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8CEH

Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2 in the presence of sordarin

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1040S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP50,Small ribosomal subunit protein eS24-A
2140S ribosomal protein S25-Apolymer10812067.31UniProt (Q3E792)
Pfam (PF03297)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP45,S31,Small ribosomal subunit protein eS25-A,YS23
3240S ribosomal protein S26polymer11913538.91UniProt (A0A6A5PUG0)
Pfam (PF01283)
In PDB
Saccharomyces cerevisiae (baker's yeast)
4340S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP61,Small ribosomal subunit protein eS27-A,YS20
5440S ribosomal protein S28-Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)
In PDB
Saccharomyces cerevisiae (baker's yeast)S33,Small ribosomal subunit protein eS28-A,YS27
65HLJ1_G0030400.mRNA.1.CDS.1polymer566675.71UniProt (A0A6A5PV92)
Pfam (PF00253)
In PDB
Saccharomyces cerevisiae (baker's yeast)HLJ1_G0038740.mRNA.1.CDS.1,HN1_G0030180.mRNA.1.CDS.1,JXXY16_1_G0039900.mRNA.1.CDS.1,SX2_G0030120.mRNA.1.CDS.1,XXYS1_4_G0042270.mRNA.1.CDS.1,Y55_G0030330.mRNA.1.CDS.1
7640S ribosomal protein S30-Apolymer637137.51UniProt (P0CX33)
Pfam (PF04758)
In PDB
Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS30-A
87Guanine nucleotide-binding protein subunit beta-like proteinpolymer31934841.21UniProt (P38011)
Pfam (PF00400)
In PDB
Saccharomyces cerevisiae (baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1
98Ubiquitin-40S ribosomal protein S31polymer15217254.21UniProt (A0A6A5PU37)
Pfam (PF00240)
Pfam (PF01599)
In PDB
Saccharomyces cerevisiae (baker's yeast)
10A60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
In PDB
Saccharomyces cerevisiae (baker's yeast)L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15
11AA25S ribosomal RNApolymer33961098082.81GenBank (1262303)Saccharomyces cerevisiae (baker's yeast)
12AaElongation factor 2polymer84293549.31UniProt (A0A6A5Q7K2)
Pfam (PF00009)
Pfam (PF03144)
Pfam (PF14492)
Pfam (PF03764)
Pfam (PF00679)
In PDB
Saccharomyces cerevisiae (baker's yeast)
13B60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
In PDB
Saccharomyces cerevisiae (baker's yeast)L20A,Large ribosomal subunit protein uL22-A,YL17
14BB5S ribosomal RNApolymer12138951.11GenBank (1329886537)Saccharomyces cerevisiae (baker's yeast)
15BbTransfer RNA Phepolymer7624743.81GenBank (176419)Saccharomyces cerevisiae (baker's yeast)
16C60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL18-A,RP28
17CC5.8S ribosomal RNApolymer15850682.91GenBank (1331532632)Saccharomyces cerevisiae (baker's yeast)
18CcTransfer RNA fMetpolymer7724801.81GenBank (170517292)Escherichia coli
19D60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
In PDB
Saccharomyces cerevisiae (baker's yeast)L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14
20DD60S acidic ribosomal protein P0polymer31233749.11UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)
In PDB
Saccharomyces cerevisiae (baker's yeast)A0,L10e,Large ribosomal subunit protein uL10
21DdMessenger RNApolymer3912744.81Saccharomyces cerevisiae
22E60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
In PDB
Saccharomyces cerevisiae (baker's yeast)L18a,Large ribosomal subunit protein eL20-A
23EE60S ribosomal protein L2-Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB
Saccharomyces cerevisiae (baker's yeast)L5,Large ribosomal subunit protein uL2-A,RP8,YL6
24Ee60S ribosomal protein L12-Apolymer16517850.61UniProt (P0CX53)
Pfam (PF03946)
Pfam (PF00298)
In PDB
Saccharomyces cerevisiae (baker's yeast)L15,Large ribosomal subunit protein uL11-A,YL23
25F60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL21-A
26FF60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
27G60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
In PDB
Saccharomyces cerevisiae (baker's yeast)L1c,Large ribosomal subunit protein eL22-A,RP4,YL31
28GG60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB
Saccharomyces cerevisiae (baker's yeast)L2,Large ribosomal subunit protein uL4-A,RP2,YL2
29H60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
In PDB
Saccharomyces cerevisiae (baker's yeast)L17a,Large ribosomal subunit protein uL14-A,YL32
