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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
1XEukaryotic translation initiation factor 6polymer26428598.01UniProt (Q12522)
Pfam (PF01912)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)eIF-6
2A25S Ribosomal RNApolymer33961097493.91REF (831416132)Saccharomyces cerevisiae S288c
3B5S Ribosomal RNApolymer12138951.11GenBank (1039024045)Saccharomyces cerevisiae
4C5.8S Ribosomal RNApolymer15850682.91GenBank (1102645687)Saccharomyces cerevisiae
5D60S ribosomal protein L2-Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
6E60S 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
7F60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,RP2,YL2
8G60S 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
9H60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
10I60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF00327)
Pfam (PF08079)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
11J60S 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
12K60S ribosomal protein L9-Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
13L60S 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
14M60S ribosomal protein L11-Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,RP39,YL22
15N60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16O60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
17a60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
18b60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
19c60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
20d60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
21e60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
22f60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
23g60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
24h60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
25i60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
26j60S ribosomal protein L24-Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
27k60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
28l60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
29m60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
30n60S ribosomal protein L28polymer14916761.71UniProt (P02406)
Pfam (PF00828)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
31o60S ribosomal protein L29polymer596691.91UniProt (P05747)
Pfam (PF01779)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
32p60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
33q60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
34r60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
35s60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
36t60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
37u60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
38v60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
39w60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
40x60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
41y60S ribosomal protein L39polymer516358.61UniProt (P04650)
Pfam (PF00832)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
42zUbiquitin-60S ribosomal protein L40polymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
43Q60S ribosomal protein L42-Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
44R60S ribosomal protein L43-Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
45SRibosomal Protein uL1polymer21718485.71Saccharomyces cerevisiae
46V60S ribosomal export protein NMD3polymer52459995.91UniProt (P38861)
Pfam (PF04981)
Pfam (PF21193)
Pfam (PF21192)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nonsense-mediated mRNA decay protein 3
47WLarge subunit GTPase 1polymer65171945.91UniProt (P53145)
Pfam (PF01926)
In PDB		Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
48A, W, B, C, D...MAGNESIUM IONnon-polymer24.3160Chemie (MG)
49APOTASSIUM IONnon-polymer39.12Chemie (K)
50WPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTERnon-polymer522.21Chemie (GNP)
51waterwater18.06Chemie (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 139see remark 999
Unk 136Pro 140see remark 999
Unk 137Glu 141see remark 999
Unk 138Trp 142see remark 999
Unk 139Asn 143see remark 999
Unk 140Glu 144see remark 999
Unk 141Gly 145see remark 999
Unk 142Met 146see remark 999
Unk 143Ser 147see remark 999
Unk 144Lys 148see remark 999
Unk 145Phe 149see remark 999
Unk 146Gln 150see remark 999
Unk 147Leu 151see remark 999
Unk 148Asp 152see remark 999
Unk 149Arg 153see remark 999
Unk 150Gln 154see remark 999
Unk 151Glu 155see remark 999
Unk 152Lys 156see remark 999
Unk 153Glu 157see remark 999
Unk 154Ala 158see remark 999
Unk 155Phe 159see remark 999
Unk 156Leu 160see remark 999
Unk 157Glu 161see remark 999
Unk 158Trp 162see remark 999
Unk 159Arg 163see remark 999
Unk 160Arg 164see remark 999
Unk 161Lys 165see remark 999
Unk 162Leu 166see remark 999
Unk 163Ala 167see remark 999
Unk 164His 168see remark 999
Unk 165Leu 169see remark 999
Unk 166Gln 170see remark 999
Unk 167Glu 171see remark 999
Unk 168Ser 172see remark 999
Unk 169Asn 173see remark 999
Unk 170Glu 174see remark 999
Unk 171Asp 175see remark 999
Unk 172Leu 176see remark 999
Unk 173Leu 177see remark 999
Unk 174Leu 178see remark 999
Unk 175Thr 179see remark 999
Unk 276Leu 313see remark 999
Unk 277Glu 314see remark 999
Unk 278Glu 315see remark 999
Unk 279Leu 316see remark 999
Unk 280Phe 317see remark 999
Unk 281Leu 318see remark 999
Unk 282Ser 319see remark 999
Unk 283Lys 320see remark 999
Unk 284Ala 321see remark 999
Unk 285Pro 322see remark 999
Unk 286Asn 323see remark 999
Unk 287Glu 324see remark 999
Unk 288Pro 325see remark 999
Unk 289Leu 326see remark 999
Unk 290Leu 327see remark 999
Unk 291Pro 328see remark 999
Unk 292Pro 329see remark 999
Unk 293Leu 330see remark 999
Unk 294Pro 331see remark 999
Unk 295Gly 332see remark 999
Unk 296Gln 333see remark 999
Unk 297Pro 334see remark 999
Unk 298Pro 335see remark 999
Unk 299Leu 336see remark 999
Unk 504His 504see remark 999
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.

218853

PDB entries from 2024-04-24

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