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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5T6R

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3 Complex

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A25S Ribosomal RNApolymer33961097493.91GenBank (834774822)Saccharomyces cerevisiae
2B5S Ribosomal RNApolymer12138951.11GenBank (1039024045)Saccharomyces cerevisiae
3C5.8S Ribosomal RNApolymer15850682.91GenBank (1060743159)Saccharomyces cerevisiae
4D60S ribosomal protein L2-Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
5E60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
6F60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,RP2,YL2
7G60S ribosomal protein L5polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
8H60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
9I60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF00327)
Pfam (PF08079)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
10J60S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
11K60S ribosomal protein L9-Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
12L60S ribosomal protein L10polymer22125410.51UniProt (P41805)
Pfam (PF00252)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
13M60S ribosomal protein L11-Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,RP39,YL22
14N60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
15O60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16a60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
17b60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
18c60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
19d60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
20e60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
21f60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
22g60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
23h60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
24i60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
25j60S ribosomal protein L24-Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
26k60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
27l60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
28m60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
29n60S ribosomal protein L28polymer14916761.71UniProt (P02406)
Pfam (PF00828)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
30o60S ribosomal protein L29polymer596691.91UniProt (P05747)
Pfam (PF01779)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
31p60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
32q60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
33r60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
34s60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
35t60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
36u60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
37v60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
38w60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
39x60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
40y60S ribosomal protein L39polymer516358.61UniProt (P04650)
Pfam (PF00832)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
41zUbiquitin-60S ribosomal protein L40polymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
42Q60S ribosomal protein L42-Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
43R60S ribosomal protein L43-Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
44SRibosomal Protein uL1polymer21017890.01Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
45VMaltose binding protein, 60S ribosomal export protein Nmd3 fusionpolymer917103321.61UniProt (A0A0F8NYV9)
UniProt (P38861)
Pfam (PF01547)
Pfam (PF04981)
Pfam (PF21193)
Pfam (PF21192)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nonsense-mediated mRNA decay protein 3
46A, C, iMAGNESIUM IONnon-polymer24.386Chemie (MG)
47APOTASSIUM IONnon-polymer39.13Chemie (K)
48waterwater18.012Chemie (HOH)
Sequence modifications
V: -398 - -16 (UniProt: A0A0F8NYV9)
PDBExternal DatabaseDetails
Ile -396Thr 3conflict
His -15-linker
His -14-linker
His -13-linker
His -12-linker
His -11-linker
His -10-linker
His -9-linker
His -8-linker
His -7-linker
His -6-linker
Glu -5-linker
Asn -4-linker
Leu -3-linker
Tyr -2-linker
Phe -1-linker
Gln 0-linker
Gly 1-linker
V: 2 - 518 (UniProt: P38861)
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains45
Total formula weight2048590.5
Non-Polymers*Number of molecules89
Total formula weight2207.5
All*Total formula weight2050798.0
*Water molecules are not included.

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PDB entries from 2024-04-17

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