8PVA image
Entry Detail
PDB ID:
8PVA
EMDB ID:
Keywords:
Title:
Structure of bacterial ribosome determined by cryoEM at 100 keV
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-07-17
Release Date:
2023-11-29
Method Details:
Experimental Method:
Resolution:
4.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:VA (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:WA (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:XA (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:YA (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL31A
Chain IDs:ZA (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:E-site tRNA
Chain IDs:DB (auth: 5)
Chain Length:2
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:16S rRNA
Chain IDs:A
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS2
Chain IDs:B
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS3
Chain IDs:C
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS4
Chain IDs:D
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS5
Chain IDs:E
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS6, fully modified isoform
Chain IDs:F
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS7
Chain IDs:G
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS8
Chain IDs:H
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS9
Chain IDs:I
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS10
Chain IDs:J
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS11
Chain IDs:K
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS12
Chain IDs:L
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS13
Chain IDs:M
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS14
Chain IDs:N
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS15
Chain IDs:O
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS16
Chain IDs:P
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS17
Chain IDs:Q
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS18
Chain IDs:R
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein uS19
Chain IDs:S
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS20
Chain IDs:T
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Small ribosomal subunit protein bS21
Chain IDs:U
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:AB (auth: X)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:A-site tRNA-val
Chain IDs:BB (auth: Y)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:P-site tRNA-fMet
Chain IDs:CB (auth: Z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:23S rRNA
Chain IDs:V (auth: a)
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:W (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL2
Chain IDs:X (auth: c)
Chain Length:273
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL3
Chain IDs:Y (auth: d)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL4
Chain IDs:Z (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL5
Chain IDs:AA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL6
Chain IDs:BA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein bL9
Chain IDs:CA (auth: h)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL13
Chain IDs:DA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:EA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:FA (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:Large ribosomal subunit protein uL16
Chain IDs:GA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:HA (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:IA (auth: n)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:JA (auth: o)
Chain Length:89
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:KA (auth: p)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:LA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:MA (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:NA (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:OA (auth: t)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:PA (auth: u)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:QA (auth: v)
Chain Length:85
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:RA (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:SA (auth: x)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:TA (auth: y)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:UA (auth: z)
Chain Length:57
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG A G modified residue
4D4 GA ARG modified residue
4OC A C modified residue
5MC A C modified residue
D2T L ASP modified residue
G7M A G modified residue
MA6 A A modified residue
MEQ Y GLN modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
Primary Citation

Abstact

Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.

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Primary Citation of related structures