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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6D6R

Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(A)		Exosome complex component RRP45polymer47352828.01UniProt (Q06265)
Pfam (PF01138)
Pfam (PF03725)		Homo sapiens (Human)EXOSC9,Autoantigen PM/Scl 1,Exosome component 9,P75 polymyositis-scleroderma overlap syndrome-associated autoantigen,Polymyositis/scleroderma autoantigen 1,Polymyositis/scleroderma autoantigen 75 kDa,PM/Scl-75
2B
(B)		Exosome complex component RRP41polymer24926831.51UniProt (Q9NPD3)
Pfam (PF01138)
Pfam (PF03725)		Homo sapiens (Human)EXOSC4,Exosome component 4,Ribosomal RNA-processing protein 41,p12A
3C
(C)		Exosome complex component RRP43polymer27830285.81UniProt (Q96B26)
Pfam (PF01138)
Pfam (PF03725)		Homo sapiens (Human)EXOSC8,Exosome component 8,Opa-interacting protein 2,OIP-2,Ribosomal RNA-processing protein 43,p9
4D
(D)		Exosome complex component RRP46polymer23725480.21UniProt (Q9NQT4)
Pfam (PF01138)
Pfam (PF03725)		Homo sapiens (Human)EXOSC5,Chronic myelogenous leukemia tumor antigen 28,Exosome component 5,Ribosomal RNA-processing protein 46,p12B
5E
(E)		Exosome complex component RRP42polymer29332072.61UniProt (Q15024)
Pfam (PF03725)
Pfam (PF01138)		Homo sapiens (Human)EXOSC7,Exosome component 7,Ribosomal RNA-processing protein 42,p8
6F
(F)		Exosome complex component MTR3polymer27228267.11UniProt (Q5RKV6)
Pfam (PF01138)		Homo sapiens (Human)EXOSC6,Exosome component 6,mRNA transport regulator 3 homolog,hMtr3,p11
7G
(G)		Exosome complex component RRP40polymer27729796.41UniProt (Q9NQT5)
Pfam (PF21261)
Pfam (PF21262)
Pfam (PF15985)		Homo sapiens (Human)EXOSC3,Exosome component 3,Ribosomal RNA-processing protein 40,p10
8H
(H)		Exosome complex component RRP4polymer29633184.41UniProt (Q13868)
Pfam (PF14382)
Pfam (PF21266)
Pfam (PF15985)		Homo sapiens (Human)EXOSC2,Exosome component 2,Ribosomal RNA-processing protein 4
9I
(I)		Exosome complex component CSL4polymer19721691.01UniProt (Q9Y3B2)
Pfam (PF14382)
Pfam (PF10447)		Homo sapiens (Human)EXOSC1,Exosome component 1
10J
(J)		Exosome component 10polymer76186754.91UniProt (Q01780)
Pfam (PF08066)
Pfam (PF01612)
Pfam (PF00570)		Homo sapiens (Human)EXOSC10,Autoantigen PM/Scl 2,P100 polymyositis-scleroderma overlap syndrome-associated autoantigen,Polymyositis/scleroderma autoantigen 100 kDa,PM/Scl-100,Polymyositis/scleroderma autoantigen 2
11K
(K)		Exosome complex exonuclease RRP44polymer960109267.91UniProt (Q9Y2L1)
Pfam (PF13638)
Pfam (PF17216)
Pfam (PF17849)
Pfam (PF00773)
Pfam (PF17215)		Homo sapiens (Human)DIS3,Protein DIS3 homolog,Ribosomal RNA-processing protein 44
12L
(L)		M-phase phosphoprotein 6polymer16219268.01UniProt (Q99547)
Pfam (PF10175)		Homo sapiens (Human)MPP6, MPHOSPH6
13M
(M)		Exosome RNA helicase MTR4polymer1045118225.01UniProt (P42285)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF21408)
Pfam (PF13234)
Pfam (PF08148)		Homo sapiens (Human)MTR4, MTREX,ATP-dependent RNA helicase DOB1,ATP-dependent RNA helicase SKIV2L2,Superkiller viralicidic activity 2-like 2,TRAMP-like complex helicase
14N
(N)		RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')polymer165143.21synthetic construct
15O
(O)		DNA/RNA (62-MER)polymer6219487.11synthetic construct
16P
(K)		ZINC IONnon-polymer65.41Chemie (ZN)
17Q
(K)		MAGNESIUM IONnon-polymer24.31Chemie (MG)
18R
(M)		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTERnon-polymer506.21Chemie (ANP)
Sequence modifications
A: 1 - 456 (UniProt: Q06265)
PDBExternal DatabaseDetails
Met -16-expression tag
Gly -15-expression tag
Ser -14-expression tag
Ser -13-expression tag
His -12-expression tag
His -11-expression tag
His -10-expression tag
His -9-expression tag
His -8-expression tag
His -7-expression tag
Ser -6-expression tag
Gln -5-expression tag
Asp -4-expression tag
Pro -3-expression tag
Asn -2-expression tag
Ser -1-expression tag
His 0-expression tag
B: 0 - 244 (UniProt: Q9NPD3)
PDBExternal DatabaseDetails
Met -4-expression tag
Ala -3-expression tag
Asp -2-expression tag
Pro -1-expression tag
C: 1 - 276 (UniProt: Q96B26)
PDBExternal DatabaseDetails
Asp -1-expression tag
Pro 0-expression tag
D: 1 - 235 (UniProt: Q9NQT4)
PDBExternal DatabaseDetails
Ser -1-expression tag
Leu 0-expression tag
E: 1 - 291 (UniProt: Q15024)
PDBExternal DatabaseDetails
Asp -1-expression tag
Pro 0-expression tag
G: 1 - 275 (UniProt: Q9NQT5)
PDBExternal DatabaseDetails
Asp -1-expression tag
Pro 0-expression tag
His 225Tyr 225variant
H: 1 - 293 (UniProt: Q13868)
PDBExternal DatabaseDetails
Asp -2-expression tag
Pro -1-expression tag
His 0-expression tag
I: 1 - 195 (UniProt: Q9Y3B2)
PDBExternal DatabaseDetails
Asp -1-expression tag
Pro 0-expression tag
J: 1 - 648 (UniProt: Q01780)
PDBExternal DatabaseDetails
Ser 0-expression tag
Asn 313Asp 313engineered mutation
J: 661 - 760 (UniProt: Q01780)
PDBExternal DatabaseDetails
Ser 649-linker
Arg 650-linker
Gly 651-linker
Ser 652-linker
Gly 653-linker
Ser 654-linker
Gly 655-linker
Ser 656-linker
Gly 657-linker
Ser 658-linker
Gly 659-linker
Ser 660-linker
K: 1 - 958 (UniProt: Q9Y2L1)
PDBExternal DatabaseDetails
Gly -1-expression tag
Ser 0-expression tag
Asn 146Asp 146engineered mutation
Ser 269Asn 269variant
Asn 487Asp 487engineered mutation
Asn 843Lys 843variant
L: 1 - 160 (UniProt: Q99547)
PDBExternal DatabaseDetails
Asp -1-expression tag
Pro 0-expression tag
M: 1 - 1042 (UniProt: P42285)
PDBExternal DatabaseDetails
Ser -2-expression tag
Gly -1-expression tag
Asp 0-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains15
Total formula weight638582.9
Non-Polymers*Number of molecules3
Total formula weight595.9
All*Total formula weight639178.8
*Water molecules are not included.

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PDB entries from 2026-01-28

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