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8K2D

Cryo-EM structure of the yeast 80S ribosome with tigecycline, eEF2, Stm1 and eIF5A

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(C2)
18S rRNApolymer1800579761.91Saccharomyces cerevisiae (baker's yeast)
2B
(C1)
23S rRNApolymer33961097493.91GenBank (834774822)Saccharomyces cerevisiae (baker's yeast)
3C
(C4)
5S rRNApolymer12138951.11GenBank (1039024045)Saccharomyces cerevisiae (baker's yeast)5S rRNA
4D
(C3)
5.8S rRNApolymer15850682.91GenBank (1267176494)Saccharomyces cerevisiae (baker's yeast)
5E
(SA)
Small ribosomal subunit protein uS2Apolymer25228051.31UniProt (P32905)
Pfam (PF00318)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S0-A,Nucleic acid-binding protein NAB1A
6F
(SB)
40S ribosomal protein S1-Apolymer25528798.51UniProt (P33442)
Pfam (PF01015)
Saccharomyces cerevisiae (baker's yeast)RP10A,Small ribosomal subunit protein eS1-A
7G
(SC)
40S ribosomal protein S2polymer25427490.81UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
Saccharomyces cerevisiae (baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5
8H
(SD)
Small ribosomal subunit protein uS3polymer24026542.81UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S3,RP13,YS3
9I
(SE)
40S ribosomal protein S4-Apolymer26129469.31UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
Saccharomyces cerevisiae (baker's yeast)RP5,S7,Small ribosomal subunit protein eS4-A,YS6
10J
(SF)
Small ribosomal subunit protein uS7polymer22525072.61UniProt (P26783)
Pfam (PF00177)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S5,RP14,S2,YS8
11K
(SG)
40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)
Saccharomyces cerevisiae (baker's yeast)RP9,S10,Small ribosomal subunit protein eS6-A,YS4
12L
(SH)
40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
Saccharomyces cerevisiae (baker's yeast)RP30,RP40,Small ribosomal subunit protein eS7-A
13M
(SI)
40S ribosomal protein S8-Apolymer20022537.81UniProt (P0CX39)
Pfam (PF01201)
Saccharomyces cerevisiae (baker's yeast)RP19,S14,Small ribosomal subunit protein eS8-A,YS9
14N
(SJ)
40S ribosomal protein S9-Apolymer19722487.91UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
Saccharomyces cerevisiae (baker's yeast)RP21,S13,Small ribosomal subunit protein uS4-A,YP28,YS11
15O
(SK)
Small ribosomal subunit protein eS10Apolymer10512757.41UniProt (Q08745)
Pfam (PF03501)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S10-A
16P
(SL)
Small ribosomal subunit protein uS17Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
Saccharomyces cerevisiae (Baker's yeast)40S ribosomal protein S11-A,RP41,S18,YS12
17Q
(SM)
Small ribosomal subunit protein eS12polymer14315488.61UniProt (P48589)
Pfam (PF01248)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S12
18R
(SN)
40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
Saccharomyces cerevisiae (baker's yeast)S27a,Small ribosomal subunit protein uS15,YS15
19S
(SO)
40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)
Saccharomyces cerevisiae (baker's yeast)RP59A,Small ribosomal subunit protein uS11-A
20T
(SP)
Small ribosomal subunit protein uS19polymer14216031.91UniProt (Q01855)
Pfam (PF00203)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S15,RIG protein,RP52,S21,YS21
21U
(SQ)
Small ribosomal subunit protein uS9Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S16-A,RP61R
22V
(SR)
Small ribosomal subunit protein eS17Apolymer13615820.41UniProt (P02407)
Pfam (PF00833)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S17-A,RP51A
23W
(SS)
Small ribosomal subunit protein uS13Apolymer14617071.61UniProt (P0CX55)
Pfam (PF00416)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S18-A
24X
(ST)
Small ribosomal subunit protein eS19Apolymer14415942.11UniProt (P07280)
Pfam (PF01090)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S19-A,RP55A,S16a,YP45,YS16A
25Y
(SU)
Small ribosomal subunit protein uS10polymer12113929.01UniProt (P38701)
Pfam (PF00338)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S20
26Z
(SV)
Small ribosomal subunit protein eS21Apolymer879758.81UniProt (P0C0V8)
Pfam (PF01249)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S21-A,S26,YS25
27AA
(SW)
40S ribosomal protein S22-Apolymer13014650.11UniProt (P0C0W1)
Pfam (PF00410)
Saccharomyces cerevisiae (baker's yeast)RP50,S24,Small ribosomal subunit protein uS8-A,YP58,YS22
28BA
(SX)
40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
