8ZFI | pdb_00008zfi

Structure of E.coli ribosome in complex with an engineered arrest peptide and trigger factor

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structure of E.coli ribosome in complex with an engineered arrest peptide and trigger factor

Sriramoju, M.K., Ko, T.P., Draczkowski, P., Hsu, S.T.D.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28A [auth 0]78Escherichia coliMutation(s): 0 
Gene Names: rpmB, b3637, JW3612
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29B [auth 1]63Escherichia coliMutation(s): 0 
Gene Names: rpmC, b3312, JW3274
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30C [auth 2]59Escherichia coliMutation(s): 0 
Gene Names: rpmD, b3302, JW3264
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32D [auth 4]57Escherichia coliMutation(s): 0 
Gene Names: rpmF, b1089, JW1075
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33E [auth 5]55Escherichia coliMutation(s): 0 
Gene Names: rpmG, b3636, JW3611
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34F [auth 6]46Escherichia coliMutation(s): 0 
Gene Names: rpmH, rimA, ssaF, b3703, JW3680
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35G [auth 7]65Escherichia coliMutation(s): 0 
Gene Names: rpmI, b1717, JW1707
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36H [auth 8]38Escherichia coliMutation(s): 0 
Gene Names: rpmJ, b3299, JW3261
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2J [auth B]241Escherichia coliMutation(s): 0 
Gene Names: rpsB, b0169, JW0164
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3K [auth C]233Escherichia coliMutation(s): 0 
Gene Names: rpsC, b3314, JW3276
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4L [auth D]206Escherichia coliMutation(s): 0 
Gene Names: rpsD, ramA, b3296, JW3258
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5M [auth E]167Escherichia coliMutation(s): 0 
Gene Names: rpsE, spc, b3303, JW3265
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, fully modified isoformN [auth F]135Escherichia coliMutation(s): 0 
Gene Names: rpsF, b4200, JW4158
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7O [auth G]179Escherichia coliMutation(s): 0 
Gene Names: rpsG, b3341, JW3303
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8P [auth H]130Escherichia coliMutation(s): 0 
Gene Names: rpsH, b3306, JW3268
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9Q [auth I]130Escherichia coliMutation(s): 0 
Gene Names: rpsI, b3230, JW3199
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10R [auth J]103Escherichia coliMutation(s): 0 
Gene Names: rpsJ, nusE, b3321, JW3283
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11S [auth K]129Escherichia coliMutation(s): 0 
Gene Names: rpsK, b3297, JW3259
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12T [auth L]124Escherichia coliMutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13U [auth M]118Escherichia coliMutation(s): 0 
Gene Names: rpsM, b3298, JW3260
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14V [auth N]101Escherichia coliMutation(s): 0 
Gene Names: rpsN, b3307, JW3269
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15W [auth O]89Escherichia coliMutation(s): 0 
Gene Names: rpsO, secC, b3165, JW3134
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16X [auth P]82Escherichia coliMutation(s): 0 
Gene Names: rpsP, b2609, JW2590
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Y [auth Q]84Escherichia coliMutation(s): 0 
Gene Names: rpsQ, neaA, b3311, JW3273
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Z [auth R]75Escherichia coliMutation(s): 0 
Gene Names: rpsR, b4202, JW4160
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19AA [auth S]92Escherichia coliMutation(s): 0 
Gene Names: rpsS, b3316, JW3278
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20BA [auth T]87Escherichia coliMutation(s): 0 
Gene Names: rpsT, b0023, JW0022
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21CA [auth U]71Escherichia coliMutation(s): 0 
Gene Names: rpsU, b3065, JW3037
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2IA [auth c]273Escherichia coliMutation(s): 0 
Gene Names: rplB, b3317, JW3279
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3JA [auth d]209Escherichia coliMutation(s): 0 
Gene Names: rplC
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4KA [auth e]201Escherichia coliMutation(s): 0 
Gene Names: rplD, eryA, b3319, JW3281
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5LA [auth f]179Escherichia coliMutation(s): 0 
Gene Names: rplE, b3308, JW3270
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6MA [auth g]177Escherichia coliMutation(s): 0 
Gene Names: rplF, b3305, JW3267
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9NA [auth h]149Escherichia coliMutation(s): 0 
Gene Names: rplI, b4203, JW4161
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13OA [auth k]142Escherichia coliMutation(s): 0 
Gene Names: rplM, b3231, JW3200
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14PA [auth l]123Escherichia coliMutation(s): 0 
Gene Names: rplN, b3310, JW3272
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15QA [auth m]144Escherichia coliMutation(s): 0 
Gene Names: rplO, b3301, JW3263
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16RA [auth n]136Escherichia coliMutation(s): 0 
Gene Names: rplP, b3313, JW3275
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17SA [auth o]127Escherichia coliMutation(s): 0 
Gene Names: rplQ, b3294, JW3256
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18TA [auth p]117Escherichia coliMutation(s): 0 
Gene Names: rplR, b3304, JW3266
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19UA [auth q]115Escherichia coliMutation(s): 0 
Gene Names: rplS, b2606, JW2587
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20VA [auth r]118Escherichia coliMutation(s): 0 
Gene Names: rplT, pdzA, b1716, JW1706
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21WA [auth s]103Escherichia coliMutation(s): 0 
Gene Names: rplU, b3186, JW3153
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
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UniProt GroupP0AG48
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22XA [auth t]110Escherichia coliMutation(s): 0 
Gene Names: rplV, eryB, b3315, JW3277
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23YA [auth u]100Escherichia coliMutation(s): 0 
Gene Names: rplW, b3318, JW3280
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24ZA [auth v]104Escherichia coliMutation(s): 0 
Gene Names: rplX, b3309, JW3271
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AB [auth w]94Escherichia coliMutation(s): 0 
Gene Names: rplY, b2185, JW2173
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27CB [auth y]85Escherichia coliMutation(s): 0 
Gene Names: rpmA, b3185, JW3152
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
eRAP-NCDB [auth z]49Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Trigger factorEB [auth V]432Escherichia coliMutation(s): 0 
Gene Names: tig, b0436, JW0426
EC: 5.2.1.8
UniProt
Find proteins for P0A850 (Escherichia coli (strain K12))
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Entity ID: 9
MoleculeChains LengthOrganismImage
16S rRNAI [auth A]1,533Escherichia coli
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Entity ID: 30
MoleculeChains LengthOrganismImage
E-site tRNADA [auth X]76Escherichia coli
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Entity ID: 31
MoleculeChains LengthOrganismImage
P-site tRNA (Chain-Y), A-site tRNA-PRO (Chain-Z)EA [auth Y],
FA [auth Z]		77Escherichia coli
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Entity ID: 32
MoleculeChains LengthOrganismImage
5S rRNAGA [auth a]120Escherichia coli
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Entity ID: 33
MoleculeChains LengthOrganismImage
RNA (2903-MER)HA [auth b]2,904Escherichia coli
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNABB [auth x]14Escherichia coli
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.8.9.3
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)TaiwanAS-CDA-109-L08, AS-CFII-111-210
Ministry of Science and Technology (MoST, Taiwan)Taiwan110-2113-M-001-050-MY3 and 110-2311-B-001-013-MY3, 110-2811-M-001-584, 111-2811-M-001-125, 112-2811-M-001-087

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release