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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)
Pfam (PF25476)		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)
PubChem (177679032)
PubChem (135400627)
PubChem (135487750)
PubChem (136088935)
PubChem (136803486)
PubChem (135398633)
PubChem (135544356)
PubChem (135547949)
PubChem (135600366)
PubChem (135749822)
PubChem (136005188)
PubChem (136073923)
PubChem (136240914)
PubChem (136664747)
PubChem (136772743)
PubChem (136772744)
PubChem (136803487)
PubChem (137286749)
PubChem (164715984)
PubChem (171699466)
60HB, KB
(b, m)		MAGNESIUM IONnon-polymer24.32Chemie (MG)
PubChem (888)
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.

251801

PDB entries from 2026-04-08

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