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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

5T62

Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis: 60S-Nmd3-Tif6-Lsg1 Complex

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(X)		Eukaryotic translation initiation factor 6polymer26428598.01UniProt (Q12522)
Pfam (PF01912)		Saccharomyces cerevisiae S288CeIF-6
2B
(A)		TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequencepolymer33961097493.91GenBank (329138943)Saccharomyces cerevisiae S288C
3C
(B)		5S Ribosomal RNApolymer12138951.11GenBank (1039024045)Saccharomyces cerevisiae (brewer's yeast)
4D
(C)		5.8S Ribosomal RNApolymer15850682.91GenBank (1102645687)Saccharomyces cerevisiae (brewer's yeast)
5E
(D)		60S ribosomal protein L2-Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)		Saccharomyces cerevisiae S288CL5,RP8,YL6
6F
(E)		60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)		Saccharomyces cerevisiae S288CMaintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
7G
(F)		60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)		Saccharomyces cerevisiae S288CL2,RP2,YL2
8H
(G)		60S ribosomal protein L5polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)		Saccharomyces cerevisiae S288CL1,L1a,Ribosomal 5S RNA-binding protein,YL3
9I
(H)		60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)		Saccharomyces cerevisiae S288CL17,RP18,YL16
10J
(I)		60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF00327)
Pfam (PF08079)		Saccharomyces cerevisiae S288CL6,RP11,YL8
11K
(J)		60S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)		Saccharomyces cerevisiae S288CL4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
12L
(K)		60S ribosomal protein L9-Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)		Saccharomyces cerevisiae S288CL8,RP24,YL11
13M
(L)		60S ribosomal protein L10polymer22125410.51UniProt (P41805)
Pfam (PF00252)		Saccharomyces cerevisiae S288CL9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
14N
(M)		60S ribosomal protein L11-Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)		Saccharomyces cerevisiae S288CL16,RP39,YL22
15O
(N)		60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)		Saccharomyces cerevisiae S288C
16P
(O)		60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)		Saccharomyces cerevisiae S288C
17Q
(a)		60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)		Saccharomyces cerevisiae S288CL13,RP15R,YL10,YP18
18R
(b)		60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)		Saccharomyces cerevisiae S288CL13a,L21,RP22,YL15
19S
(c)		60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)		Saccharomyces cerevisiae S288CL20A,YL17
20T
(d)		60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)		Saccharomyces cerevisiae S288CRP28
21U
(e)		60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)		Saccharomyces cerevisiae S288CL23,RP15L,RP33,YL14
22V
(f)		60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)		Saccharomyces cerevisiae S288CL18a
23W
(g)		60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)		Saccharomyces cerevisiae S288C
24X
(h)		60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)		Saccharomyces cerevisiae S288CL1c,RP4,YL31
25Y
(i)		60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)		Saccharomyces cerevisiae S288CL17a,YL32
26Z
(j)		60S ribosomal protein L24-Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)		Saccharomyces cerevisiae S288CL30,RP29,YL21
27AA
(k)		60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)		Saccharomyces cerevisiae S288CRP16L,YL25,YP42'
28BA
(l)		60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)		Saccharomyces cerevisiae S288CL33,YL33
29CA
(m)		60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)		Saccharomyces cerevisiae S288C
30DA
(n)		60S ribosomal protein L28polymer14916761.71UniProt (P02406)
Pfam (PF00828)		Saccharomyces cerevisiae S288CL27a,L29,RP44,RP62,YL24
31EA
(o)		60S ribosomal protein L29polymer596691.91UniProt (P05747)
Pfam (PF01779)		Saccharomyces cerevisiae S288CYL43
32FA
(p)		60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)		Saccharomyces cerevisiae S288CL32,RP73,YL38
33GA
(q)		60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)		Saccharomyces cerevisiae S288CL34,YL28
34HA
(r)		60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)		Saccharomyces cerevisiae S288C
35IA
(s)		60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)		Saccharomyces cerevisiae S288CL37,RP47,YL37
36JA
