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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5DAT

Complex of yeast 80S ribosome with hypusine-containing 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 (Baker's yeast)
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
12C0, c040S ribosomal protein S10-Apolymer10512757.42UniProt (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 (Baker's yeast)RP41,S18,YS12
14C2, c240S ribosomal protein S12polymer12413327.32UniProt (P48589)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (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 S15polymer13715448.12UniProt (Q01855)
Pfam (PF00203)
In PDB		Saccharomyces cerevisiae (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
24D240S ribosomal protein S22-Apolymer12914518.91UniProt (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 S31polymer768703.52UniProt (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 (Baker's yeast)
373, 75S ribosomal RNApolymer12138951.12GenBank (834774822)Saccharomyces cerevisiae S288c (Baker's yeast)
384, 85.8S ribosomal RNApolymer15850682.92GenBank (940534893)Saccharomyces cerevisiae S288c (Baker's yeast)
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)
51M560S ribosomal protein L15-Apolymer20424480.31UniProt (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-A (eL34)polymer11913412.82UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae 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
80d240S ribosomal protein S22-Apolymer13014682.01UniProt (P0C0W1)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
81m260S ribosomal protein L12-A (uL11)polymer15012783.81Saccharomyces cerevisiae S288c (Baker's yeast)
82m560S ribosomal protein L15-Apolymer20324351.21UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
83p060S acidic ribosomal protein P0polymer22024101.71UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
In PDB		Saccharomyces cerevisiae S288c (Baker's yeast)A0,L10E
84p1, p260S ribosomal protein P1 alpha/P2 betapolymer474017.92Saccharomyces cerevisiae S288c (Baker's yeast)
85fEukaryotic translation initiation factor 5A-1polymer15717222.41UniProt (P23301)
Pfam (PF21485)
Pfam (PF01287)
In PDB		Saccharomyces cerevisiae S288c (Baker's yeast)eIF-5A-1,Hypusine-containing protein HP2,eIF-4D
86l160S ribosomal protein L1-A (uL1)polymer21318145.31Saccharomyces cerevisiae S288c (Baker's yeast)
871, 2, c7, 5, 7...MAGNESIUM IONnon-polymer24.31108Chemie (MG)
886, 5, 1, 2, 8...osmium (III) hexamminenon-polymer286.41166Chemie (OHX)
89q0, d6, q2, O7, d7...ZINC IONnon-polymer65.416Chemie (ZN)
90waterwater18.012Chemie (HOH)
Sequence modifications
M5: 2 - 205 (UniProt: P05748)
PDBExternal DatabaseDetails
Lys 170-insertion
d2: 2 - 131 (UniProt: P0C0W1)
PDBExternal DatabaseDetails
Tyr 47-insertion
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains164
Total formula weight6291702.2
Non-Polymers*Number of molecules2290
Total formula weight361878.1
All*Total formula weight6653580.2
*Water molecules are not included.

218853

PDB entries from 2024-04-24

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