2NVU: NEDD8-activating enzyme E1 regulatory subunit

Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex. Determined by X-ray diffraction at 2.8 Å resolution. Released 30 Jan 2007.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 13,090
Mol. weight: 188.89 kDa
Ligands: MG, ZN, ATP
Released: 30 Jan 2007

Explore 2NVU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NVU contains 91 α-helices and 84 β-strands across 5 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: 33 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	14-29	16
β-strand	32-36	5	1
α-helix	40-50	11
β-strand	56-60	5	1
β-strand	64	1	2
α-helix	67-71	5
α-helix	78-80	3
β-strand	84	1	2
α-helix	85-93	9
β-strand	101-105	5	1
α-helix	109-115	7
α-helix	119-121	3
β-strand	125-129	5	1
α-helix	133-145	13
β-strand	150-156	7	1
β-strand	159-165	7	1
β-strand	169-171	3	3
α-helix	190-197	8
α-helix	206-210	5
α-helix	214-225	12
α-helix	237-248	12
β-strand	253	1	4
α-helix	258	1
β-strand	259	1	4
α-helix	260	1
α-helix	263-275	13
α-helix	277-279	3
α-helix	283-289	7
α-helix	292-295	4
α-helix	303-316	14
α-helix	323-325	3
α-helix	336-358	23
α-helix	362-368	7
α-helix	377-385	9
α-helix	387-389	3
β-strand	391-393	3	3
α-helix	395-397	3
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-438	16
α-helix	447-449	3
α-helix	450-467	18
α-helix	476-485	10
α-helix	491-510	20
β-strand	514	1	5
β-strand	519-523	5	1
β-strand	528-532	5	1

Chain B: 43 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	1003-1004	2
β-strand	1008-1011	4	6
α-helix	1019-1032	14
β-strand	1036-1039	4	6
α-helix	1044-1053	10
β-strand	1060-1064	5	6
α-helix	1065-1073	9
β-strand	1077	1	7
α-helix	1084-1087	4
β-strand	1090	1	8
α-helix	1094-1097	4
β-strand	1099-1100	2	9
β-strand	1103-1104	2	9
β-strand	1106-1113	8	6
β-strand	1115-1118	4	10
β-strand	1129	1	11
α-helix	1133-1141	9
β-strand	1146-1148	3	10
α-helix	1155-1164	10
β-strand	1168-1172	5	12
β-strand	1177-1183	7	12
α-helix	1187-1201	15
α-helix	1211-1218	8
β-strand	1223-1228	6	10
β-strand	1246	1	10
α-helix	1247-1248	2
β-strand	1250	1	11
β-strand	1260-1267	8	6
β-strand	1268	1	7
α-helix	1275-1282	8
α-helix	1288-1295	8
β-strand	1305	1	8
α-helix	1306-1309	4
α-helix	1321-1327	7
α-helix	1329	1
β-strand	1330	1	6
α-helix	1337-1352	16
α-helix	1358-1369	12
α-helix	2018-2025	8
α-helix	2040-2047	8
β-strand	2051-2054	4	13
α-helix	2059-2068	10
β-strand	2074-2079	6	13
β-strand	2082	1	14
α-helix	2085-2089	5
α-helix	2096-2098	3
β-strand	2102	1	14
α-helix	2103-2114	12
β-strand	2119-2124	6	13
α-helix	2127-2129	3
α-helix	2132-2136	5
β-strand	2140-2143	4	13
α-helix	2148-2160	13
β-strand	2164-2165	2	15
β-strand	2168-2169	2	15
α-helix	2171-2173	3
β-strand	2177-2183	7	13
β-strand	2186-2192	7	13
α-helix	2204-2206	3
α-helix	2208-2210	3
α-helix	2215-2220	6
α-helix	2225-2231	7
α-helix	2232-2236	5
α-helix	2237-2240	4
α-helix	2254-2270	17
α-helix	2278-2286	9
α-helix	2293-2312	20
α-helix	2316-2318	3
β-strand	2321-2325	5	13
β-strand	2328	1	5
β-strand	2331-2335	5	13
α-helix	2337-2340	4
α-helix	2349-2350	2
β-strand	2351-2355	5	16
β-strand	2360	1	17
α-helix	2361-2370	10
β-strand	2380-2385	6	16
β-strand	2388-2393	6	16
α-helix	2398-2404	7
α-helix	2405-2409	5
β-strand	2411	1	17
β-strand	2422-2426	5	16
β-strand	2434-2440	7	16

