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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5DC3

Complex of yeast 80S ribosome with non-modified eIF5A

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
12, 618S ribosomal RNApolymer1800579761.92REF (831416132)Saccharomyces cerevisiae S288c
2S0, s040S ribosomal protein S0-Apolymer25127920.12UniProt (P32905)
Pfam (PF00318)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleic acid-binding protein NAB1A
3S1, s140S ribosomal protein S1-Apolymer25428667.32UniProt (P33442)
Pfam (PF01015)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP10A
4S2, s240S ribosomal protein S2polymer25327359.62UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,YS5
5S3, s340S ribosomal protein S3polymer23926411.62UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP13,YS3
6S4, s440S ribosomal protein S4-Apolymer26029338.12UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP5,S7,YS6
7S5, s540S ribosomal protein S5polymer22424941.42UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP14,S2,YS8
8S6, s640S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
9S7, s740S ribosomal protein S7-Apolymer18921527.02UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP30,RP40
10S8, s840S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP19,S14,YS9
11S9, s940S ribosomal protein S9-Apolymer19622356.72UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP21,S13,YP28,YS11
12C040S ribosomal protein S10-Apolymer10512757.41UniProt (Q08745)
Pfam (PF03501)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
13C1, c140S ribosomal protein S11-Apolymer15517654.72UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP41,S18,YS12
14C2, c240S ribosomal protein S12polymer14215357.42UniProt (P48589)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
15C3, c340S ribosomal protein S13polymer15016928.72UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S27a,YS15
16C4, c440S ribosomal protein S14-Apolymer13614431.52UniProt (P06367)
Pfam (PF00411)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP59A
17C5, c540S ribosomal protein S15polymer14115900.72UniProt (Q01855)
Pfam (PF00203)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RIG protein,RP52,S21,YS21
18C6, c640S ribosomal protein S16-Apolymer14215746.32UniProt (P0CX51)
Pfam (PF00380)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61R
19C7, c740S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP51A
20C8, c840S ribosomal protein S18-Apolymer14516940.42UniProt (P0CX55)
Pfam (PF00416)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
21C9, c940S ribosomal protein S19-Apolymer14315810.92UniProt (P07280)
Pfam (PF01090)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP55A,S16a,YP45,YS16A
22D0, d040S ribosomal protein S20polymer12013797.92UniProt (P38701)
Pfam (PF00338)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
23D1, d140S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S26,YS25
24D2, d240S ribosomal protein S22-Apolymer12914518.92UniProt (P0C0W1)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
25D3, d340S ribosomal protein S23-Apolymer14415942.72UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP37,S28,YS14
26D4, d440S ribosomal protein S24-Apolymer13415231.62UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50
27D5, d540S ribosomal protein S25-Apolymer10711936.12UniProt (Q3E792)
Pfam (PF03297)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP45,S31,YS23
28D6, d640S ribosomal protein S26-Bpolymer9711023.02UniProt (P39939)
Pfam (PF01283)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
29D7, d740S ribosomal protein S27-Apolymer818762.22UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61,YS20
30D8, d840S ribosomal protein S28-Apolymer667474.72UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S33,YS27
31D9, d940S ribosomal protein S29-Apolymer556544.52UniProt (P41057)
Pfam (PF00253)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S36,YS29
32E0, e040S ribosomal protein S30-Apolymer627006.32UniProt (P0CX33)
Pfam (PF04758)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
33E1, e1Ubiquitin-40S ribosomal protein S31polymer768717.52UniProt (P05759)
Pfam (PF01599)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
34SR, sRGuanine nucleotide-binding protein subunit beta-like proteinpolymer31834710.02UniProt (P38011)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
35SM, sMSuppressor protein STM1polymer27330048.02UniProt (P39015)
Pfam (PF09598)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (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
361, 525S ribosomal RNApolymer33961097493.92REF (831416132)Saccharomyces cerevisiae S288c
373, 75S ribosomal RNApolymer12138951.12GenBank (834774822)Saccharomyces cerevisiae
384, 85.8S ribosomal RNApolymer15850682.92GenBank (940534893)Saccharomyces cerevisiae
39L2, l260S ribosomal protein L2-Apolymer25327332.42UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
40L3, l360S ribosomal protein L3polymer38643719.62UniProt (P14126)
Pfam (PF00297)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
41L4, l460S ribosomal protein L4-Apolymer36139027.92UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,RP2,YL2
42L5, l560S ribosomal protein L5polymer29633633.62UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
