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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8V87

60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1125S ribosomal RNApolymer33961097493.91GenBank (2211412803)Saccharomyces cerevisiae BY4741
225.8S ribosomal RNApolymer15850682.91GenBank (1772891209)Saccharomyces cerevisiae BY4741
33ATP-dependent RNA helicase DBP10polymer995113126.51UniProt (Q12389)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF08147)
In PDB		Saccharomyces cerevisiae BY4741
46ITS2 RNApolymer23274308.41Saccharomyces cerevisiae BY4741
5760S ribosomal subunit assembly/export protein LOC1polymer20423652.61UniProt (P43586)
In PDB		Saccharomyces cerevisiae BY4741Localization of ASH1 mRNA protein 1
68Nucleolar complex protein 2polymer71081719.31UniProt (P39744)
Pfam (PF03715)
In PDB		Saccharomyces cerevisiae BY4741
7ARibosome biogenesis protein BRX1polymer29133585.41UniProt (Q08235)
Pfam (PF04427)
In PDB		Saccharomyces cerevisiae BY4741
8B60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein uL3,Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
9C60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Saccharomyces cerevisiae BY4741L2,Large ribosomal subunit protein uL4-A,RP2,YL2
10DATP-dependent RNA helicase HAS1polymer50556798.31UniProt (Q03532)
Pfam (PF00271)
Pfam (PF13959)
Pfam (PF00270)
In PDB		Saccharomyces cerevisiae BY4741Helicase associated with SET1 protein 1
11E60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae BY4741L17,Large ribosomal subunit protein eL6-A,RP18,YL16
12F60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae BY4741L6,Large ribosomal subunit protein uL30-A,RP11,YL8
13GLarge ribosomal subunit protein eL8Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae BY4741
14HLarge ribosomal subunit protein uL6Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae BY4741
15INucleolar complex-associated protein 3polymer66375689.01UniProt (Q07896)
Pfam (PF07540)
Pfam (PF03914)
In PDB		Saccharomyces cerevisiae BY4741
16JrRNA-processing protein EBP2polymer42749842.61UniProt (P36049)
Pfam (PF05890)
In PDB		Saccharomyces cerevisiae BY4741EBNA1-binding protein homolog
17KProteasome-interacting protein CIC1polymer37642596.71UniProt (P38779)
Pfam (PF00687)
In PDB		Saccharomyces cerevisiae BY4741
18L60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein eL13-A
19M60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein eL14-A
20NLarge ribosomal subunit protein eL15Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae BY4741
21OLarge ribosomal subunit protein uL13Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae BY4741
22P60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae BY4741L20A,Large ribosomal subunit protein uL22-A,YL17
23Q60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein eL18-A,RP28
24R60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae BY4741L23,Large ribosomal subunit protein eL19-A,RP15L,RP33,YL14
25SLarge ribosomal subunit protein eL20Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae BY4741
26U60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae BY4741L1c,Large ribosomal subunit protein eL22-A,RP4,YL31
27V60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae BY4741L17a,Large ribosomal subunit protein uL14-A,YL32
28WRibosome assembly factor MRT4polymer23627098.01UniProt (P33201)
Pfam (PF00466)
Pfam (PF17777)
In PDB		Saccharomyces cerevisiae BY4741
29X60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein uL23,RP16L,YL25,YP42'
30Y60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae BY4741L33,Large ribosomal subunit protein uL24-A,YL33
31Z60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein eL27-A
32aLarge ribosomal subunit protein uL1Apolymer21724524.81UniProt (P0CX43)
Pfam (PF00687)
In PDB		Saccharomyces cerevisiae BY4741
33bNucleolar GTP-binding protein 1polymer64774531.21UniProt (Q02892)