Saccharomyces cerevisiae (baker's yeast)RP37,S28,Small ribosomal subunit protein uS12-A,YS14
29CA
(SY)
40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
Saccharomyces cerevisiae (baker's yeast)RP50,Small ribosomal subunit protein eS24-A
30DA
(SZ)
Small ribosomal subunit protein eS25Apolymer10812067.31UniProt (Q3E792)
Pfam (PF03297)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S25-A,RP45,S31,YS23
31EA
(Sa)
Small ribosomal subunit protein eS26Bpolymer11913480.91UniProt (P39939)
Pfam (PF01283)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S26-B
32FA
(Sb)
40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
Saccharomyces cerevisiae (baker's yeast)RP61,Small ribosomal subunit protein eS27-A,YS20
33GA
(Sc)
Small ribosomal subunit protein eS28Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S28-A,S33,YS27
34HA
(Sd)
Small ribosomal subunit protein uS14Apolymer566675.71UniProt (P41057)
Pfam (PF00253)
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S29-A,S36,YS29
35IA
(Se)
40S ribosomal protein S30-Apolymer637137.51UniProt (P0CX33)
Pfam (PF04758)
Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS30-A
36JA
(Sf)
Ubiquitin-ribosomal protein eS31 fusion proteinpolymer15217254.21UniProt (P05759)
Pfam (PF00240)
Pfam (PF01599)
Saccharomyces cerevisiae (baker's yeast)
37KA
(Sg)
Small ribosomal subunit protein RACK1polymer31934841.21UniProt (P38011)
Pfam (PF00400)
Saccharomyces cerevisiae (baker's yeast)Guanine nucleotide-binding protein subunit beta-like protein,Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
38LA
(LA)
Large ribosomal subunit protein uL2Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L2-A,L5,RP8,YL6
39MA
(LB)
Large ribosomal subunit protein uL3polymer38743850.81UniProt (P14126)
Pfam (PF00297)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
40NA
(LC)
Large ribosomal subunit protein uL4Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
Saccharomyces cerevisiae (Baker's yeast)60S ribosomal protein L4-A,L2,RP2,YL2
41OA
(LD)
Large ribosomal subunit protein uL18polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L5,L1,L1a,Ribosomal 5S RNA-binding protein,YL3
42PA
(LE)
Large ribosomal subunit protein eL6Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L6-A,L17,RP18,YL16
43QA
(LF)
Large ribosomal subunit protein uL30Apolymer24427686.31UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L7-A,L6,RP11,YL8
44RA
(LG)
Large ribosomal subunit protein eL8Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L8-A,L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
45SA
(LH)
Large ribosomal subunit protein uL6Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L9-A,L8,RP24,YL11
46TA
(LI)
Large ribosomal subunit protein uL16polymer22125410.51UniProt (P41805)
Pfam (PF00252)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L10,L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
47UA
(LJ)
Large ribosomal subunit protein uL5Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L11-A,L16,RP39,YL22
48VA
(LK)
Large ribosomal subunit protein uL11Apolymer16517850.61UniProt (P0CX53)
Pfam (PF03946)
Pfam (PF00298)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L12-A,L15,YL23
49WA
(LL)
Large ribosomal subunit protein eL13Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L13-A
50XA
(LM)
Large ribosomal subunit protein eL14Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L14-A
51YA
(LN)
Large ribosomal subunit protein eL15Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L15-A,L13,RP15R,YL10,YP18
52ZA
(LO)
Large ribosomal subunit protein uL13Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L16-A,L13a,L21,RP22,YL15
53AB
(LP)
Large ribosomal subunit protein uL22Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L17-A,L20A,YL17
54BB
(LQ)
Large ribosomal subunit protein eL18Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L18-A,RP28
55CB
(LR)
Large ribosomal subunit protein eL19Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L19-A,L23,RP15L,RP33,YL14
56DB
(LS)
Large ribosomal subunit protein eL20Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L20-A,L18a
57EB
(LT)
Large ribosomal subunit protein eL21Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L21-A
58FB
(LU)
Large ribosomal subunit protein eL22Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L22-A,L1c,RP4,YL31
59GB
(LV)
Large ribosomal subunit protein uL14Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L23-A,L17a,YL32
