3DBL: NEDD8-activating enzyme E1 regulatory subunit

Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln). Determined by X-ray diffraction at 2.9 Å resolution. Released 12 Aug 2008.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 12
Atoms: 32,577
Mol. weight: 474 kDa
Ligands: ZN
Released: 12 Aug 2008

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

Secondary structure: helices and β-sheets

3DBL contains 220 α-helices and 177 β-strands across 12 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, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	14-29	16
β-strand	32-35	4	1
α-helix	40-50	11
β-strand	56-60	5	1
β-strand	64	1	2
α-helix	69-72	4
α-helix	78-80	3
β-strand	84	1	2
α-helix	85-94	10
β-strand	101-105	5	1
α-helix	109-115	7
α-helix	117-122	6
β-strand	125-129	5	1
α-helix	133-145	13
β-strand	150-155	6	1
β-strand	159-165	7	1
β-strand	169-171	3	3
α-helix	190-197	8
α-helix	209-211	3
α-helix	214-227	14
α-helix	237-248	12
α-helix	263-270	8
α-helix	272-275	4
α-helix	283-290	8
α-helix	292-295	4
α-helix	303-316	14
α-helix	323-325	3
α-helix	336-366	31
α-helix	377-385	9
β-strand	391-393	3	3
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	449-467	19
α-helix	476-485	10
α-helix	491-510	20
β-strand	514	1	4
α-helix	515-516	2
β-strand	519-523	5	1
β-strand	528-532	5	1

Chain B: 25 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
α-helix	41-48	8
β-strand	51-54	4	5
α-helix	59-68	10
β-strand	74-78	5	5
β-strand	82	1	6
α-helix	85-87	3
α-helix	96-98	3
β-strand	102	1	6
α-helix	103-114	12
β-strand	119-123	5	5
α-helix	127-129	3
β-strand	130	1	7
α-helix	132-135	4
β-strand	140-143	4	5
α-helix	148-159	12
β-strand	164-165	2	8
β-strand	168-169	2	8
α-helix	170	1
α-helix	171-173	3
β-strand	177-183	7	5
β-strand	186-192	7	5
α-helix	201-206	6
α-helix	208-209	2
α-helix	215-219	5
α-helix	225-231	7
α-helix	232-236	5
α-helix	237-239	3
β-strand	242	1	9
β-strand	244	1	9
α-helix	254-270	17
α-helix	278-286	9
α-helix	293-312	20
α-helix	316-318	3
β-strand	322-325	4	5
β-strand	328	1	4
β-strand	331-334	4	5
β-strand	351-352	2	10
β-strand	360	1	11
α-helix	361-370	10
β-strand	381-384	4	10
β-strand	389-393	5	10
α-helix	398-402	5
α-helix	405-408	4
β-strand	411	1	11
α-helix	417-418	2
β-strand	422-427	6	10
β-strand	430-437	8	10

Chain C: 27 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	14-29	16
β-strand	32-35	4	14
α-helix	40-50	11
β-strand	56-60	5	14
β-strand	64	1	15
α-helix	67-72	6
α-helix	78-80	3
β-strand	84	1	15
α-helix	85-94	10
β-strand	101	1	14
β-strand	104-105	2	14
α-helix	109-112	4
α-helix	119-122	4
β-strand	126-129	4	14
α-helix	133-146	14
β-strand	150-156	7	14
β-strand	159-165	7	14
β-strand	169-171	3	16
α-helix	190-198	9
α-helix	214-228	15
α-helix	237-248	12
α-helix	263-270	8
α-helix	272-275	4
α-helix	283-289	7
α-helix	292-295	4
α-helix	303-316	14
α-helix	336-367	32
α-helix	372-374	3
α-helix	379-385	7
β-strand	391-393	3	16
α-helix	395-397	3
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	447-467	21
α-helix	476-485	10
α-helix	491-510	20
β-strand	514	1	17
β-strand	519-523	5	14
β-strand	528-532	5	14