Pfam (PF17835)
Pfam (PF06858)
Pfam (PF08155)
In PDB		Saccharomyces cerevisiae BY4741
34c60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae BY4741L32,Large ribosomal subunit protein eL30,RP73,YL38
35d60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae BY4741L34,Large ribosomal subunit protein eL31-A,YL28
36e60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein eL32
37f60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae BY4741L37,Large ribosomal subunit protein eL33-A,RP47,YL37
38g60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein eL34-A
39h60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein uL29-A
40i60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae BY4741L39,Large ribosomal subunit protein eL36-A,YL39
41j60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae BY4741L43,Large ribosomal subunit protein eL37-A,YL35,YP55
42k60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae BY4741Large ribosomal subunit protein eL38
43l60S ribosome subunit biogenesis protein NIP7polymer18120411.71UniProt (Q08962)
Pfam (PF17833)
Pfam (PF03657)
In PDB		Saccharomyces cerevisiae BY4741
44mRibosome biogenesis protein ERB1polymer80791830.61UniProt (Q04660)
Pfam (PF08145)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae BY4741Eukaryotic ribosome biogenesis protein 1
45nPescadillo homologpolymer60569984.11UniProt (P53261)
Pfam (PF06732)
Pfam (PF16589)
In PDB		Saccharomyces cerevisiae BY4741Nucleolar protein 7,Ribosomal RNA-processing protein 13
46oRibosome biogenesis protein 15polymer22025499.21UniProt (P53927)
Pfam (PF00076)
In PDB		Saccharomyces cerevisiae BY4741Nucleolar protein 15
47pYTM1 isoform 1polymer46051426.61UniProt (A0A8H4BV53)
Pfam (PF08154)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae BY4741
48q25S rRNA (cytosine(2870)-C(5))-methyltransferasepolymer61869912.21UniProt (P40991)
Pfam (PF17125)
Pfam (PF01189)
In PDB		Saccharomyces cerevisiae BY4741Nucleolar protein 2
49rRibosome biogenesis protein NSA2polymer26129786.81UniProt (P40078)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae BY4741NOP7-associated protein 2
50sNuclear GTP-binding protein NUG1polymer52057798.71UniProt (P40010)
Pfam (PF08701)
Pfam (PF01926)
In PDB		Saccharomyces cerevisiae BY4741Nuclear GTPase 1
51tRibosome biogenesis protein RLP7polymer32236621.11UniProt (P40693)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae BY4741Ribosomal protein L7-like
52uRibosome biogenesis protein RLP24polymer19924027.71UniProt (Q07915)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae BY4741
53vNucleolar protein 16polymer23126954.41UniProt (P40007)
Pfam (PF09420)
In PDB		Saccharomyces cerevisiae BY4741
54w27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferasepolymer84196656.21UniProt (P25582)
Pfam (PF01728)
Pfam (PF11861)
Pfam (PF07780)
In PDB		Saccharomyces cerevisiae BY47412'-O-ribose RNA methyltransferase SPB1,AdoMet-dependent rRNA methyltransferase SPB1,S-adenosyl-L-methionine-dependent methyltransferase,Suppressor of PAB1 protein 1
55yEukaryotic translation initiation factor 6polymer24526476.61UniProt (Q12522)
Pfam (PF01912)
In PDB		Saccharomyces cerevisiae BY4741eIF-6
56zUPF0642 protein YBL028Cpolymer10612435.41UniProt (P38202)
Pfam (PF10338)
In PDB		Saccharomyces cerevisiae BY4741
573ADENOSINE-5'-DIPHOSPHATEnon-polymer427.21Chemie (ADP)
583, bMAGNESIUM IONnon-polymer24.32Chemie (MG)
59bGUANOSINE-5'-DIPHOSPHATEnon-polymer443.21Chemie (GDP)
60bPOTASSIUM IONnon-polymer39.11Chemie (K)
61g, jZINC IONnon-polymer65.42Chemie (ZN)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains56
Total formula weight2996631.6
Non-Polymers*Number of molecules7
Total formula weight1088.9
All*Total formula weight2997720.5
*Water molecules are not included.

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PDB entries from 2024-06-12

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