3DBR: NEDD8-activating enzyme E1 regulatory subunit

Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg). Determined by X-ray diffraction at 3.05 Å resolution. Released 12 Aug 2008.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 12
Atoms: 32,424
Mol. weight: 474 kDa
Ligands: ZN
Released: 12 Aug 2008

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

Secondary structure: helices and β-sheets

3DBR contains 204 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: 27 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	14-28	15
β-strand	32-35	4	1
α-helix	40-50	11
β-strand	56-60	5	1
β-strand	64	1	2
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	150-156	7	1
β-strand	159-165	7	1
β-strand	169-171	3	3
α-helix	190-197	8
α-helix	214-227	14
α-helix	237-248	12
α-helix	264-270	7
α-helix	272-275	4
α-helix	283-289	7
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	395-397	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	515-517	3
β-strand	520-523	4	1
β-strand	528-531	4	1

Chain B: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
α-helix	41-48	8
β-strand	50-54	5	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	121-123	3	5
α-helix	127-129	3
β-strand	130	1	7
α-helix	132-135	4
β-strand	140-143	4	5
α-helix	148-160	13
β-strand	164-165	2	8
β-strand	168-169	2	8
β-strand	177-183	7	5
β-strand	186-192	7	5
α-helix	202-206	5
α-helix	208-209	2
α-helix	215-220	6
α-helix	225-230	6
α-helix	231-236	6
α-helix	237-239	3
α-helix	254-270	17
α-helix	278-286	9
α-helix	293-312	20
α-helix	316-318	3
β-strand	321-325	5	5
β-strand	328	1	4
β-strand	331-335	5	5
β-strand	351	1	9
β-strand	354	1	10
α-helix	362-370	9
β-strand	381-386	6	9
β-strand	388-393	6	9
α-helix	398-402	5
α-helix	405-408	4
β-strand	423-427	5	9
β-strand	430-436	7	9
β-strand	439	1	10

Chain C: 27 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-30	17
β-strand	33-35	3	13
α-helix	40-50	11
β-strand	56	1	14
β-strand	59	1	13
β-strand	64	1	15
α-helix	67-70	4
α-helix	78-80	3
β-strand	84	1	15
α-helix	85-96	12
β-strand	101	1	14
α-helix	109-114	6
α-helix	117-122	6
β-strand	125-128	4	13
α-helix	133-146	14
β-strand	150-156	7	13
β-strand	159-165	7	13
β-strand	169-171	3	16
α-helix	190-198	9
α-helix	214-228	15
α-helix	237-248	12
α-helix	264-275	12
α-helix	283-289	7
α-helix	292-295	4
α-helix	303-316	14
α-helix	323-325	3
α-helix	336-367	32
α-helix	372-374	3
α-helix	377-385	9
α-helix	387-389	3
β-strand	391-393	3	16
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-437	15
α-helix	450-467	18
α-helix	476-485	10
α-helix	491-510	20
β-strand	514	1	17
β-strand	519-523	5	13
β-strand	528-532	5	13

Chain D: 20 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	41-47	7
β-strand	50-54	5	18
α-helix	59-69	11
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	121-123	3	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	184	1	21
β-strand	186-192	7	18
α-helix	198-199	2
α-helix	215	1
α-helix	216-220	5
α-helix	225-229	5
α-helix	254-270	17
α-helix	278-285	8
β-strand	291	1	21
α-helix	293-312	20
β-strand	321-325	5	18
β-strand	328	1	17
β-strand	331-335	5	18
β-strand	351-355	5	22
β-strand	360	1	23
α-helix	362-370	9
β-strand	380-384	5	22
β-strand	389-393	5	22
α-helix	398-404	7
α-helix	405-408	4
β-strand	411	1	23
α-helix	413-415	3
β-strand	422-426	5	22
β-strand	434-440	7	22

Chain E: 29 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	14-28	15
β-strand	32-35	4	26
α-helix	40-50	11
β-strand	56-60	5	26
β-strand	64	1	27
α-helix	65	1
α-helix	67-72	6
α-helix	78-80	3
β-strand	84	1	27
α-helix	85-95	11
β-strand	101	1	26
β-strand	104-105	2	26
α-helix	109-115	7
α-helix	117-122	6
β-strand	125-129	5	26
α-helix	133-146	14
β-strand	150-156	7	26
β-strand	159-165	7	26
β-strand	169-171	3	28
α-helix	190-197	8
α-helix	214-227	14
α-helix	239-248	10
α-helix	263-265	3
α-helix	266-269	4
α-helix	272-275	4
α-helix	283-290	8
α-helix	292-295	4
α-helix	303-316	14
α-helix	336-368	33
α-helix	372-374	3
α-helix	377-385	9
β-strand	391-393	3	28
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	447-449	3
α-helix	450-468	19
α-helix	476-484	9
α-helix	491-510	20
β-strand	514	1	29
β-strand	519-523	5	26
β-strand	528-532	5	26

