3DQV: NEDD8

Name: PDB 3DQV: Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation
Published: 2008-09-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation. Determined by X-ray diffraction at 3.0 Å resolution. Released 30 Sept 2008.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 8,839
Mol. weight: 134.12 kDa
Ligands: ZN
Released: 30 Sept 2008

Explore 3DQV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DQV contains 48 α-helices and 58 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	101-107	7	1
β-strand	112-117	6	1
β-strand	122	1	2
α-helix	123-133	11
α-helix	138-140	3
β-strand	143-145	3	1
β-strand	148-149	2	1
α-helix	150-151	2
β-strand	155	1	2
β-strand	166-169	4	1

Chain B: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	101-106	6	11
β-strand	112-117	6	11
β-strand	122	1	12
α-helix	123-133	11
α-helix	138-140	3
β-strand	141-145	5	11
β-strand	148-149	2	11
α-helix	150-151	2
β-strand	155	1	12
α-helix	156-159	4
β-strand	166-171	6	11
α-helix	172	1

Chain C: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	1407-1416	10
β-strand	1417	1	3
α-helix	1420-1423	4
α-helix	1427-1440	14
α-helix	1441-1443	3
α-helix	1448-1463	16
β-strand	1467	1	3
α-helix	1470-1482	13
α-helix	1487-1512	26
α-helix	1523-1525	3
β-strand	1526-1527	2	4
β-strand	1530-1532	3	5
α-helix	1546-1548	3
α-helix	1549-1563	15
β-strand	1569-1573	5	5
β-strand	1579-1583	5	4
β-strand	1590-1596	7	4
α-helix	1597-1604	8
β-strand	1614-1615	2	6
α-helix	1616-1623	8
α-helix	1627-1638	12
β-strand	1648-1650	3	6
α-helix	1657-1659	3
β-strand	1665-1668	4	6
β-strand	1683-1687	5	4
α-helix	1695-1725	31
β-strand	1728-1729	2	7
α-helix	1731-1741	11
α-helix	1750-1762	13
β-strand	1766-1768	3	7
β-strand	1776-1778	3	7

Chain D: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	1405-1416	12
β-strand	1417	1	13
α-helix	1420-1424	5
α-helix	1427-1439	13
α-helix	1441-1443	3
α-helix	1447-1463	17
β-strand	1467	1	13
α-helix	1470-1482	13
α-helix	1487-1513	27
β-strand	1526-1532	7	14
α-helix	1549-1552	4
α-helix	1554-1563	10
β-strand	1569-1573	5	14
β-strand	1579-1585	7	14
β-strand	1590-1596	7	14
α-helix	1597-1604	8
β-strand	1613-1615	3	15
α-helix	1616-1623	8
α-helix	1627-1638	12
β-strand	1648-1650	3	15
β-strand	1665-1668	4	15
β-strand	1675	1	16
β-strand	1680	1	16
β-strand	1686-1687	2	14
α-helix	1695-1701	7
α-helix	1704-1724	21
β-strand	1728-1730	3	17
α-helix	1731-1741	11
α-helix	1750-1762	13
β-strand	1766-1768	3	17
β-strand	1775-1778	4	17

Chain R: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	24-28	5	4
β-strand	31-35	5	5
α-helix	36-38	3
β-strand	41	1	8
β-strand	48	1	8
α-helix	54-58	5
β-strand	73	1	9
α-helix	82-85	4
β-strand	93	1	10
β-strand	100	1	10
β-strand	103	1	9

Chain Y: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	22-35	14	14
α-helix	36-38	3
β-strand	41	1	18
β-strand	48	1	18
α-helix	55-58	4
α-helix	60	1
β-strand	70-71	2	19
β-strand	79-80	2	19
α-helix	82-85	4
β-strand	93	1	20
β-strand	100	1	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD8	A, B	protein	81	Homo sapiens	Q15843 (AlphaFold model)
Cullin-5	C, D	protein	382	Homo sapiens	Q93034 (AlphaFold model)
Rbx1	R, Y	protein	106	Homo sapiens	P62877 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3DQV_1 NEDD8 (chains A, B)
GSGGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKT
AADYKIMGGSVLHLVLALRGG

Sequence of entity 2 (C, D), FASTA

>3DQV_2 Cullin-5 (chains C, D)
GSESKCPEELANYCDMLLRKTPLSKKLTSEEIEAKLKEVLKKLKYVQNKDVFMRYHKAHL
TRRLILDISADSEIEENMVEWLREVGMPADYVNKLARMFQDIKVSEDLNQAFKEMHKNNK
LALPADSVNIKILNAGAWSRSSEKVFVSLPTELEDLIPEVEEFYKKNHSGRKLHWHHLMS
NGIITFKNEVGQYDLEVTTFQLAVLFAWNQRPREKISFENLKLATELPDAELRRTLWSLV
AFPKLKRQVLLYEPQVNSPKDFTEGTLFSVNQEFSLIKNAKVQKRGKINLIGRLQLTTER
MREEENEGIVQLRILRTQEAIIQIMKMRKKISNAQLQTELVEILKNMFLPQKKMIKEQIE
WLIEHKYIRRDESDINTFIYMA

Sequence of entity 3 (R, Y), FASTA

>3DQV_3 Rbx1 (chains R, Y)
GSMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQAS
ATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Duda, D.M., Borg, L.A., Scott, D.C. et al. Cell (2008) 134:995-1006. DOI 10.1016/j.cell.2008.07.022 · PubMed

Other PDB entries of the same protein (UniProt Q15843 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1NDD 1.6 Å, Structure of NEDD8
4FBJ 1.6 Å, Structure of the Cif:Nedd8 complex - Photorhabdus luminescens Cycle Inhibiting Factor in…
8WZN 1.8 Å, ParkinK211N in complex with phospho NEDD8
2BKR 1.9 Å, NEDD8 NEDP1 complex
4F8C 1.95 Å, Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor…
1XT9 2.2 Å, Crystal Structure of Den1 in complex with Nedd8
8WZO 2.25 Å, Parkin in complex with phospho NEDD8
4HCP 2.52 Å, crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8
8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
2NVU 2.8 Å, Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like…
3DBH 2.85 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…
3DBL 2.9 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…

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