60HB
(LW)
Large ribosomal subunit protein eL24Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L24-A,L30,RP29,YL21
61IB
(LX)
Large ribosomal subunit protein uL23polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L25,RP16L,YL25,YP42'
62JB
(LY)
Large ribosomal subunit protein uL24Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L26-A,L33,YL33
63KB
(LZ)
Large ribosomal subunit protein eL27Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L27-A
64LB
(La)
Large ribosomal subunit protein uL15polymer14916761.71UniProt (P02406)
Pfam (PF00828)
Saccharomyces cerevisiae (Baker's yeast)60S ribosomal protein L28,L27a,L29,RP44,RP62,YL24
65MB
(Lb)
Large ribosomal subunit protein eL29polymer596691.91UniProt (P05747)
Pfam (PF01779)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L29,YL43
66NB
(Lc)
Large ribosomal subunit protein eL30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L30,L32,RP73,YL38
67OB
(Ld)
Large ribosomal subunit protein eL31Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L31-A,L34,YL28
68PB
(Le)
Large ribosomal subunit protein eL32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L32
69QB
(Lf)
Large ribosomal subunit protein eL33Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L33-A,L37,RP47,YL37
70RB
(Lg)
Large ribosomal subunit protein eL34Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L34-A
71SB
(Lh)
Large ribosomal subunit protein uL29Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L35-A
72TB
(Li)
Large ribosomal subunit protein eL36Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L36-A,L39,YL39
73UB
(Lj)
Large ribosomal subunit protein eL37Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L37-A,L43,YL35,YP55
74VB
(Lk)
Large ribosomal subunit protein eL38polymer788845.61UniProt (P49167)
Pfam (PF01781)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L38
75WB
(Ll)
Large ribosomal subunit protein eL39polymer516358.61UniProt (P04650)
Pfam (PF00832)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L39,L46,YL40
76XB
(Lm)
Ubiquitin-ribosomal protein eL40A fusion proteinpolymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
Saccharomyces cerevisiae (baker's yeast)
77YB
(Ln)
Large ribosomal subunit protein eL41Apolymer253354.21UniProt (P0CX86)
Pfam (PF05162)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L41-A,L47,YL41
78ZB
(Lo)
Large ribosomal subunit protein eL42Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L42-A,L41,YL27,YP44
79AC
(Lp)
Large ribosomal subunit protein eL43Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L43-A,L37a,YL35
80BC
(CE)
Eukaryotic translation initiation factor 5A-1polymer15717222.41UniProt (P23301)
Pfam (PF21485)
Pfam (PF01287)
Saccharomyces cerevisiae (baker's yeast)eIF-5A-1,Hypusine-containing protein HP2,eIF-4D
81CC
(L1)
Large ribosomal subunit protein uL1Apolymer21724524.81UniProt (P0CX43)
Pfam (PF00687)
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L1-A,L10a
82DC
(P0)
Large ribosomal subunit protein uL10polymer31233749.11UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)
Saccharomyces cerevisiae (baker's yeast)60S acidic ribosomal protein P0,A0,L10e
83EC
(CD)
Elongation factor 2polymer84293407.11UniProt (P32324)
Pfam (PF00009)
Pfam (PF03144)
Pfam (PF14492)
Pfam (PF03764)
Pfam (PF00679)
Saccharomyces cerevisiae (baker's yeast)EF-2,Eukaryotic elongation factor 2,eEF2,Ribosomal translocase,Translation elongation factor 2
84FC
(CS)
Suppressor protein STM1polymer27330048.01UniProt (P39015)
Pfam (PF09598)
Saccharomyces cerevisiae (baker's yeast)3BP1,GU4 nucleic-binding protein 2,G4p2 protein,POP2 multicopy suppressor protein 4,Ribosomal subunits association factor,AF,TOM1 suppressor protein 1,Triplex-binding protein 1
85GC, QC, RC, SC, TC...
(C2, SM, Sa, Sb, Lg...)
ZINC IONnon-polymer65.49Chemie (ZN)
86HC, IC, JC, KC, LC...
(C1)
TIGECYCLINEnon-polymer587.76Chemie (T1C)
87NC, OC, PC, YC
(C1, C3, CD)
MAGNESIUM IONnon-polymer24.34Chemie (MG)
88ZC
(CD)
GUANOSINE-5'-DIPHOSPHATEnon-polymer443.21Chemie (GDP)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains84
Total formula weight3322589.9
Non-Polymers*Number of molecules20
Total formula weight4655.1
All*Total formula weight3327245.0
*Water molecules are not included.

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PDB entries from 2025-08-27

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