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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
1A
(A)		25S Ribosomal RNApolymer33961097493.91GenBank (834774822)Saccharomyces cerevisiae
2B
(B)		5S Ribosomal RNApolymer12138951.11GenBank (1039024045)Saccharomyces cerevisiae
3C
(C)		5.8S Ribosomal RNApolymer15850682.91GenBank (1060743159)Saccharomyces cerevisiae
4D
(D)		60S ribosomal protein L2-Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
5E
(E)		60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
6F
(F)		60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,RP2,YL2
7G
(G)		60S ribosomal protein L5polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
8H
(H)		60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
9I
(I)		60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF00327)
Pfam (PF08079)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
10J
(J)		60S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
11K
(K)		60S ribosomal protein L9-Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
12L
(L)		60S ribosomal protein L10polymer22125410.51UniProt (P41805)
Pfam (PF00252)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
13M
(M)		60S ribosomal protein L11-Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,RP39,YL22
14N
(N)		60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
15O
(O)		60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16P
(a)		60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
17Q
(b)		60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
18R
(c)		60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
19S
(d)		60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
20T
(e)		60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
21U
(f)		60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
22V
(g)		60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
23W
(h)		60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
24X
(i)		60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
25Y
(j)		60S ribosomal protein L24-Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
26Z
(k)		60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
27AA
(l)		60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
28BA
(m)		60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
29CA
(n)		60S ribosomal protein L28polymer14916761.71UniProt (P02406)
Pfam (PF00828)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
30DA
(o)		60S ribosomal protein L29polymer596691.91UniProt (P05747)
Pfam (PF01779)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
31EA
(p)		60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
32FA
(q)		60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
33GA
(r)		60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
34HA
(s)		60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
35IA
(t)		60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
36JA
(u)		60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
37KA
(v)		60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
38LA
(w)		60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
39MA
(x)		60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
40NA
(y)		60S ribosomal protein L39polymer516358.61UniProt (P04650)
Pfam (PF00832)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
41OA
(z)		Ubiquitin-60S ribosomal protein L40polymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
42PA
(Q)		60S ribosomal protein L42-Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
43QA
(R)		60S ribosomal protein L43-Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
44RA
(S)		Ribosomal Protein uL1polymer21017890.01Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
45SA
(V)		Maltose binding protein, 60S ribosomal export protein Nmd3 fusionpolymer917103321.61UniProt (A0A0F8NYV9)
UniProt (P38861)
Pfam (PF01547)
Pfam (PF04981)
Pfam (PF21193)
Pfam (PF21192)		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nonsense-mediated mRNA decay protein 3
46AB, AC, AD, BB, BC...
(A, C, i)		MAGNESIUM IONnon-polymer24.386Chemie (MG)
47AE, BE, ZD
(A)		POTASSIUM IONnon-polymer39.13Chemie (K)
48EE, FE, GE
(A, c, e)		waterwater18.012Chemie (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 2025-06-11

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