(t)		60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)		Saccharomyces cerevisiae S288C
37KA
(u)		60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)		Saccharomyces cerevisiae S288C
38LA
(v)		60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)		Saccharomyces cerevisiae S288CL39,YL39
39MA
(w)		60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)		Saccharomyces cerevisiae S288CL43,YL35,YP55
40NA
(x)		60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)		Saccharomyces cerevisiae S288C
41OA
(y)		60S ribosomal protein L39polymer516358.61UniProt (P04650)
Pfam (PF00832)		Saccharomyces cerevisiae S288CL46,YL40
42PA
(z)		Ubiquitin-60S ribosomal protein L40polymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)		Saccharomyces cerevisiae S288C
43QA
(Q)		60S ribosomal protein L42-Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)		Saccharomyces cerevisiae S288CL41,YL27,YP44
44RA
(R)		60S ribosomal protein L43-Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)		Saccharomyces cerevisiae S288CL37a,YL35
45SA
(S)		Ribosomal Protein uL1polymer21718485.71Saccharomyces cerevisiae
46TA
(V)		60S ribosomal export protein NMD3polymer52459995.91UniProt (P38861)
Pfam (PF04981)
Pfam (PF21193)
Pfam (PF21192)		Saccharomyces cerevisiae S288CNonsense-mediated mRNA decay protein 3
47UA
(W)		Large subunit GTPase 1polymer65171945.91UniProt (P53145)
Pfam (PF01926)		Saccharomyces cerevisiae S288C
48AB, AC, AD, AE, AF...
(A, W, B, C, D...)		MAGNESIUM IONnon-polymer24.3160Chemie (MG)
49NG, OG
(A)		POTASSIUM IONnon-polymer39.12Chemie (K)
50AH
(W)		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTERnon-polymer522.21Chemie (GNP)
51CH, DH
(A, e)		waterwater18.06Chemie (HOH)
Sequence modifications
X: 1 - 245 (UniProt: Q12522)
PDBExternal DatabaseDetails
Met -18-initiating methionine
Gly -17-expression tag
Ser -16-expression tag
Ser -15-expression tag
His -14-expression tag
His -13-expression tag
His -12-expression tag
His -11-expression tag
His -10-expression tag
His -9-expression tag
Ser -8-expression tag
Leu -7-expression tag
Arg -6-expression tag
Arg -5-expression tag
Ala -4-expression tag
Ser -3-expression tag
Leu -2-expression tag
Gly -1-expression tag
Ser 0-expression tag
V: 1 - 518 (UniProt: P38861)
PDBExternal DatabaseDetails
His -5-expression tag
His -4-expression tag
His -3-expression tag
His -2-expression tag
His -1-expression tag
His 0-expression tag
W: -3 - 640 (UniProt: P53145)
PDBExternal DatabaseDetails
Unk 135Arg 139conflict
Unk 136Pro 140conflict
Unk 137Glu 141conflict
Unk 138Trp 142conflict
Unk 139Asn 143conflict
Unk 140Glu 144conflict
Unk 141Gly 145conflict
Unk 142Met 146conflict
Unk 143Ser 147conflict
Unk 144Lys 148conflict
Unk 145Phe 149conflict
Unk 146Gln 150conflict
Unk 147Leu 151conflict
Unk 148Asp 152conflict
Unk 149Arg 153conflict
Unk 150Gln 154conflict
Unk 151Glu 155conflict
Unk 152Lys 156conflict
Unk 153Glu 157conflict
Unk 154Ala 158conflict
Unk 155Phe 159conflict
Unk 156Leu 160conflict
Unk 157Glu 161conflict
Unk 158Trp 162conflict
Unk 159Arg 163conflict
Unk 160Arg 164conflict
Unk 161Lys 165conflict
Unk 162Leu 166conflict
Unk 163Ala 167conflict
Unk 164His 168conflict
Unk 165Leu 169conflict
Unk 166Gln 170conflict
Unk 167Glu 171conflict
Unk 168Ser 172conflict
Unk 169Asn 173conflict
Unk 170Glu 174conflict
Unk 171Asp 175conflict
Unk 172Leu 176conflict
Unk 173Leu 177conflict
Unk 174Leu 178conflict
Unk 175Thr 179conflict
Unk 276Leu 313conflict
Unk 277Glu 314conflict
Unk 278Glu 315conflict
Unk 279Leu 316conflict
Unk 280Phe 317conflict
Unk 281Leu 318conflict
Unk 282Ser 319conflict
Unk 283Lys 320conflict
Unk 284Ala 321conflict
Unk 285Pro 322conflict
Unk 286Asn 323conflict
Unk 287Glu 324conflict
Unk 288Pro 325conflict
Unk 289Leu 326conflict
Unk 290Leu 327conflict
Unk 291Pro 328conflict
Unk 292Pro 329conflict
Unk 293Leu 330conflict
Unk 294Pro 331conflict
Unk 295Gly 332conflict
Unk 296Gln 333conflict
Unk 297Pro 334conflict
Unk 298Pro 335conflict
Unk 299Leu 336conflict
Unk 504His 504conflict
Ala 641-expression tag
Ala 642-expression tag
Ala 643-expression tag
Leu 644-expression tag
Glu 645-expression tag
His 646-expression tag
His 647-expression tag
His 648-expression tag
His 649-expression tag
His 650-expression tag
His 651-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains47
Total formula weight2106404.4
Non-Polymers*Number of molecules163
Total formula weight4489.2
All*Total formula weight2110893.6
*Water molecules are not included.

246905

PDB entries from 2025-12-31

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