Chain F: 20 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
α-helix	41-48	8
β-strand	50-54	5	30
α-helix	59-69	11
β-strand	74-78	5	30
β-strand	82	1	31
α-helix	86-89	4
β-strand	102	1	31
α-helix	103-114	12
α-helix	120	1
β-strand	121-123	3	30
β-strand	130	1	32
α-helix	132-135	4
β-strand	140-142	3	30
α-helix	148-160	13
β-strand	164-165	2	33
β-strand	168-169	2	33
α-helix	171-173	3
β-strand	177-183	7	30
β-strand	185-192	8	30
β-strand	194	1	34
β-strand	197	1	34
α-helix	204-206	3
α-helix	215-218	4
α-helix	227-234	8
α-helix	238-240	3
α-helix	254-270	17
α-helix	278-286	9
α-helix	293-312	20
α-helix	316-319	4
β-strand	321-325	5	30
β-strand	328	1	29
β-strand	331-335	5	30
β-strand	351-354	4	35
β-strand	360	1	36
α-helix	362-370	9
β-strand	380-382	3	37
β-strand	383-384	2	38
β-strand	389-390	2	38
α-helix	398-404	7
α-helix	405-408	4
β-strand	411	1	36
β-strand	419	1	39
β-strand	421	1	39
β-strand	422	1	35
β-strand	424-427	4	37
β-strand	430-434	5	37
β-strand	436-439	4	35

Chain G: 27 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	9-12	4
α-helix	14-28	15
β-strand	32-35	4	42
α-helix	40-50	11
β-strand	56-60	5	42
β-strand	64	1	43
α-helix	67-71	5
β-strand	84	1	43
α-helix	85-94	10
β-strand	101-105	5	42
α-helix	109-115	7
α-helix	117-122	6
β-strand	125-129	5	42
α-helix	133-145	13
β-strand	150-156	7	42
β-strand	159-165	7	42
β-strand	169	1	44
α-helix	190-197	8
α-helix	214-227	14
α-helix	237-248	12
α-helix	264-267	4
α-helix	271-273	3
α-helix	283-289	7
α-helix	292-295	4
α-helix	303-316	14
α-helix	323-325	3
α-helix	340-368	29
α-helix	377-386	10
α-helix	387-389	3
β-strand	393	1	44
α-helix	395-397	3
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	450-467	18
α-helix	477-484	8
α-helix	491-510	20
β-strand	514	1	45
β-strand	519-523	5	42
β-strand	528-532	5	42

Chain H: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	12-13	2
α-helix	18-25	8
α-helix	41-48	8
β-strand	51-54	4	46
α-helix	59-70	12
β-strand	75-78	4	46
β-strand	82	1	47
α-helix	85-87	3
β-strand	102	1	47
α-helix	103-114	12
β-strand	121-123	3	46
β-strand	130	1	32
α-helix	135-137	3
β-strand	140-143	4	46
α-helix	148-159	12
β-strand	164-165	2	48
β-strand	168-169	2	48
α-helix	170	1
α-helix	171-173	3
β-strand	177-183	7	46
β-strand	186-192	7	46
α-helix	208-210	3
α-helix	215-217	3
α-helix	227-234	8
α-helix	254-270	17
α-helix	278-286	9
α-helix	288-290	3
α-helix	293-312	20
β-strand	321-325	5	46
β-strand	328	1	45
β-strand	331-335	5	46
β-strand	352-354	3	49
α-helix	361-363	3
α-helix	367-370	4
α-helix	372-374	3
β-strand	380-382	3	50
β-strand	383-384	2	51
β-strand	389-390	2	51
α-helix	398-402	5
α-helix	405-407	3
α-helix	413-415	3
β-strand	424-427	4	50
β-strand	430-435	6	50
β-strand	437-439	3	49

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

>3DBR_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

>3DBR_2 NEDD8-activating enzyme E1 catalytic subunit (chains B, D, F, H)
MKLDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLA
LSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQ
DFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGN
AQVILPGMTACIECTLELYPPQVNFPMATIASMPRLPEHCIEYVRMLQWPKEQPFGEGVP
LDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVF
KIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYL
TNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADV
TTPQTVLFKLHFTS

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

>3DBR_3 NEDD8 (chains I, J, K, L)
GSRRASVGSGGSMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGK
QMNDEKTAADYKILGGSVLHLVLRLRGG

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…
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
1R4N 3.6 Å, APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP

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