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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8I9Y

Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(C1)		RNA (3341-MER)polymer33411079977.11Chaetomium thermophilum
2B
(C2)		RNA (319-MER)polymer319102607.41Chaetomium thermophilum
3C
(CA)		Brix domain-containing proteinpolymer31636482.01UniProt (G0RXZ3)
Pfam (PF04427)		Chaetomium thermophilum
4D
(CB)		Ribosome biogenesis protein C8F11.04polymer39143700.51UniProt (G0S7X0)
Pfam (PF00687)		Chaetomium thermophilum
5E
(CC)		Ribosome biogenesis protein ERB1polymer80190998.01UniProt (G0SCK6)
Pfam (PF08145)
Pfam (PF00400)		Chaetomium thermophilumEukaryotic ribosome biogenesis protein 1
6F
(CD)		Ribosome biogenesis protein YTM1polymer49552989.21UniProt (G0SFB5)
Pfam (PF00400)
Pfam (PF08154)		Chaetomium thermophilum
7G
(CE)		RNA helicasepolymer59866830.91UniProt (G0RYU9)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF13959)		Chaetomium thermophilum
8H
(CF)		Ribosome assembly factor mrt4polymer27030551.51UniProt (G0S616)
Pfam (PF00466)
Pfam (PF17777)		Chaetomium thermophilummRNA turnover protein 4
9I
(CG)		60S ribosome subunit biogenesis protein NIP7polymer18420686.01UniProt (G0S435)
Pfam (PF17833)
Pfam (PF03657)		Chaetomium thermophilum
10J
(CH)		Nucleolar GTP-binding protein 1polymer66175621.51UniProt (G0S8F1)
Pfam (PF17835)
Pfam (PF06858)
Pfam (PF08155)		Chaetomium thermophilum
11K
(CI)		Putative RNA-binding proteinpolymer41445884.41UniProt (G0S1H0)
Pfam (PF00076)		Chaetomium thermophilum
12L
(CJ)		Pescadillo homologpolymer67977167.31UniProt (G0SHX6)
Pfam (PF06732)
Pfam (PF00533)		Chaetomium thermophilumNucleolar protein 7 homolog
13M
(CK)		Ribosome biogenesis protein NSA2 homologpolymer26129724.61UniProt (G0S081)
Pfam (PF01201)		Chaetomium thermophilum
14N
(CL)		Putative GTP binding proteinpolymer55861523.91UniProt (G0SEW3)
Pfam (PF08701)
Pfam (PF01926)		Chaetomium thermophilum
15EA, O
(CM, LF)		60S ribosomal protein l7-like proteinpolymer24928821.82UniProt (G0SFL0)
Pfam (PF08079)
Pfam (PF00327)		Chaetomium thermophilum
16P
(CN)		Eukaryotic translation initiation factor 6polymer24626468.81UniProt (G0S683)
Pfam (PF01912)		Chaetomium thermophilum
17Q
(CO)		DUF2423 domain-containing proteinpolymer12013262.41UniProt (G0SHK0)
Pfam (PF10338)		Chaetomium thermophilum
18R
(CP)		RNA methyltransferase nop2-like proteinpolymer75183658.31UniProt (G0SHQ0)
Pfam (PF22458)
Pfam (PF01189)		Chaetomium thermophilum
19S
(CQ)		Ribosome biogenesis protein RLP24polymer22526434.31UniProt (G0S497)
Pfam (PF01246)		Chaetomium thermophilum
20T
(CR)		Nucleolar protein 16polymer23726960.51UniProt (G0S832)
Pfam (PF09420)		Chaetomium thermophilum
21U
(CS)		AdoMet-dependent rRNA methyltransferase SPB1polymer83495511.01UniProt (G0SGD8)
Pfam (PF01728)
Pfam (PF11861)
Pfam (PF07780)		Chaetomium thermophilum
22V
(CT)		Nucleolar complex-associated protein 3polymer68877953.91UniProt (G0S5L0)
Pfam (PF07540)
Pfam (PF03914)		Chaetomium thermophilum
23W
(CU)		rRNA-processing protein EBP2polymer45150255.61UniProt (G0SGC2)
Pfam (PF05890)		Chaetomium thermophilum
24X
(CV)		Putative 60S ribosomal proteinpolymer14715960.51UniProt (G0SHJ6)
Pfam (PF01778)		Chaetomium thermophilum
25Y
(CX)		60S ribosomal subunit-like proteinpolymer20322678.61UniProt (G0SGJ0)Chaetomium thermophilum
