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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6EM5

State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of nucleolar pre-60S ribosomes

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
125.8S ribosomal RNApolymer15850682.91GenBank (1214879358)Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
26Internal Transcribed Spacer 2polymer23274308.41GenBank (1102641490)Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
3L60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL13-A
4M60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL14-A
5N60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,Large ribosomal subunit protein eL15-A,RP15R,YL10,YP18
6Q60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL18-A,RP28
7R60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14
8S60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a,Large ribosomal subunit protein eL20-A
9T60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL21-A
10U60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,Large ribosomal subunit protein eL22-A,RP4,YL31
11Z60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL27-A
12c60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,Large ribosomal subunit protein eL30,RP73,YL38
13d60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,Large ribosomal subunit protein eL31-A,YL28
14e60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL32
15f60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,Large ribosomal subunit protein eL33-A,RP47,YL37
16g60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL34-A
17i60S ribosomal protein L36-Bpolymer10011162.31UniProt (O14455)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,Large ribosomal subunit protein eL36-B,YL39
18j60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,Large ribosomal subunit protein eL37-A,YL35,YP55
19k60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein eL38
20E60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,Large ribosomal subunit protein eL6-A,RP18,YL16
21G60S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
In PDB		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
22O60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,Large ribosomal subunit protein uL13-A,RP22,YL15
23V60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,Large ribosomal subunit protein uL14-A,YL32
24X60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein uL23,RP16L,YL25,YP42'
25Y60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,Large ribosomal subunit protein uL24-A,YL33
26h60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein uL29-A
27B60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
28C60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,Large ribosomal subunit protein uL4-A,RP2,YL2
29H60S ribosomal protein L9-Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,Large ribosomal subunit protein uL6-A,RP24,YL11
30ARibosome biogenesis protein BRX1polymer29133585.41UniProt (Q08235)
Pfam (PF04427)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
31KProteasome-interacting protein CIC1polymer37642596.71UniProt (P38779)
Pfam (PF00687)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Core interacting component 1
32mRibosome biogenesis protein ERB1polymer80791830.61UniProt (Q04660)
Pfam (PF08145)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Eukaryotic ribosome biogenesis protein 1
33DATP-dependent RNA helicase HAS1polymer50556798.31UniProt (Q03532)
Pfam (PF13959)
Pfam (PF00270)
Pfam (PF00271)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Helicase associated with SET1 protein 1
34WRibosome assembly factor MRT4polymer23627098.01UniProt (P33201)
Pfam (PF00466)
Pfam (PF17777)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)mRNA turnover protein 4
35l60S ribosome subunit biogenesis protein NIP7polymer18120411.71UniProt (Q08962)
Pfam (PF17833)
Pfam (PF03657)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nuclear import protein 7
36bNucleolar GTP-binding protein 1polymer64774531.21UniProt (Q02892)
Pfam (PF17835)
Pfam (PF06858)
Pfam (PF08155)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
37oRibosome biogenesis protein 15polymer22025499.21UniProt (P53927)
Pfam (PF00076)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleolar protein 15
38nPescadillo homologpolymer60569984.11UniProt (P53261)
Pfam (PF06732)
Pfam (PF16589)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleolar protein 7,Ribosomal RNA-processing protein 13
39rRibosome biogenesis protein NSA2polymer26129786.81UniProt (P40078)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)NOP7-associated protein 2
40sNuclear GTP-binding protein NUG1polymer52057798.71UniProt (P40010)
Pfam (PF08701)
Pfam (PF01926)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nuclear GTPase 1
41tRibosome biogenesis protein RLP7polymer32236621.11UniProt (P40693)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal protein L7-like
42yEukaryotic translation initiation factor 6polymer24526476.61UniProt (Q12522)
Pfam (PF01912)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)eIF-6
43zUPF0642 protein YBL028Cpolymer10612435.41UniProt (P38202)
Pfam (PF10338)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
44pRibosome biogenesis protein YTM1polymer46051426.61UniProt (Q12024)
Pfam (PF08154)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Microtubule-associated protein YTM1
45q25S rRNA (cytosine(2870)-C(5))-methyltransferasepolymer61869912.21UniProt (P40991)
Pfam (PF01189)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleolar protein 2
46uRibosome biogenesis protein RLP24polymer19924027.71UniProt (Q07915)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosomal protein L24-like
47vNucleolar protein 16polymer23126954.41UniProt (P40007)
Pfam (PF09420)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
48w27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferasepolymer84196656.21UniProt (P25582)
Pfam (PF01728)
Pfam (PF11861)
Pfam (PF07780)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)2'-O-ribose RNA methyltransferase SPB1,AdoMet-dependent rRNA methyltransferase SPB1,S-adenosyl-L-methionine-dependent methyltransferase,Suppressor of PAB1 protein 1
49INucleolar complex-associated protein 3polymer66375689.01UniProt (Q07896)
Pfam (PF07540)
Pfam (PF03914)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
50JrRNA-processing protein EBP2polymer42749842.61UniProt (P36049)
Pfam (PF05890)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)EBNA1-binding protein homolog
51xRibosome production factor 1polymer29535184.41UniProt (P38805)
Pfam (PF04427)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Ribosome biogenesis protein RPF1
523Protein MAK16polymer30635754.61UniProt (P10962)
Pfam (PF01778)
Pfam (PF04874)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Maintenance of killer protein 16
534Ribosomal RNA-processing protein 1polymer27833250.51UniProt (P35178)
Pfam (PF05997)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
545Ribosome biogenesis protein NSA1polymer46351982.51UniProt (P53136)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)NOP7-associated protein 1
55125S ribosomal RNApolymer33961097493.91GenBank (834774822)Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
56F60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,Large ribosomal subunit protein uL30-A,RP11,YL8
57P60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,Large ribosomal subunit protein uL22-A,YL17
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains57
Total formula weight2928070.6
All*Total formula weight2928070.6
*Water molecules are not included.

222624

PDB entries from 2024-07-17

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