30HH60S ribosomal protein L5polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
In PDB
Saccharomyces cerevisiae (baker's yeast)L1,L1a,Large ribosomal subunit protein uL18,Ribosomal 5S RNA-binding protein,YL3
31I60S ribosomal protein L24-Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)
In PDB
Saccharomyces cerevisiae (baker's yeast)L30,Large ribosomal subunit protein eL24-A,RP29,YL21
32II60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
In PDB
Saccharomyces cerevisiae (baker's yeast)L17,Large ribosomal subunit protein eL6-A,RP18,YL16
33J60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL23,RP16L,YL25,YP42'
34JJ60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB
Saccharomyces cerevisiae (baker's yeast)L6,Large ribosomal subunit protein uL30-A,RP11,YL8
35K60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB
Saccharomyces cerevisiae (baker's yeast)L33,Large ribosomal subunit protein uL24-A,YL33
36KK60S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
In PDB
Saccharomyces cerevisiae (baker's yeast)L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5
37L60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL27-A
38LLRPL9A isoform 1polymer19121605.11UniProt (A0A8H4FCT7)
Pfam (PF00347)
In PDB
Saccharomyces cerevisiae (baker's yeast)
39M60S ribosomal protein L28polymer14916761.71UniProt (P02406)
Pfam (PF00828)
In PDB
Saccharomyces cerevisiae (baker's yeast)L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24
40MM60S ribosomal protein L10polymer22125410.51UniProt (P41805)
Pfam (PF00252)
In PDB
Saccharomyces cerevisiae (baker's yeast)L9,Large ribosomal subunit protein uL16,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
41N60S ribosomal protein L29polymer596691.91UniProt (P05747)
Pfam (PF01779)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL29,YL43
42NN60S ribosomal protein L11-Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)
In PDB
Saccharomyces cerevisiae (baker's yeast)L16,Large ribosomal subunit protein uL5-A,RP39,YL22
43O60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
In PDB
Saccharomyces cerevisiae (baker's yeast)L32,Large ribosomal subunit protein eL30,RP73,YL38
44OO60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL13-A
45P60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
In PDB
Saccharomyces cerevisiae (baker's yeast)L34,Large ribosomal subunit protein eL31-A,YL28
46PP60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL14-A
47PpPolypeptidepolymer2296.41Saccharomyces cerevisiae
48Q60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL32
49QQ60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
In PDB
Saccharomyces cerevisiae (baker's yeast)L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18
50R60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
In PDB
Saccharomyces cerevisiae (baker's yeast)L37,Large ribosomal subunit protein eL33-A,RP47,YL37
51S60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL34-A
52T60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein uL29-A
53U60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)
In PDB
Saccharomyces cerevisiae (baker's yeast)L39,Large ribosomal subunit protein eL36-A,YL39
54V60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
In PDB
Saccharomyces cerevisiae (baker's yeast)L43,Large ribosomal subunit protein eL37-A,YL35,YP55
55W60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)
In PDB
Saccharomyces cerevisiae (baker's yeast)Large ribosomal subunit protein eL38
56X60S ribosomal protein L39polymer516358.61UniProt (P04650)
Pfam (PF00832)
In PDB
Saccharomyces cerevisiae (baker's yeast)L46,Large ribosomal subunit protein eL39,YL40
57YUbiquitin-60S ribosomal protein L40polymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
In PDB
Saccharomyces cerevisiae (baker's yeast)
58Z60S ribosomal protein L41polymer253354.21UniProt (A0A8H8UMB4)
Pfam (PF05162)
In PDB
Saccharomyces cerevisiae (baker's yeast)
59a60S ribosomal protein L42-Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)
In PDB
Saccharomyces cerevisiae (baker's yeast)L41,Large ribosomal subunit protein eL42-A,YL27,YP44
60b60S ribosomal protein L43-Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)
In PDB
Saccharomyces cerevisiae (baker's yeast)L37a,Large ribosomal subunit protein eL43-A,YL35