26Z
(CY)		Putative NOC2 family proteinpolymer78889766.21UniProt (G0SD05)
Pfam (PF03715)		Chaetomium thermophilum
27AA
(Cz)		rRNA-processing proteinpolymer12314710.41UniProt (G0SCP3)
Pfam (PF03879)		Chaetomium thermophilum
28BA
(LB)		60S ribosomal protein L3-like proteinpolymer39244456.91UniProt (G0RXW1)
Pfam (PF00297)		Chaetomium thermophilum
29CA
(LC)		60S ribosomal protein L4-like proteinpolymer36539439.91UniProt (G0SFC3)
Pfam (PF00573)
Pfam (PF14374)		Chaetomium thermophilum
30DA
(LE)		60S ribosomal protein L6polymer20022133.01UniProt (G0S0D6)
Pfam (PF01159)		Chaetomium thermophilum
31FA
(LG)		60S ribosomal protein L8polymer26229744.51UniProt (G0SAJ9)
Pfam (PF01248)		Chaetomium thermophilum
32GA
(LH)		60S ribosomal protein l9-like proteinpolymer19221582.11UniProt (G0S0E5)
Pfam (PF00347)		Chaetomium thermophilum
33HA
(LK)		60S ribosomal protein L12-like proteinpolymer16517802.71UniProt (G0SGH8)
Pfam (PF03946)
Pfam (PF00298)		Chaetomium thermophilum
34IA
(LL)		60S ribosomal protein L13polymer21324191.21UniProt (G0S992)
Pfam (PF01294)		Chaetomium thermophilum
35JA
(LM)		60S ribosomal protein L14-like proteinpolymer14216111.91UniProt (G0S1R0)
Pfam (PF01929)		Chaetomium thermophilum
36KA
(LN)		Ribosomal protein L15polymer20324307.31UniProt (G0RZ88)
Pfam (PF00827)		Chaetomium thermophilum
37LA
(LO)		60S ribosomal protein L16-like proteinpolymer20422993.21UniProt (G0SH61)
Pfam (PF00572)		Chaetomium thermophilum
38MA
(LP)		60S ribosomal protein l17-like proteinpolymer18721072.21UniProt (G0SGY1)
Pfam (PF00237)		Chaetomium thermophilum
39NA
(LQ)		Ribosomal protein L18-like proteinpolymer21324195.51UniProt (G0S9B5)
Pfam (PF17135)		Chaetomium thermophilum
40OA
(LR)		Ribosomal protein L19polymer2898317092.31UniProt (G0S9T3)
Pfam (PF12074)
Pfam (PF13513)
Pfam (PF21040)
Pfam (PF10274)
Pfam (PF01280)		Chaetomium thermophilum
41PA
(LS)		60S ribosomal protein L20polymer17420341.91UniProt (G0SCE2)
Pfam (PF01775)		Chaetomium thermophilum
42QA
(LT)		60S ribosomal protein l21-like proteinpolymer16018159.21UniProt (G0S0Z3)
Pfam (PF01157)		Chaetomium thermophilum
43RA
(LU)		60S ribosomal protein L22-like proteinpolymer12714302.61UniProt (G0SDS8)
Pfam (PF01776)		Chaetomium thermophilum
44SA
(LV)		60S ribosomal protein l23-like proteinpolymer13914674.41UniProt (G0SI44)
Pfam (PF00238)		Chaetomium thermophilum
45TA
(LX)		60S ribosomal protein L25-like proteinpolymer15617175.31UniProt (G0S507)
Pfam (PF03939)
Pfam (PF00276)		Chaetomium thermophilum
46UA
(LY)		60S ribosomal protein L26-like proteinpolymer13815565.31UniProt (G0RYN9)
Pfam (PF16906)
Pfam (PF00467)		Chaetomium thermophilum
47VA
(LZ)		60S ribosomal protein L27polymer13515803.71UniProt (G0RZE9)
Pfam (PF01777)		Chaetomium thermophilum
48WA
(Lc)		60S ribosomal protein l30-like proteinpolymer10811602.61UniProt (G0SEI0)
Pfam (PF01248)		Chaetomium thermophilum
49XA
(Ld)		Putative 60S ribosomal proteinpolymer12013872.21UniProt (G0SD68)
Pfam (PF01198)		Chaetomium thermophilum
50YA
(Le)		60S ribosomal protein L32-like proteinpolymer13115096.01UniProt (G0S6V4)
Pfam (PF01655)		Chaetomium thermophilum
51ZA
(Lf)		60S ribosomal protein l33-like proteinpolymer10912330.31UniProt (G0SCL3)
Pfam (PF01247)		Chaetomium thermophilum
52AB
(Lg)		Ribosomal protein l34-like proteinpolymer11913493.01UniProt (G0SFN0)
