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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
1C218S rRNApolymer1800579761.91Saccharomyces cerevisiae (baker's yeast)
2C123S rRNApolymer33961097493.91GenBank (834774822)Saccharomyces cerevisiae (baker's yeast)
3C45S rRNApolymer12138951.11GenBank (1039024045)Saccharomyces cerevisiae (baker's yeast)5S rRNA
4C35.8S rRNApolymer15850682.91GenBank (1267176494)Saccharomyces cerevisiae (baker's yeast)
5SASmall ribosomal subunit protein uS2Apolymer25228051.31UniProt (P32905)
Pfam (PF00318)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S0-A,Nucleic acid-binding protein NAB1A
6SB40S ribosomal protein S1-Apolymer25528798.51UniProt (P33442)
Pfam (PF01015)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP10A,Small ribosomal subunit protein eS1-A
7SC40S ribosomal protein S2polymer25427490.81UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
In PDB
Saccharomyces cerevisiae (baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5
8SDSmall ribosomal subunit protein uS3polymer24026542.81UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S3,RP13,YS3
9SE40S ribosomal protein S4-Apolymer26129469.31UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP5,S7,Small ribosomal subunit protein eS4-A,YS6
10SFSmall ribosomal subunit protein uS7polymer22525072.61UniProt (P26783)
Pfam (PF00177)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S5,RP14,S2,YS8
11SG40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP9,S10,Small ribosomal subunit protein eS6-A,YS4
12SH40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP30,RP40,Small ribosomal subunit protein eS7-A
13SI40S ribosomal protein S8-Apolymer20022537.81UniProt (P0CX39)
Pfam (PF01201)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP19,S14,Small ribosomal subunit protein eS8-A,YS9
14SJ40S ribosomal protein S9-Apolymer19722487.91UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP21,S13,Small ribosomal subunit protein uS4-A,YP28,YS11
15SKSmall ribosomal subunit protein eS10Apolymer10512757.41UniProt (Q08745)
Pfam (PF03501)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S10-A
16SLSmall ribosomal subunit protein uS17Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB
Saccharomyces cerevisiae (Baker's yeast)40S ribosomal protein S11-A,RP41,S18,YS12
17SMSmall ribosomal subunit protein eS12polymer14315488.61UniProt (P48589)
Pfam (PF01248)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S12
18SN40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB
Saccharomyces cerevisiae (baker's yeast)S27a,Small ribosomal subunit protein uS15,YS15
19SO40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP59A,Small ribosomal subunit protein uS11-A
20SPSmall ribosomal subunit protein uS19polymer14216031.91UniProt (Q01855)
Pfam (PF00203)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S15,RIG protein,RP52,S21,YS21
21SQSmall ribosomal subunit protein uS9Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S16-A,RP61R
22SRSmall ribosomal subunit protein eS17Apolymer13615820.41UniProt (P02407)
Pfam (PF00833)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S17-A,RP51A
23SSSmall ribosomal subunit protein uS13Apolymer14617071.61UniProt (P0CX55)
Pfam (PF00416)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S18-A
24STSmall ribosomal subunit protein eS19Apolymer14415942.11UniProt (P07280)
Pfam (PF01090)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S19-A,RP55A,S16a,YP45,YS16A
25SUSmall ribosomal subunit protein uS10polymer12113929.01UniProt (P38701)
Pfam (PF00338)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S20
26SVSmall ribosomal subunit protein eS21Apolymer879758.81UniProt (P0C0V8)
Pfam (PF01249)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S21-A,S26,YS25
27SW40S ribosomal protein S22-Apolymer13014650.11UniProt (P0C0W1)
Pfam (PF00410)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP50,S24,Small ribosomal subunit protein uS8-A,YP58,YS22
28SX40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP37,S28,Small ribosomal subunit protein uS12-A,YS14
29SY40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP50,Small ribosomal subunit protein eS24-A
30SZSmall ribosomal subunit protein eS25Apolymer10812067.31UniProt (Q3E792)
Pfam (PF03297)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S25-A,RP45,S31,YS23
31SaSmall ribosomal subunit protein eS26Bpolymer11913480.91UniProt (P39939)
Pfam (PF01283)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S26-B
32Sb40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP61,Small ribosomal subunit protein eS27-A,YS20
33ScSmall ribosomal subunit protein eS28Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S28-A,S33,YS27
34SdSmall ribosomal subunit protein uS14Apolymer566675.71UniProt (P41057)
Pfam (PF00253)
In PDB
Saccharomyces cerevisiae (baker's yeast)40S ribosomal protein S29-A,S36,YS29
35Se40S ribosomal protein S30-Apolymer637137.51UniProt (P0CX33)
Pfam (PF04758)
In PDB
Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS30-A
36SfUbiquitin-ribosomal protein eS31 fusion proteinpolymer15217254.21UniProt (P05759)
Pfam (PF00240)
Pfam (PF01599)
In PDB
Saccharomyces cerevisiae (baker's yeast)
37SgSmall ribosomal subunit protein RACK1polymer31934841.21UniProt (P38011)
Pfam (PF00400)
In PDB
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
38LALarge ribosomal subunit protein uL2Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L2-A,L5,RP8,YL6
39LBLarge ribosomal subunit protein uL3polymer38743850.81UniProt (P14126)
Pfam (PF00297)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
40LCLarge ribosomal subunit protein uL4Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB
Saccharomyces cerevisiae (Baker's yeast)60S ribosomal protein L4-A,L2,RP2,YL2
41LDLarge ribosomal subunit protein uL18polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L5,L1,L1a,Ribosomal 5S RNA-binding protein,YL3
