3GZN: NEDD8-activating enzyme

Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924. Determined by X-ray diffraction at 3.0 Å resolution. Released 2 Feb 2010.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 6
Atoms: 16,050
Mol. weight: 244.27 kDa
Ligands: ZN, B39
Released: 2 Feb 2010

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

Secondary structure: helices and β-sheets

3GZN contains 114 α-helices and 82 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: 28 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-36	16
β-strand	39-43	5	1
α-helix	47-57	11
β-strand	63-67	5	1
β-strand	71	1	2
α-helix	74-79	6
α-helix	85-87	3
β-strand	91	1	2
α-helix	92-100	9
α-helix	101-103	3
β-strand	108-112	5	1
α-helix	116-122	7
α-helix	124-129	6
β-strand	132-136	5	1
α-helix	140-152	13
β-strand	157-163	7	1
β-strand	166-172	7	1
β-strand	176-178	3	3
α-helix	197-204	8
α-helix	221-236	16
α-helix	244-256	13
β-strand	260	1	4
α-helix	265	1
β-strand	266	1	4
α-helix	267	1
α-helix	270-278	9
α-helix	290-296	7
α-helix	299-302	4
α-helix	310-323	14
α-helix	330-332	3
α-helix	343-375	33
α-helix	384-392	9
α-helix	393-395	3
β-strand	398-400	3	3
α-helix	405-409	5
α-helix	416-423	8
α-helix	430-446	17
α-helix	457-474	18
α-helix	483-492	10
α-helix	498-517	20
β-strand	521	1	5
β-strand	526-530	5	1
β-strand	535-539	5	1

Chain B: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	39-46	8
α-helix	62-69	8
β-strand	71-75	5	6
α-helix	79-89	11
β-strand	95-99	5	6
β-strand	103	1	7
α-helix	106-110	5
α-helix	117-119	3
β-strand	123	1	7
α-helix	124-135	12
β-strand	140-144	5	6
α-helix	153-156	4
β-strand	161-165	5	6
α-helix	169-181	13
β-strand	185-186	2	8
β-strand	189-190	2	8
α-helix	192-194	3
β-strand	198-204	7	6
β-strand	207-213	7	6
α-helix	225-227	3
α-helix	229-230	2
α-helix	236-241	6
α-helix	246-251	6
α-helix	252-257	6
α-helix	258-261	4
α-helix	275-291	17
α-helix	299-307	9
α-helix	309-311	3
α-helix	314-333	20
α-helix	337-339	3
β-strand	342-346	5	6
β-strand	349	1	5
β-strand	352-356	5	6
α-helix	358-361	4
β-strand	372-376	5	9
α-helix	383-391	9
β-strand	401-405	5	9
β-strand	410-414	5	9
α-helix	421-424	4
α-helix	426-429	4
β-strand	443-448	6	9
β-strand	451-461	11	9

Chain C: 32 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	16-19	4
α-helix	21-36	16
β-strand	39-43	5	10
α-helix	47-57	11
β-strand	63-67	5	10
β-strand	71	1	11
α-helix	74-79	6
α-helix	85-87	3
β-strand	91	1	11
α-helix	92-101	10
β-strand	108-112	5	10
α-helix	116-122	7
α-helix	124-129	6
β-strand	132-136	5	10
α-helix	140-152	13
β-strand	157-163	7	10
β-strand	166-172	7	10
β-strand	176-178	3	12
α-helix	197-204	8
α-helix	208-210	3
α-helix	214-217	4
α-helix	221-234	14
α-helix	244-256	13
α-helix	259	1
β-strand	260	1	13
α-helix	265	1
β-strand	266	1	13
α-helix	267	1
α-helix	270-277	8
α-helix	278-280	3
α-helix	290-296	7
α-helix	299-302	4
α-helix	310-323	14
α-helix	330-332	3
α-helix	343-375	33
α-helix	379-381	3
α-helix	384-392	9
β-strand	398-400	3	12
α-helix	405-409	5
α-helix	416-422	7
α-helix	430-446	17
α-helix	457-474	18
α-helix	483-492	10
α-helix	498-517	20
β-strand	521	1	14
β-strand	526-530	5	10
β-strand	535-539	5	10

Chain D: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	39-46	8
α-helix	61-69	9
β-strand	71-75	5	15
α-helix	79-89	11
β-strand	95-100	6	15
β-strand	103	1	16
α-helix	106-110	5
α-helix	117-119	3
β-strand	123	1	16
α-helix	124-135	12
β-strand	140-145	6	15
α-helix	148-150	3
α-helix	153-157	5
β-strand	161-165	5	15
α-helix	169-182	14
β-strand	185-186	2	17
β-strand	189-190	2	17
α-helix	192-194	3
β-strand	198-204	7	15
β-strand	207-213	7	15
α-helix	222-227	6
α-helix	236-240	5
α-helix	246-252	7
α-helix	253-257	5
α-helix	258-261	4
α-helix	275-291	17
α-helix	299-306	8
α-helix	309-311	3
α-helix	314-333	20
α-helix	337-339	3
β-strand	342-346	5	15
β-strand	349	1	14
β-strand	352-356	5	15
α-helix	358-361	4
β-strand	372-376	5	18
α-helix	383-391	9
β-strand	401-405	5	18
β-strand	410-414	5	18
α-helix	419-425	7
α-helix	426-429	4
β-strand	443-448	6	18
β-strand	451-461	11	18

Chains I and J: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1-6	6	19
β-strand	12-17	6	19
β-strand	22	1	20
α-helix	23-34	12
α-helix	38-40	3
β-strand	43-45	3	19
β-strand	48-49	2	19
β-strand	55	1	20
α-helix	57-59	3
β-strand	66-69	4	19
β-strand	75	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD8-activating enzyme E1 regulatory subunit	A, C	protein	534	Homo sapiens	Q13564 (AlphaFold model)
NEDD8-activating enzyme E1 catalytic subunit	B, D	protein	463	Homo sapiens	Q8TBC4 (AlphaFold model)
NEDD8	I, J	protein	82	Homo sapiens	Q15843 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3GZN_1 NEDD8-activating enzyme E1 regulatory subunit (chains A, C)
MAQLGKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTII
DGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFF
CRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNAL
EDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEK
EDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQ
TPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNH
VAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPD
NEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVH
EFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL

Sequence of entity 2 (B, D), FASTA

>3GZN_2 NEDD8-activating enzyme E1 catalytic subunit (chains B, D)
MADGEEPEKKRRRIEELLAEKMAVDGGCGDTGDWEGRWNHVKKFLERSGPFTHPDFEPST
ESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDI
GRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLI
SLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIA
SMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYR
LTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAER
KENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTS
IEERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHFTS

Sequence of entity 3 (I, J), FASTA

>3GZN_3 NEDD8 (chains I, J)
HHHHHHMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEK
TAADYKILGGSVLHLVLALRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
B39	[(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimid…	C21 H25 N5 O4 S	2

Primary citation

Substrate-assisted inhibition of ubiquitin-like protein-activating enzymes: the NEDD8 E1 inhibitor MLN4924 forms a NEDD8-AMP mimetic in situ. Brownell, J.E., Sintchak, M.D., Gavin, J.M. et al. Mol Cell (2010) 37:102-111. DOI 10.1016/j.molcel.2009.12.024 · 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…
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…
1R4M 3.0 Å, APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex
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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