ISDA

Entry Detail

PDB ID:

6WOO

EMDB ID:

EMD-21859

Keywords:

RIBOSOME

Title:

CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP

Biological Source:

Source Organism:

Saccharomyces cerevisiae

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2020-04-25

Release Date:

2020-09-23

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:eIF5B
Chain IDs:DC (auth: 1)
Chain Length:600
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P39730 Pfam ID:PF00009, PF11987, PF14578

Polymer Type:polyribonucleotide
Description:18S ribosomal RNA
Chain IDs:CC (auth: 2)
Chain Length:1796
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Description:Met-tRNA-iMet
Chain IDs:EC (auth: 3)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:FC (auth: 4)
Chain Length:6
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Description:25S ribosomal RNA
Chain IDs:A (auth: 5)
Chain Length:3271
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:B (auth: 7)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Polymer Type:polyribonucleotide
Description:5.8S ribosomal rRNA
Chain IDs:C (auth: 8)
Chain Length:157
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Protein Blast

Polymer Type:polypeptide(L)
Description:uL2
Chain IDs:D (auth: A)
Chain Length:249
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX45 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Description:uS2
Chain IDs:VA (auth: AA)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P46654 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Description:uL3
Chain IDs:E (auth: B)
Chain Length:384
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P14126 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Description:eS1
Chain IDs:WA (auth: BB)
Chain Length:81
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P23248 Pfam ID:PF01015

Protein Blast

Polymer Type:polypeptide(L)
Description:uL4
Chain IDs:F (auth: C)
Chain Length:97
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P10664 Pfam ID:PF00573, PF14374

Protein Blast

Polymer Type:polypeptide(L)
Description:uS5
Chain IDs:XA (auth: CC)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P25443 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Description:uL18
Chain IDs:G (auth: D)
Chain Length:295
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P26321 Pfam ID:PF17144, PF14204

Protein Blast

Polymer Type:polypeptide(L)
Description:uS3
Chain IDs:YA (auth: DD)
Chain Length:53
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05750 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Description:eL6
Chain IDs:H (auth: E)
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q02326 Pfam ID:PF01159

Protein Blast

Polymer Type:polypeptide(L)
Description:eS4
Chain IDs:ZA (auth: EE)
Chain Length:53
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121

Protein Blast

Polymer Type:polypeptide(L)
Description:uL30
Chain IDs:I (auth: F)
Chain Length:222
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05737 Pfam ID:PF08079, PF00327

Protein Blast

Polymer Type:polypeptide(L)
Description:uS7
Chain IDs:AB (auth: FF)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:A0A1L4AA68 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Description:eL8
Chain IDs:J (auth: G)
Chain Length:233
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P17076 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Description:eS6
Chain IDs:BB (auth: GG)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX37 Pfam ID:PF01092

Protein Blast

Polymer Type:polypeptide(L)
Description:uL6
Chain IDs:K (auth: H)
Chain Length:116
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P51401 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Description:eS7
Chain IDs:CB (auth: HH)
Chain Length:184
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P26786 Pfam ID:PF01251

Protein Blast

Polymer Type:polypeptide(L)
Description:uL16
Chain IDs:L (auth: I)
Chain Length:216
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P41805 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Description:eS8
Chain IDs:DB (auth: II)
Chain Length:199
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX39 Pfam ID:PF01201

Protein Blast

Polymer Type:polypeptide(L)
Description:uL5
Chain IDs:M (auth: J)
Chain Length:168
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q3E757 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Description:uS4
Chain IDs:EB (auth: JJ)
Chain Length:182
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05755 Pfam ID:PF00163, PF01479

Polymer Type:polypeptide(L)
Description:L10
Chain IDs:UA (auth: K)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Protein Blast

Polymer Type:polypeptide(L)
Description:eS10
Chain IDs:FB (auth: KK)
Chain Length:96
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q08745 Pfam ID:PF03501

Protein Blast

Polymer Type:polypeptide(L)
Description:eL13
Chain IDs:N (auth: L)
Chain Length:49
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q12690 Pfam ID:PF01294

Protein Blast

Polymer Type:polypeptide(L)
Description:uS17
Chain IDs:GB (auth: LL)
Chain Length:145
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX47 Pfam ID:PF16205, PF00366

Protein Blast

Polymer Type:polypeptide(L)
Description:eL14
Chain IDs:O (auth: M)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P36105 Pfam ID:PF00467, PF01929