42LELarge ribosomal subunit protein eL6Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L6-A,L17,RP18,YL16
43LFLarge ribosomal subunit protein uL30Apolymer24427686.31UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L7-A,L6,RP11,YL8
44LGLarge ribosomal subunit protein eL8Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L8-A,L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
45LHLarge ribosomal subunit protein uL6Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L9-A,L8,RP24,YL11
46LILarge ribosomal subunit protein uL16polymer22125410.51UniProt (P41805)
Pfam (PF00252)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L10,L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
47LJLarge ribosomal subunit protein uL5Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L11-A,L16,RP39,YL22
48LKLarge ribosomal subunit protein uL11Apolymer16517850.61UniProt (P0CX53)
Pfam (PF03946)
Pfam (PF00298)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L12-A,L15,YL23
49LLLarge ribosomal subunit protein eL13Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L13-A
50LMLarge ribosomal subunit protein eL14Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L14-A
51LNLarge ribosomal subunit protein eL15Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L15-A,L13,RP15R,YL10,YP18
52LOLarge ribosomal subunit protein uL13Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L16-A,L13a,L21,RP22,YL15
53LPLarge ribosomal subunit protein uL22Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L17-A,L20A,YL17
54LQLarge ribosomal subunit protein eL18Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L18-A,RP28
55LRLarge ribosomal subunit protein eL19Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L19-A,L23,RP15L,RP33,YL14
56LSLarge ribosomal subunit protein eL20Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L20-A,L18a
57LTLarge ribosomal subunit protein eL21Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L21-A
58LULarge ribosomal subunit protein eL22Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L22-A,L1c,RP4,YL31
59LVLarge ribosomal subunit protein uL14Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L23-A,L17a,YL32
60LWLarge ribosomal subunit protein eL24Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L24-A,L30,RP29,YL21
61LXLarge ribosomal subunit protein uL23polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L25,RP16L,YL25,YP42'
62LYLarge ribosomal subunit protein uL24Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L26-A,L33,YL33
63LZLarge ribosomal subunit protein eL27Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L27-A
64LaLarge ribosomal subunit protein uL15polymer14916761.71UniProt (P02406)
Pfam (PF00828)
In PDB
Saccharomyces cerevisiae (Baker's yeast)60S ribosomal protein L28,L27a,L29,RP44,RP62,YL24
65LbLarge ribosomal subunit protein eL29polymer596691.91UniProt (P05747)
Pfam (PF01779)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L29,YL43
66LcLarge ribosomal subunit protein eL30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L30,L32,RP73,YL38
67LdLarge ribosomal subunit protein eL31Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L31-A,L34,YL28
68LeLarge ribosomal subunit protein eL32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L32
69LfLarge ribosomal subunit protein eL33Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L33-A,L37,RP47,YL37
70LgLarge ribosomal subunit protein eL34Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L34-A
71LhLarge ribosomal subunit protein uL29Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L35-A
72LiLarge ribosomal subunit protein eL36Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L36-A,L39,YL39
73LjLarge ribosomal subunit protein eL37Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L37-A,L43,YL35,YP55
74LkLarge ribosomal subunit protein eL38polymer788845.61UniProt (P49167)
Pfam (PF01781)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L38
75LlLarge ribosomal subunit protein eL39polymer516358.61UniProt (P04650)
Pfam (PF00832)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L39,L46,YL40
76LmUbiquitin-ribosomal protein eL40A fusion proteinpolymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
In PDB
Saccharomyces cerevisiae (baker's yeast)
77LnLarge ribosomal subunit protein eL41Apolymer253354.21UniProt (P0CX86)
Pfam (PF05162)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L41-A,L47,YL41
78LoLarge ribosomal subunit protein eL42Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L42-A,L41,YL27,YP44
79LpLarge ribosomal subunit protein eL43Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L43-A,L37a,YL35
80CEEukaryotic translation initiation factor 5A-1polymer15717222.41UniProt (P23301)
Pfam (PF21485)
Pfam (PF01287)
In PDB
Saccharomyces cerevisiae (baker's yeast)eIF-5A-1,Hypusine-containing protein HP2,eIF-4D
81L1Large ribosomal subunit protein uL1Apolymer21724524.81UniProt (P0CX43)
Pfam (PF00687)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S ribosomal protein L1-A,L10a
82P0Large ribosomal subunit protein uL10polymer31233749.11UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)
In PDB
Saccharomyces cerevisiae (baker's yeast)60S acidic ribosomal protein P0,A0,L10e
83CDElongation factor 2polymer84293407.11UniProt (P32324)
Pfam (PF00009)
Pfam (PF03144)
Pfam (PF14492)
Pfam (PF03764)
Pfam (PF00679)
In PDB
Saccharomyces cerevisiae (baker's yeast)EF-2,Eukaryotic elongation factor 2,eEF2,Ribosomal translocase,Translation elongation factor 2
84CSSuppressor protein STM1polymer27330048.01UniProt (P39015)
Pfam (PF09598)
In PDB
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
85C2, SM, Sa, Sb, Lg...ZINC IONnon-polymer65.49Chemie (ZN)
86C1TIGECYCLINEnon-polymer587.76Chemie (T1C)
87C1, C3, CDMAGNESIUM IONnon-polymer24.34Chemie (MG)
88CDGUANOSINE-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.

223166

PDB entries from 2024-07-31

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