3JCJ image
Entry Detail
PDB ID:
3JCJ
Keywords:
Title:
Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2015-12-18
Release Date:
2016-03-09
Method Details:
Experimental Method:
Resolution:
3.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:A (auth: 0)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:B (auth: 1)
Chain Length:75
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:C (auth: 2)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:D (auth: 3)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:messenger RNA
Chain IDs:E (auth: 4)
Chain Length:52
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:F (auth: A)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:G (auth: B)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:H (auth: C)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:I (auth: D)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:J (auth: E)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:K (auth: F)
Chain Length:890
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:L (auth: G)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L11
Chain IDs:M (auth: H)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:N (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:O (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:P (auth: K)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:Q (auth: L)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:R (auth: M)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:S (auth: N)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:T (auth: O)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:U (auth: P)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:V (auth: Q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:W (auth: R)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:X (auth: S)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:Y (auth: T)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:Z (auth: U)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:AA (auth: V)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:BA (auth: W)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:CA (auth: X)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:DA (auth: Y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:EA (auth: Z)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:FA (auth: a)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:GA (auth: b)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:HA (auth: c)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:IA (auth: d)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L10
Chain IDs:JA (auth: e)
Chain Length:165
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Translation initiation factor IF-2
Chain IDs:KA (auth: f)
Chain Length:890
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:LA (auth: g)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:MA (auth: h)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:NA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:OA (auth: k)
Chain Length:167
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:PA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:QA (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6
Chain IDs:RA (auth: n)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:SA (auth: o)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:TA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:UA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:VA (auth: r)
Chain Length:102
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:WA (auth: s)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:XA (auth: t)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:YA (auth: u)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:tRNA
Chain IDs:ZA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:AB (auth: w)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:BB (auth: x)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:CB (auth: y)
Chain Length:59
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:DB (auth: z)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
4SU ZA U 4-THIOURIDINE-5'-MONOPHOSPHATE
5MU ZA U 5-METHYLURIDINE 5'-MONOPHOSPHATE
H2U ZA U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
PSU ZA U PSEUDOURIDINE-5'-MONOPHOSPHATE
Primary Citation
Structures of ribosome-bound initiation factor 2 reveal the mechanism of subunit association.
Sci Adv 2 e1501502 e1501502 (2016)
PMID: 26973877 DOI: 10.1126/sciadv.1501502

Abstact

Throughout the four phases of protein biosynthesis-initiation, elongation, termination, and recycling-the ribosome is controlled and regulated by at least one specified translational guanosine triphosphatase (trGTPase). Although the structural basis for trGTPase interaction with the ribosome has been solved for the last three steps of translation, the high-resolution structure for the key initiation trGTPase, initiation factor 2 (IF2), complexed with the ribosome, remains elusive. We determine the structure of IF2 complexed with a nonhydrolyzable guanosine triphosphate analog and initiator fMet-tRNAi (Met) in the context of the Escherichia coli ribosome to 3.7-Å resolution using cryo-electron microscopy. The structural analysis reveals previously unseen intrinsic conformational modes of the 70S initiation complex, establishing the mutual interplay of IF2 and initator transfer RNA (tRNA) with the ribsosome and providing the structural foundation for a mechanistic understanding of the final steps of translation initiation.

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Primary Citation of related structures