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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6FT6

Structure of the Nop53 pre-60S particle bound to the exosome nuclear cofactors

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(2)		7S ribosomal RNApolymer16251999.81GenBank (1279395616)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
2B
(A)		60S ribosomal protein L2-Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,Large ribosomal subunit protein uL2-A,RP8,YL6
3C
(B)		60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
4D
(C)		60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,Large ribosomal subunit protein uL4-A,RP2,YL2
5E
(D)		60S ribosomal protein L5polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Large ribosomal subunit protein uL18,Ribosomal 5S RNA-binding protein,YL3
6F
(E)		60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,Large ribosomal subunit protein eL6-A,RP18,YL16
7G
(F)		60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,Large ribosomal subunit protein uL30-A,RP11,YL8
8H
(G)		60S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Large ribosomal subunit protein eL8-A,Maintenance of killer protein 7,RP6,YL5
9I
(H)		60S ribosomal protein L9-Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,Large ribosomal subunit protein uL6-A,RP24,YL11
10J
(I)		Bud site selection protein 20polymer16618547.01UniProt (Q08004)
Pfam (PF12171)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
11K
(J)		60S ribosomal protein L11-Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,Large ribosomal subunit protein uL5-A,RP39,YL22
12L
(L)		60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL13-A
13M
(M)		60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL14-A
14N
(N)		60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18
15O
(O)		60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15
16P
(P)		60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,Large ribosomal subunit protein uL22-A,YL17
17Q
(Q)		60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL18-A,RP28
18R
(R)		60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14
19S
(S)		60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a,Large ribosomal subunit protein eL20-A
20T
(T)		60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL21-A
21U
(U)		60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,Large ribosomal subunit protein eL22-A,RP4,YL31
22V
(V)		60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,Large ribosomal subunit protein uL14-A,YL32
23W
(W)		Ribosome assembly factor MRT4polymer23627098.01UniProt (P33201)
Pfam (PF00466)
Pfam (PF17777)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)mRNA turnover protein 4
24X
(X)		60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein uL23,RP16L,YL25,YP42'
25Y
(Y)		60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,Large ribosomal subunit protein uL24-A,YL33
26Z
(Z)		60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL27-A
27AA
(a)		60S ribosomal protein L28polymer14916761.71UniProt (P02406)
Pfam (PF00828)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,Large ribosomal subunit protein uL15,RP44,RP62,YL24
28BA
(b)		Nucleolar GTP-binding protein 1polymer64774531.21UniProt (Q02892)
Pfam (PF17835)
Pfam (PF06858)
Pfam (PF08155)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
29CA
(c)		60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,Large ribosomal subunit protein eL30,RP73,YL38
30DA
(d)		60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,Large ribosomal subunit protein eL31-A,YL28
31EA
(e)		60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL32
32FA
(f)		60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,Large ribosomal subunit protein eL33-A,RP47,YL37
33GA
(g)		60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL34-A
34HA
(h)		60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein uL29-A
35IA
(i)		60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,Large ribosomal subunit protein eL36-A,YL39
36JA
(j)		60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,Large ribosomal subunit protein eL37-A,YL35,YP55
37KA
(k)		60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL38
38LA
(l)		60S ribosomal protein L39polymer516358.61UniProt (P04650)
Pfam (PF00832)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,Large ribosomal subunit protein eL39,YL40
39MA
(m)		Nucleolar GTP-binding protein 2polymer48655585.61UniProt (P53742)
Pfam (PF08153)
Pfam (PF01926)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
40NA
(n)		Pescadillo homologpolymer60569984.11UniProt (P53261)
Pfam (PF06732)
Pfam (PF16589)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleolar protein 7,Ribosomal RNA-processing protein 13
41OA
(p)		60S ribosomal protein L43-Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,Large ribosomal subunit protein eL43-A,YL35
42PA
(r)		Ribosome biogenesis protein NSA2polymer26129786.81UniProt (P40078)
Pfam (PF01201)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)NOP7-associated protein 2
43QA
(s)		Nuclear GTP-binding protein NUG1polymer52057798.71UniProt (P40010)
Pfam (PF08701)
Pfam (PF01926)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nuclear GTPase 1
44RA
(u)		Ribosome biogenesis protein RLP24polymer19924027.71UniProt (Q07915)
Pfam (PF01246)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal protein L24-like
45SA
(v)		Ribosome biogenesis protein RPF2polymer34439665.81UniProt (P36160)
Pfam (PF04427)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
46TA
(w)		Regulator of ribosome biosynthesispolymer20323001.41UniProt (Q08746)
Pfam (PF04939)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
47UA
(x)		Ribosome assembly protein 4polymer51557106.81UniProt (P25382)
Pfam (PF08154)
Pfam (PF00400)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Notchless protein homolog 1,Ribosome biogenesis factor RSA4
48VA
(y)		Eukaryotic translation initiation factor 6polymer24526476.61UniProt (Q12522)
Pfam (PF01912)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)eIF-6
49WA
(z)		UPF0642 protein YBL028Cpolymer10612435.41UniProt (P38202)
Pfam (PF10338)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
50XA
(1)		25S ribosomal RNApolymer33961097493.91GenBank (834774822)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
51YA
(3)		5S ribosomal RNApolymer12138951.11GenBank (1329886537)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
52ZA
(4)		Probable metalloprotease ARX1polymer59365290.31UniProt (Q03862)Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Associated with ribosomal export complex protein 1
53AB
(5)		rRNA-processing protein CGR1polymer12014460.11UniProt (P53188)
Pfam (PF03879)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Coiled-coil growth-regulated protein 1
54BB
(KK)		Exosome complex exonuclease RRP6polymer73384160.61UniProt (Q12149)
Pfam (PF08066)
Pfam (PF01612)
Pfam (PF00570)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal RNA-processing protein 6
55CB
(LL)		Exosome complex protein LRP1polymer18421086.31UniProt (P38801)
Pfam (PF04000)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Like an rRNA processing protein 1,Yeast C1D domain-containing protein,rRNA processing protein 47
56DB
(MM)		ATP-dependent RNA helicase DOB1polymer1011115230.61UniProt (P47047)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF21408)
Pfam (PF13234)
Pfam (PF08148)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)mRNA transport regulator MTR4
57EB
(NN)		MPP6polymer11954.21Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
58FB, IB, LB, MB
(I, j, p, u)		ZINC IONnon-polymer65.44Chemie (ZN)
59GB, JB
(b, m)		GUANOSINE-5'-TRIPHOSPHATEnon-polymer523.22Chemie (GTP)
60HB, KB
(b, m)		MAGNESIUM IONnon-polymer24.32Chemie (MG)
Sequence modifications
2: 1 - 156 (GenBank: 1279395616)
PDBExternal DatabaseDetails
A 157-expression tag
A 158-expression tag
A 159-expression tag
A 160-expression tag
U 161-expression tag
U 162-expression tag
MM: 80 - 1073 (UniProt: P47047)
PDBExternal DatabaseDetails
Met 1-initiating methionine
Asp 2-expression tag
Ser 3-expression tag
Thr 4-expression tag
Asp 5-expression tag
Leu 6-expression tag
Phe 7-expression tag
Asp 8-expression tag
Val 9-expression tag
Phe 10-expression tag
Glu 11-expression tag
Glu 12-expression tag
Thr 13-expression tag
Pro 14-expression tag
Val 15-expression tag
Glu 16-expression tag
Leu 17-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains57
Total formula weight2669329.1
Non-Polymers*Number of molecules8
Total formula weight1356.6
All*Total formula weight2670685.7
*Water molecules are not included.

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PDB entries from 2025-06-11

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