Protein Blast

Polymer Type:polypeptide(L)
Description:eS12
Chain IDs:HB (auth: MM)
Chain Length:124
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P48589 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Description:eL15
Chain IDs:P (auth: N)
Chain Length:202
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05748 Pfam ID:PF00827

Protein Blast

Polymer Type:polypeptide(L)
Description:uS15
Chain IDs:IB (auth: NN)
Chain Length:150
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05756 Pfam ID:PF08069, PF00312

Protein Blast

Polymer Type:polypeptide(L)
Description:uL13
Chain IDs:Q (auth: O)
Chain Length:101
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P26784 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Description:uS11
Chain IDs:JB (auth: OO)
Chain Length:127
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P39516 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Description:uL22
Chain IDs:R (auth: P)
Chain Length:180
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05740 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Description:uS19
Chain IDs:KB (auth: PP)
Chain Length:103
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q01855 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Description:eL18
Chain IDs:S (auth: Q)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX49 Pfam ID:PF17135

Protein Blast

Polymer Type:polypeptide(L)
Description:uS19
Chain IDs:LB (auth: QQ)
Chain Length:141
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX51 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Description:eL19
Chain IDs:T (auth: R)
Chain Length:195
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX82 Pfam ID:PF01280

Protein Blast

Polymer Type:polypeptide(L)
Description:eS17
Chain IDs:MB (auth: RR)
Chain Length:123
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P14127 Pfam ID:PF00833

Protein Blast

Polymer Type:polypeptide(L)
Description:eL20
Chain IDs:U (auth: S)
Chain Length:169
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX23 Pfam ID:PF01775

Protein Blast

Polymer Type:polypeptide(L)
Description:uS13
Chain IDs:NB (auth: SS)
Chain Length:136
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX55 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Description:eL21
Chain IDs:V (auth: T)
Chain Length:158
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q02753 Pfam ID:PF01157

Protein Blast

Polymer Type:polypeptide(L)
Description:eS19
Chain IDs:OB (auth: TT)
Chain Length:143
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P07280 Pfam ID:PF01090

Protein Blast

Polymer Type:polypeptide(L)
Description:eL22
Chain IDs:W (auth: U)
Chain Length:100
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05749 Pfam ID:PF01776

Protein Blast

Polymer Type:polypeptide(L)
Description:uS10
Chain IDs:PB (auth: UU)
Chain Length:106
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38701 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Description:uL14
Chain IDs:X (auth: V)
Chain Length:132
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX41 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Description:eS21
Chain IDs:QB (auth: VV)
Chain Length:87
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0C0V8 Pfam ID:PF01249

Protein Blast

Polymer Type:polypeptide(L)
Description:eL24
Chain IDs:Y (auth: W)
Chain Length:62
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P04449 Pfam ID:PF01246

Protein Blast

Polymer Type:polypeptide(L)
Description:uS8
Chain IDs:RB (auth: WW)
Chain Length:129
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0C0W1 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Description:uL23
Chain IDs:Z (auth: X)
Chain Length:121
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P04456 Pfam ID:PF03939, PF00276

Protein Blast

Polymer Type:polypeptide(L)
Description:uS12
Chain IDs:SB (auth: XX)
Chain Length:144
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX29 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Description:uL24
Chain IDs:AA (auth: Y)
Chain Length:125
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05743 Pfam ID:PF16906, PF00467

Protein Blast

Polymer Type:polypeptide(L)
Description:eS24
Chain IDs:TB (auth: YY)
Chain Length:134
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX31 Pfam ID:PF01282

Protein Blast

Polymer Type:polypeptide(L)
Description:eL27
Chain IDs:BA (auth: Z)
Chain Length:134
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0C2H6 Pfam ID:PF01777

Protein Blast

Polymer Type:polypeptide(L)
Description:eS25
Chain IDs:UB (auth: ZZ)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q3E792 Pfam ID:PF03297

Protein Blast

Polymer Type:polypeptide(L)
Description:uL15
Chain IDs:CA (auth: a)
Chain Length:249
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P02406 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Description:eS26
Chain IDs:VB (auth: aa)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P39939 Pfam ID:PF01283

Protein Blast

Polymer Type:polypeptide(L)
Description:eL29
Chain IDs:DA (auth: b)
Chain Length:384
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05747 Pfam ID:PF01779

Protein Blast

Polymer Type:polypeptide(L)
Description:eS27
Chain IDs:WB (auth: bb)
Chain Length:81
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P35997 Pfam ID:PF01667