Chain D: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	41-48	8
β-strand	51-54	4	18
α-helix	59-68	10
β-strand	74-78	5	18
β-strand	82	1	19
α-helix	85-87	3
β-strand	102	1	19
α-helix	103-114	12
β-strand	119-123	5	18
α-helix	127-129	3
β-strand	130	1	7
α-helix	132-135	4
β-strand	140-143	4	18
α-helix	148-160	13
β-strand	164-165	2	20
β-strand	168-169	2	20
α-helix	171-173	3
β-strand	177-183	7	18
β-strand	186-192	7	18
α-helix	215-219	5
α-helix	225-231	7
α-helix	232-236	5
α-helix	237-239	3
α-helix	254-271	18
α-helix	278-286	9
α-helix	293-312	20
α-helix	316-318	3
β-strand	321-325	5	18
β-strand	328	1	17
β-strand	331-335	5	18
α-helix	337-340	4
α-helix	350	1
β-strand	351-355	5	21
β-strand	360	1	22
α-helix	361-370	10
β-strand	380-386	7	21
β-strand	388-393	6	21
α-helix	398-402	5
α-helix	405-408	4
β-strand	411	1	22
α-helix	413-415	3
β-strand	421-427	7	21
β-strand	430-440	11	21

Chain E: 29 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	14-29	16
β-strand	32-35	4	25
α-helix	40-50	11
β-strand	56-60	5	25
β-strand	64	1	26
α-helix	65-66	2
α-helix	67-72	6
α-helix	78-80	3
β-strand	84	1	26
α-helix	85-94	10
β-strand	101	1	25
β-strand	104-105	2	25
α-helix	109-115	7
α-helix	117-122	6
β-strand	125-129	5	25
α-helix	133-145	13
β-strand	150-156	7	25
β-strand	159-165	7	25
β-strand	169-171	3	27
α-helix	190-197	8
α-helix	206-209	4
α-helix	214-227	14
α-helix	237-248	12
α-helix	263-270	8
α-helix	272-275	4
α-helix	283-290	8
α-helix	292-295	4
α-helix	303-316	14
α-helix	323-325	3
α-helix	336-368	33
α-helix	378-385	8
β-strand	391-393	3	27
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	447-449	3
α-helix	450-467	18
α-helix	476-485	10
α-helix	491-510	20
β-strand	514	1	28
β-strand	519-523	5	25
β-strand	528-532	5	25

Chain F: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	41-48	8
β-strand	51-54	4	29
α-helix	59-69	11
β-strand	75-78	4	29
β-strand	82	1	30
α-helix	96-98	3
β-strand	102	1	30
α-helix	103-114	12
β-strand	121-123	3	29
α-helix	127-129	3
β-strand	130	1	31
α-helix	132-136	5
β-strand	140-143	4	29
α-helix	148-159	12
β-strand	164	1	32
β-strand	169	1	32
α-helix	171-173	3
β-strand	177-183	7	29
β-strand	186-192	7	29
α-helix	201-206	6
α-helix	208-210	3
α-helix	215-218	4
α-helix	225-231	7
α-helix	232-236	5
α-helix	237-239	3
α-helix	254-269	16
α-helix	278-285	8
α-helix	288-290	3
α-helix	293-312	20
α-helix	316-318	3
β-strand	320	1	29
β-strand	323-325	3	29
β-strand	328	1	28
β-strand	331-333	3	29
β-strand	353-354	2	33
α-helix	362-370	9
β-strand	380-381	2	34
β-strand	383-384	2	35
β-strand	389-390	2	35
α-helix	400-403	4
α-helix	405-409	5
β-strand	422	1	36
β-strand	425-427	3	34
β-strand	430-434	5	34
β-strand	437	1	36
β-strand	438-439	2	33

