9GR1 image
Deposition Date 2024-09-10
Release Date 2024-11-20
Last Version Date 2025-03-12
Entry Detail
PDB ID:
9GR1
Keywords:
GENE REGULATION
Title:
E. coli 70S-TEC complex in delivery state
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
synthetic construct (Taxon ID: 32630)
Escherichia coli BL21(DE3) (Taxon ID: 469008)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.17 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9GR1 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:A (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7N9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:B (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7P5
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:C (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7Q1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7Q6
Polymer Type:polyribonucleotide
Molecule:mRNA in SD-aSD duplex
Chain IDs:BB (auth: 4)
Chain Length:10
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:E (auth: A)
Chain Length:2925
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS2
Chain IDs:F (auth: B)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7V0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS3
Chain IDs:G (auth: C)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7V3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS4
Chain IDs:H (auth: D)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7V8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS5
Chain IDs:I (auth: E)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7W1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS6, fully modified isoform
Gene (Uniprot):rpsF
Chain IDs:J (auth: F)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P02358 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS7
Chain IDs:K (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P02359
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS8
Chain IDs:L (auth: H)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7W7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS9
Chain IDs:M (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7X3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS10
Chain IDs:N (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7R5
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS11
Chain IDs:O (auth: K)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7R9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS12
Chain IDs:P (auth: L)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7S3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS13
Chain IDs:Q (auth: M)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7S9
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS14
Chain IDs:R (auth: N)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0AG59
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS15
Chain IDs:S (auth: O)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0ADZ4
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:T (auth: P)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7T3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein uS17
Chain IDs:U (auth: Q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0AG63
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS18
Chain IDs:V (auth: R)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7T7 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:W (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7U3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS20
Chain IDs:X (auth: T)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7U7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit protein bS21
Chain IDs:Y (auth: U)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P68679
Polymer Type:polyribonucleotide
Molecule:mRNA in ribosome channel
Chain IDs:Z (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:tRNA(fmet) P-site
Chain IDs:CB (auth: Y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:Phe-NH-tRNA(Phe) A-site
Chain IDs:AA (auth: Z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:BA (auth: a)
Chain Length:2925
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:CA (auth: b)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:DA (auth: c)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P60422
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit protein uL3
Chain IDs:EA (auth: d)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P60438
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:FA (auth: e)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P60723
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:GA (auth: f)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P62399
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:HA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0AG55
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:IA (auth: h)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7R1
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:JA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0AA10
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:KA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0ADY3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:LA (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P02413
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:MA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0ADY7
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:NA (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0AG44
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:OA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0C018
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:PA (auth: o)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7K6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:QA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7L3
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:RA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0AG48
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:SA (auth: r)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P61175
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:TA (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0ADZ0
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:UA (auth: t)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P60624
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:VA (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P68919
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:WA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7L8
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:XA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7M2
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:YA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7M6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:ZA (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0AG51
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:AB (auth: z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BL21(DE3)
UniProt ID:P0A7N4
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
3AU AA U modified residue
4D4 MA ARG modified residue
4SU AA U modified residue
5MU AA U modified residue
7MG AA G modified residue
D2T P ASP modified residue
H2U AA U modified residue
MEQ EA GLN modified residue
MIA AA A modified residue
OMC CB C modified residue
PSU AA U modified residue
Ligand Molecules
K
MG
PHE
ZN
Primary Citation
Molecular basis of mRNA delivery to the bacterial ribosome.
Science 386 eado8476 eado8476 (2024)
PMID: 39607923 DOI: 10.1126/science.ado8476

Abstact

Protein synthesis begins with the formation of a ribosome-messenger RNA (mRNA) complex. In bacteria, the small ribosomal subunit (30S) is recruited to many mRNAs through base pairing with the Shine-Dalgarno (SD) sequence and RNA binding by ribosomal protein bS1. Translation can initiate on nascent mRNAs, and RNA polymerase (RNAP) can promote the recruitment of the pioneering 30S. Here, we examined 30S recruitment to nascent mRNAs using cryo-electron microscopy, single-molecule fluorescence colocalization, and in-cell cross-linking mass spectrometry. We show that bS1 delivers the mRNA to the ribosome for SD duplex formation and 30S activation. Additionally, bS1 and RNAP stimulate translation initiation. Our work provides a mechanistic framework for how the SD duplex, ribosomal proteins, and RNAP cooperate in 30S recruitment to mRNAs and establish transcription-translation coupling.

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Protein

Chemical

Disease

Primary Citation of related structures
9GR1