43L6, l660S ribosomal protein L6-Apolymer17519869.42UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
44L7, l760S ribosomal protein L7-Apolymer24327555.12UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
45L8, l860S ribosomal protein L8-Apolymer25528044.62UniProt (P17076)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
46L9, l960S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
47M0, m060S ribosomal protein L10polymer22025279.32UniProt (P41805)
Pfam (PF00252)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48M1, m160S ribosomal protein L11-Bpolymer17319654.52UniProt (Q3E757)
Pfam (PF00281)
Pfam (PF00673)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,RP39,YL22
49M3, m360S ribosomal protein L13-Apolymer19822473.02UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
50M4, m460S ribosomal protein L14-Apolymer13715063.92UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
51M5, m560S ribosomal protein L15-Apolymer20324351.22UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
52M6, m660S ribosomal protein L16-Apolymer19822116.02UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
53M7, m760S ribosomal protein L17-Apolymer18320458.32UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
54M8, m860S ribosomal protein L18-Apolymer18520478.12UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
55M9, m960S ribosomal protein L19-Apolymer18821631.12UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
56N0, n060S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
57N1, n160S ribosomal protein L21-Apolymer15918148.12UniProt (Q02753)
Pfam (PF01157)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
58N2, n260S ribosomal protein L22-Apolymer12013580.22UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
59N3, n360S ribosomal protein L23-Apolymer13614362.82UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
60N4, n460S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
61N5, n560S ribosomal protein L25polymer14115656.42UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
62N6, n660S ribosomal protein L26-Apolymer12614134.62UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
63N7, n760S ribosomal protein L27-Apolymer13515437.22UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
64N8, n860S ribosomal protein L28polymer14816630.52UniProt (P02406)
Pfam (PF00828)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
65N9, n960S ribosomal protein L29polymer586560.72UniProt (P05747)
Pfam (PF01779)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
66O0, o060S ribosomal protein L30polymer10411299.22UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
67O1, o160S ribosomal protein L31-Apolymer11212849.02UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
68O2, o260S ribosomal protein L32polymer12914678.22UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
69O3, o360S ribosomal protein L33-Apolymer10612045.92UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
70O4, o460S ribosomal protein L34-Apolymer11913412.82UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
71O5, o560S ribosomal protein L35-Apolymer11913811.42UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
72O6, o660S ribosomal protein L36-Apolymer9911020.12UniProt (P05745)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
73O7, o760S ribosomal protein L37-Apolymer879746.22UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
74O8, o860S ribosomal protein L38polymer778714.42UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
75O9, o960S ribosomal protein L39polymer506227.42UniProt (P04650)
Pfam (PF00832)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
76Q0, q0Ubiquitin-60S ribosomal protein L40polymer526032.32UniProt (P0CH08)
Pfam (PF01020)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
77Q1, q160S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L47,YL41
78Q2, q260S ribosomal protein L42-Apolymer10512115.52UniProt (P0CX27)
Pfam (PF00935)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
79Q3, q360S ribosomal protein L43-Apolymer919981.82UniProt (P0CX25)
Pfam (PF01780)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
80c040S ribosomal protein S10-Apolymer10512771.51Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
81m260S ribosomal protein L12-A (uL11)polymer15012783.81Saccharomyces cerevisiae S288c
82p060S acidic ribosomal protein P0polymer31133617.91UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)A0,L10E
83p160S ribosomal protein P1 alphapolymer474017.91Saccharomyces cerevisiae S288c
84p260S ribosomal P2 betapolymer463932.81Saccharomyces cerevisiae S288c (Baker's yeast)
85fEukaryotic translation initiation factor 5A-1polymer15717136.31UniProt (P23301)
Pfam (PF21485)
Pfam (PF01287)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)eIF-5A-1,Hypusine-containing protein HP2,eIF-4D
86D6, D7, D9, E1, O7...ZINC IONnon-polymer65.416Chemie (ZN)
Sequence modifications
E1, e1: 77 - 152 (UniProt: P05759)
PDBExternal DatabaseDetails
Ala 77Gly 77conflict
O4, o4: 2 - 120 (UniProt: P87262)
PDBExternal DatabaseDetails
-Lys 113deletion
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains163
Total formula weight6287617.0
Non-Polymers*Number of molecules16
Total formula weight1046.5
All*Total formula weight6288663.6
*Water molecules are not included.

218853

PDB entries from 2024-04-24

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