Chain C: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	11-14	4
α-helix	29-39	11
β-strand	47-50	4	18
β-strand	59-64	6	18
α-helix	69-71	3
β-strand	74	1	19
β-strand	76-81	6	18
α-helix	90-91	2
β-strand	92-95	4	18
β-strand	101	1	20
β-strand	104	1	20
β-strand	109	1	18
β-strand	110	1	20
α-helix	113-115	3
α-helix	125-137	13
α-helix	147-155	9
α-helix	157-169	13
β-strand	171-173	3	21
β-strand	176-178	3	21
α-helix	179-180	2
β-strand	182	1	19

Chain I: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	22
β-strand	12-16	5	22
β-strand	22	1	23
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	22
β-strand	48-49	2	22
α-helix	50-51	2
β-strand	55	1	23
β-strand	66-69	4	22
β-strand	75	1	13

Chain J: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	24
β-strand	11-14	4	24
β-strand	22	1	25
α-helix	24-30	7
β-strand	42-43	2	26
β-strand	44	1	27
β-strand	49	1	27
α-helix	50-51	2
β-strand	55	1	25
α-helix	56-59	4
β-strand	65-68	4	24
β-strand	69-70	2	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD8-activating enzyme E1 regulatory subunit	A	protein	536	Homo sapiens	Q13564 (AlphaFold model)
Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera	B	protein	805	Homo sapiens	P0AEX9 (AlphaFold model)
NEDD8-conjugating enzyme Ubc12	C	protein	180	Homo sapiens	P61081 (AlphaFold model)
NEDD8	I, J	protein	81	Homo sapiens	Q15843 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2NVU_1 NEDD8-activating enzyme E1 regulatory subunit (chains A)
GSMAQLGKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFT
IIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPS
FFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDN
ALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYK
EKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINIT
KQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVG
NHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDN
PDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDY
VHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL

Sequence of entity 2 (B), FASTA

>2NVU_2 Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera (chains B)
MKLMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDG
PDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLI
YNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKY
DIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNID
TSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKD
KPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQT
VDAALAAAQTNAAADWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAG
GLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPN
CNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPL
IDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQW
PKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNA
VIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSP
SAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGL
VDGQELAVADVTTPQTVLFKLHFTS

Sequence of entity 3 (C), FASTA

>2NVU_3 NEDD8-conjugating enzyme Ubc12 (chains C)
GSMIKLFSLKQQKKEEEKGSSKKASAAQLRIQKDINELNLPKTCDISFSDPDDLLNFKLV
ICPDEGFYKSGKFVFSFKVGQGYPHDPPKVKCETMVYHPNIDLEGNVALNILREDWKPVL
TINSIIYGLQYLFLEPNPEDPLNKEAAEVLQNNRRLFEQNVQRSMRGGYIGSTYFERCLK

Sequence of entity 4 (I, J), FASTA

>2NVU_4 NEDD8 (chains I, J)
GSGGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKT
AADYKILGGSVLHLVLALRGG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1

Primary citation

Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Huang, D.T., Hunt, H.W., Zhuang, M. et al. Nature (2007) 445:394-398. DOI 10.1038/nature05490 · PubMed

Other PDB entries of the same protein (UniProt Q13564 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TT5 2.6 Å, Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal…
1YOV 2.6 Å, Insights into the Ubiquitin Transfer Cascade from the refined structure of the…
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…
1R4M 3.0 Å, APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex
3GZN 3.0 Å, Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924
3DBR 3.05 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…
1R4N 3.6 Å, APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP

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