
2MA A A modified residue
2MG FA G modified residue
2MU A U modified residue
4OC A C modified residue
5MC A C modified residue
5MU A U modified residue
7MG FA G modified residue
M2G FA G modified residue
MA6 FA A modified residue
OMG A G modified residue
PSU A U modified residue
UR3 FA U modified residue
Ligand Molecules
SF4
ZN
Primary Citation
Alternative Mode of E-Site tRNA Binding in the Presence of a Downstream mRNA Stem Loop at the Entrance Channel.
Structure 26 437 445.e3 (2018)
PMID: 29456023 DOI: 10.1016/j.str.2018.01.013

Abstact

Structured mRNAs positioned downstream of the ribosomal decoding center alter gene expression by slowing protein synthesis. Here, we solved the cryo-EM structure of the bacterial ribosome bound to an mRNA containing a 3' stem loop that regulates translation. Unexpectedly, the E-site tRNA adopts two distinct orientations. In the first structure, normal interactions with the 50S and 30S E site are observed. However, in the second structure, although the E-site tRNA makes normal interactions with the 50S E site, its anticodon stem loop moves approximately 54 A away from the 30S E site to interact with the 30S head domain and 50S uL5. This position of the E-site tRNA causes the uL1 stalk to adopt a more open conformation that likely represents an intermediate state during E-site tRNA dissociation. These results suggest that structured mRNAs at the entrance channel restrict 30S subunit movement required during translation to slow E-site tRNA dissociation.

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Protein

Chemical

Disease

Primary Citation of related structures
5UQ7