Chain G: 26 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	14-30	17
β-strand	32-35	4	39
α-helix	40-50	11
β-strand	56-60	5	39
β-strand	64	1	40
α-helix	67-71	5
β-strand	84	1	40
α-helix	85-94	10
β-strand	101	1	39
α-helix	102	1
β-strand	104-105	2	39
α-helix	109-114	6
α-helix	119-122	4
β-strand	125-129	5	39
α-helix	133-144	12
β-strand	150-156	7	39
β-strand	159-165	7	39
β-strand	169-171	3	41
α-helix	190-197	8
α-helix	214-225	12
α-helix	237-248	12
α-helix	263-275	13
α-helix	283-290	8
α-helix	292-295	4
α-helix	303-316	14
α-helix	323-325	3
α-helix	338-368	31
α-helix	377-386	10
α-helix	387-389	3
β-strand	391-393	3	41
α-helix	398-401	4
α-helix	409-415	7
α-helix	423-439	17
α-helix	450-467	18
α-helix	476-484	9
α-helix	491-510	20
β-strand	514	1	42
β-strand	519-523	5	39
β-strand	528-532	5	39

Chain H: 28 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	41-48	8
β-strand	51-54	4	43
α-helix	59-70	12
β-strand	75-78	4	43
β-strand	82	1	44
α-helix	85-87	3
α-helix	96-98	3
β-strand	102	1	44
α-helix	103-114	12
β-strand	121-123	3	43
α-helix	127-129	3
β-strand	130	1	31
α-helix	132-136	5
β-strand	140-143	4	43
α-helix	148-159	12
β-strand	164-165	2	45
β-strand	168-169	2	45
α-helix	170	1
α-helix	171-173	3
β-strand	177-179	3	43
β-strand	181-183	3	46
β-strand	186-189	4	46
β-strand	191-192	2	43
α-helix	198-199	2
α-helix	201-206	6
α-helix	208-210	3
α-helix	215-219	5
α-helix	225-231	7
α-helix	232-236	5
α-helix	238-240	3
α-helix	247-249	3
α-helix	254-269	16
α-helix	278-286	9
α-helix	293-312	20
α-helix	316-319	4
β-strand	322-324	3	46
β-strand	325	1	47
β-strand	328	1	42
β-strand	331	1	47
β-strand	353-354	2	48
α-helix	367-370	4
α-helix	372-374	3
β-strand	381	1	49
β-strand	383-384	2	50
β-strand	389-390	2	50
α-helix	398-402	5
α-helix	405-407	3
α-helix	413-415	3
β-strand	425	1	49
β-strand	434	1	49
β-strand	438-439	2	48

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NEDD8-activating enzyme E1 regulatory subunit	A, C, E, G	protein	531	Homo sapiens	Q13564 (AlphaFold model)
NEDD8-activating enzyme E1 catalytic subunit	B, D, F, H	protein	434	Homo sapiens	Q8TBC4 (AlphaFold model)
NEDD8	I, J, K, L	protein	88	Homo sapiens	Q15843 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3DBL_1 NEDD8-activating enzyme E1 regulatory subunit (chains A, C, E, G)
GSMAQLGKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFT
IIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPS
FFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDN
ALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYK
EKEDFRDLIRQGILKPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPS
FWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAK
LLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEI
VLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFC
RYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL

Sequence of entity 2 (B, D, F, H), FASTA

>3DBL_2 NEDD8-activating enzyme E1 catalytic subunit (chains B, D, F, H)
MKLDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLA
LSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQ
DFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGN
ARVILPGMTACIECTLELYPPQVNFPMATIASMPRLPEHCIEYVRMLQWPKEQPFGEGVP
LDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVF
KIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYL
TNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADV
TTPQTVLFKLHFTS

Sequence of entity 3 (I, J, K, L), FASTA

>3DBL_3 NEDD8 (chains I, J, K, L)
GSRRASVGSGGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGK
QMNDEKTAADYKILGGSVLHLVLQLRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8's E1. Souphron, J., Waddell, M.B., Paydar, A. et al. Biochemistry (2008) 47:8961-8969. DOI 10.1021/bi800604c · 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…
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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