Pfam (PF01199)		Chaetomium thermophilum
53BB
(Lh)		dolichyl-diphosphooligosaccharide--protein glycotransferasepolymer935105169.21UniProt (G0S0D7)
Pfam (PF00831)
Pfam (PF02516)
Pfam (PF21436)		Chaetomium thermophilum
54CB
(Li)		60S ribosomal protein L36polymer11012784.11UniProt (G0SBN1)
Pfam (PF01158)		Chaetomium thermophilum
55DB
(Lj)		Ribosomal protein L37polymer9510660.51UniProt (G0S101)
Pfam (PF01907)		Chaetomium thermophilum
56EB
(Lk)		60S ribosomal protein L38-like proteinpolymer819521.31UniProt (G0SG89)
Pfam (PF01781)		Chaetomium thermophilum
57FB
(Ll)		60S ribosomal protein L39polymer516297.51UniProt (Q2H9R2)
Pfam (PF00832)		Chaetomium thermophilum
58GB
(Lq)		Ribosomal proteinpolymer21724055.31UniProt (G0S4Z9)
Pfam (PF00687)		Chaetomium thermophilum
59HB
(CH)		GUANOSINE-5'-TRIPHOSPHATEnon-polymer523.21Chemie (GTP)
60IB, JB
(CQ, Lj)		ZINC IONnon-polymer65.42Chemie (ZN)
Sequence modifications
CD: 1 - 495 (UniProt: G0SFB5)
PDBExternal DatabaseDetails
Asp 88Glu 88conflict
CE: 1 - 598 (UniProt: G0RYU9)
PDBExternal DatabaseDetails
Lys 543-insertion
Ser 544-insertion
Phe 545-insertion
Gly 546-insertion
Phe 547-insertion
Ser 548-insertion
Thr 549-insertion
Pro 550-insertion
Pro 551-insertion
Arg 552-insertion
Val 553-insertion
Asp 554-insertion
Ile 555-insertion
Thr 556-insertion
Leu 557-insertion
Ser 558-insertion
Ala 559-insertion
Ser 560-insertion
Leu 561-insertion
Ser 562-insertion
Arg 563-insertion
Asp 564-insertion
Lys 565-insertion
Lys 566-insertion
Pro 567-insertion
Gln 568-insertion
Gly 569-insertion
Arg 570-insertion
Arg 571-insertion
Ala 572-insertion
Tyr 573-insertion
Gly 574-insertion
Ser 575-insertion
Gln 576-insertion
Pro 577-insertion
Arg 578-insertion
Gln 579-insertion
Gly 580-insertion
Gly 581-insertion
Arg 582-insertion
Tyr 583-insertion
Lys 584-insertion
CF: 1 - 270 (UniProt: G0S616)
PDBExternal DatabaseDetails
Ile 13Thr 13conflict
Thr 139Pro 139conflict
Asn 228Ser 228conflict
Ile 259Met 259conflict
CL: 1 - 558 (UniProt: G0SEW3)
PDBExternal DatabaseDetails
Arg 69Ile 69conflict
LH: 1 - 192 (UniProt: G0S0E5)
PDBExternal DatabaseDetails
-Gly 16deletion
-Thr 17deletion
-Phe 18deletion
-Arg 19deletion
-Lys 20deletion
-Phe 21deletion
-Arg 22deletion
-Arg 23deletion
-Asn 24deletion
-Asp 25deletion
-Tyr 26deletion
-Thr 27deletion
-Phe 28deletion
-Gly 29deletion
-Arg 30deletion
-Thr 31deletion
-Arg 32deletion
-Gly 33deletion
-Arg 34deletion
-Glu 35deletion
-Lys 36deletion
-Lys 37deletion
-Arg 38deletion
-Gly 39deletion
-Thr 40deletion
-Thr 41deletion
-Ser 42deletion
-Ser 43deletion
-Lys 44deletion
-Ile 45deletion
-Gly 46deletion
-Glu 47deletion
-Leu 48deletion
-Asp 49deletion
-Ile 50deletion
-Asn 51deletion
-Gly 52deletion
Lk: 1 - 81 (UniProt: G0SG89)
PDBExternal DatabaseDetails
-Ser 22deletion
-Lys 23deletion
-Ile 24deletion
-Leu 25deletion
-Thr 26deletion
-Ile 27deletion
-Ala 28deletion
-Phe 29deletion
-Pro 30deletion
-Pro 31deletion
-Pro 32deletion
-Leu 33deletion
-Thr 34deletion
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains59
Total formula weight3392035.6
Non-Polymers*Number of molecules3
Total formula weight654.0
All*Total formula weight3392689.6
*Water molecules are not included.

239149

PDB entries from 2025-07-23

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