Protein Blast

Polymer Type:polypeptide(L)
Description:eL30
Chain IDs:EA (auth: c)
Chain Length:97
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P14120 Pfam ID:PF01248

Protein Blast

Polymer Type:polypeptide(L)
Description:eS28
Chain IDs:XB (auth: cc)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:Q3E7X9 Pfam ID:PF01200

Protein Blast

Polymer Type:polypeptide(L)
Description:eL31
Chain IDs:FA (auth: d)
Chain Length:295
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0C2H8 Pfam ID:PF01198

Protein Blast

Polymer Type:polypeptide(L)
Description:uS14
Chain IDs:YB (auth: dd)
Chain Length:53
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P41057 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Description:eL32
Chain IDs:GA (auth: e)
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38061 Pfam ID:PF01655

Protein Blast

Polymer Type:polypeptide(L)
Description:eS30
Chain IDs:ZB (auth: ee)
Chain Length:53
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX33 Pfam ID:PF04758

Protein Blast

Polymer Type:polypeptide(L)
Description:eL33
Chain IDs:HA (auth: f)
Chain Length:222
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05744 Pfam ID:PF01247

Protein Blast

Polymer Type:polypeptide(L)
Description:eS31
Chain IDs:AC (auth: ff)
Chain Length:206
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05759 Pfam ID:PF01599

Protein Blast

Polymer Type:polypeptide(L)
Description:eL34
Chain IDs:IA (auth: g)
Chain Length:233
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P87262 Pfam ID:PF01199

Protein Blast

Polymer Type:polypeptide(L)
Description:RACK1
Chain IDs:BC (auth: gg)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P38011 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Description:uL29
Chain IDs:JA (auth: h)
Chain Length:116
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX84 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Description:eL36
Chain IDs:KA (auth: i)
Chain Length:216
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05745 Pfam ID:PF01158

Protein Blast

Polymer Type:polypeptide(L)
Description:eL37
Chain IDs:LA (auth: j)
Chain Length:168
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P49166 Pfam ID:PF01907

Protein Blast

Polymer Type:polypeptide(L)
Description:eL38
Chain IDs:MA (auth: k)
Chain Length:152
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P49167 Pfam ID:PF01781

Protein Blast

Polymer Type:polypeptide(L)
Description:eL39
Chain IDs:NA (auth: l)
Chain Length:49
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P04650 Pfam ID:PF00832

Protein Blast

Polymer Type:polypeptide(L)
Description:eL40
Chain IDs:OA (auth: m)
Chain Length:51
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CH08 Pfam ID:PF01020

Polymer Type:polypeptide(L)
Description:eL41
Chain IDs:PA (auth: n)
Chain Length:202
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

Protein Blast

Polymer Type:polypeptide(L)
Description:eL42
Chain IDs:QA (auth: o)
Chain Length:101
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX27 Pfam ID:PF00935

Protein Blast

Polymer Type:polypeptide(L)
Description:eL43
Chain IDs:RA (auth: p)
Chain Length:180
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX25 Pfam ID:PF01780

Protein Blast

Polymer Type:polypeptide(L)
Description:uL1
Chain IDs:SA (auth: q)
Chain Length:217
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P0CX43 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Description:uL10
Chain IDs:TA (auth: r)
Chain Length:195
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae

UniProt ID:P05317 Pfam ID:PF00466, PF17777

Ligand Molecules

GDP

MET

U6A

Primary Citation

Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex.

Wang, J, Wang, J, Shin, B.S, Kim, J.R, Dever, T.E, Puglisi, J.D, Fernandez, I.S.Show

Nat Commun 11 5003 5003 (2020)

PMID: 33024099 DOI: 10.1038/s41467-020-18829-3

Abstact

Recognition of a start codon by the initiator aminoacyl-tRNA determines the reading frame of messenger RNA (mRNA) translation by the ribosome. In eukaryotes, the GTPase eIF5B collaborates in the correct positioning of the initiator Met-tRNAiMet on the ribosome in the later stages of translation initiation, gating entrance into elongation. Leveraging the long residence time of eIF5B on the ribosome recently identified by single-molecule fluorescence measurements, we determine the cryoEM structure of the naturally long-lived ribosome complex with eIF5B and Met-tRNAiMet immediately before transition into elongation. The structure uncovers an unexpected, eukaryotic specific and dynamic fidelity checkpoint implemented by eIF5B in concert with components of the large ribosomal subunit.

Legend

Protein

Chemical

Disease

Primary Citation of related structures