61c18S ribosomal RNApolymer1800580284.71Saccharomyces cerevisiae (baker's yeast)
62d40S ribosomal protein S0-Apolymer25228051.31UniProt (P32905)
Pfam (PF00318)
In PDB
Saccharomyces cerevisiae (baker's yeast)Nucleic acid-binding protein NAB1A,Small ribosomal subunit protein uS2-A
63e40S ribosomal protein S1-Apolymer25528798.51UniProt (P33442)
Pfam (PF01015)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP10A,Small ribosomal subunit protein eS1-A
64f40S 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
65gRPS3 isoform 1polymer24026542.81UniProt (A0A6A5Q3Q1)
Pfam (PF07650)
Pfam (PF00189)
In PDB
Saccharomyces cerevisiae (baker's yeast)
66h40S 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
67i40S ribosomal protein S5polymer22525072.61UniProt (P26783)
Pfam (PF00177)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP14,S2,Small ribosomal subunit protein uS7,YS8
68j40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP9,S10,Small ribosomal subunit protein eS6-A,YS4
69k40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP30,RP40,Small ribosomal subunit protein eS7-A
70l40S ribosomal protein S8-Bpolymer20022537.81UniProt (P0CX40)
Pfam (PF01201)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP19,S14,Small ribosomal subunit protein eS8-B,YS9
71m40S 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
72n40S ribosomal protein S10-Apolymer10512757.41UniProt (Q08745)
Pfam (PF03501)
In PDB
Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein eS10-A
73o40S ribosomal protein S11-Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP41,S18,Small ribosomal subunit protein uS17-A,YS12
74p40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF00312)
Pfam (PF08069)
In PDB
Saccharomyces cerevisiae (baker's yeast)S27a,Small ribosomal subunit protein uS15,YS15
75q40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP59A,Small ribosomal subunit protein uS11-A
76r40S ribosomal protein S15polymer14216031.91UniProt (Q01855)
Pfam (PF00203)
In PDB
Saccharomyces cerevisiae (baker's yeast)RIG protein,RP52,S21,Small ribosomal subunit protein uS19,YS21
77s40S ribosomal protein S16-Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP61R,Small ribosomal subunit protein uS9-A
78t40S ribosomal protein S17-Apolymer13615820.41UniProt (P02407)
Pfam (PF00833)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP51A,Small ribosomal subunit protein eS17-A
79u40S ribosomal protein S18-Apolymer14617071.61UniProt (P0CX55)
Pfam (PF00416)
In PDB
Saccharomyces cerevisiae (baker's yeast)Small ribosomal subunit protein uS13-A
80v40S ribosomal protein S19-Apolymer14415942.11UniProt (P07280)
Pfam (PF01090)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A
81w40S ribosomal protein S20polymer12113929.01UniProt (A0A6A5PVE9)
Pfam (PF00338)
In PDB
Saccharomyces cerevisiae (baker's yeast)BJ4_G0000330.mRNA.1.CDS.1,BJ4_G0023380.mRNA.1.CDS.1,EM14S01-3B_G0053970.mRNA.1.CDS.1,HLJ1_G0023150.mRNA.1.CDS.1,HLJ1_G0054920.mRNA.1.CDS.1,HN1_G0054660.mRNA.1.CDS.1,SX2_G0054700.mRNA.1.CDS.1,Y55_G0054930.mRNA.1.CDS.1
82x40S ribosomal protein S21-Apolymer879758.81UniProt (P0C0V8)
Pfam (PF01249)
In PDB
Saccharomyces cerevisiae (baker's yeast)S26,Small ribosomal subunit protein eS21-A,YS25
83y40S 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
84z40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
In PDB
Saccharomyces cerevisiae (baker's yeast)RP37,S28,Small ribosomal subunit protein uS12-A,YS14
852, 5, 8, S, V...ZINC IONnon-polymer65.48Chemie (ZN)
86AA, Bb, c, CC, Dd...MAGNESIUM IONnon-polymer24.3262Chemie (MG)
87AA, EE, MM, Q, a...POTASSIUM IONnon-polymer39.121Chemie (K)
88AASPERMIDINEnon-polymer145.23Chemie (SPD)
89AaGUANOSINE-5'-DIPHOSPHATEnon-polymer443.21Chemie (GDP)
90AaPHOSPHATE IONnon-polymer95.01Chemie (PO4)
91Aa[1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACIDnon-polymer494.61Chemie (SO1)
92waterwater18.0975Chemie (HOH)
Sequence modifications
Cc: 1 - 77 (GenBank: 170517292)
PDBExternal DatabaseDetails
C 18U 3030542conflict
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains84
Total formula weight3299204.7
Non-Polymers*Number of molecules297
Total formula weight9180.8
All*Total formula weight3308385.5
*Water molecules are not included.

219869

PDB entries from 2024-05-15

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