1R4N: Amyloid beta precursor protein-binding protein 1

APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP. Determined by X-ray diffraction at 3.6 Å resolution. Released 23 Dec 2003.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 12
Atoms: 31,744
Mol. weight: 469.48 kDa
Ligands: ZN, ATP
Released: 23 Dec 2003

Explore 1R4N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1R4N contains 212 α-helices and 172 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	14-28	15
β-strand	33-35	3	1
α-helix	40-50	11
β-strand	56-60	5	1
β-strand	64	1	2
α-helix	67-70	4
α-helix	78-80	3
β-strand	84	1	2
α-helix	85-96	12
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	239-248	10
α-helix	263-275	13
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
α-helix	387-389	3
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	477-485	9
α-helix	491-506	16
α-helix	507-511	5
β-strand	514	1	4
α-helix	515-516	2
β-strand	520-523	4	1
β-strand	528-531	4	1

Chain B: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
α-helix	41-48	8
β-strand	51-54	4	5
α-helix	59-70	12
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	148-160	13
β-strand	164-165	2	8
β-strand	168-169	2	8
α-helix	171-173	3
β-strand	177-183	7	5
β-strand	186-192	7	5
β-strand	194	1	9
β-strand	197	1	9
α-helix	202-206	5
α-helix	208-210	3
α-helix	215-219	5
α-helix	225-234	10
α-helix	236-239	4
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	1	5
β-strand	351	1	10
α-helix	365-370	6
β-strand	380-383	4	11
β-strand	390-394	5	11
α-helix	601-604	4
α-helix	703-706	4
β-strand	903-904	2	11
β-strand	914-915	2	11
β-strand	916	1	10

Chain C: 27 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	14-28	15
β-strand	33-35	3	14
α-helix	40-50	11
β-strand	56-60	5	14
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	101-105	5	14
α-helix	109-115	7
α-helix	117-122	6
β-strand	125-129	5	14
α-helix	133-145	13
β-strand	150-156	7	14
β-strand	159-165	7	14
β-strand	169-171	3	16
α-helix	190-197	8
α-helix	214-227	14
α-helix	239-248	10
α-helix	263-275	13
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
α-helix	387-389	3
β-strand	391-393	3	16
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	449-468	20
α-helix	477-485	9
α-helix	491-506	16
α-helix	507-511	5
β-strand	514	1	17
β-strand	520-523	4	14
β-strand	528-531	4	14

Chain D: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
α-helix	41-48	8
β-strand	50-54	5	18
α-helix	59-70	12
β-strand	74-78	5	18
β-strand	82	1	19
α-helix	85-87	3
α-helix	96-98	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
β-strand	194	1	21
β-strand	197	1	21
α-helix	204-206	3
α-helix	208-210	3
α-helix	215-219	5
α-helix	225-234	10
α-helix	236-239	4
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	18
β-strand	328	1	17
β-strand	331	1	18
β-strand	351	1	22
α-helix	365-370	6
β-strand	380-383	4	23
β-strand	390-394	5	23
α-helix	601-604	4
α-helix	703-706	4
β-strand	903-904	2	23
β-strand	914	1	23
β-strand	916	1	22

Chain E: 27 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	14-28	15
β-strand	33-35	3	26
α-helix	40-50	11
β-strand	56-60	5	26
β-strand	64	1	27
α-helix	67-72	6
α-helix	78-80	3
β-strand	84	1	27
α-helix	85-96	12
β-strand	101-105	5	26
α-helix	109-115	7
α-helix	117-122	6
β-strand	125-129	5	26
α-helix	133-145	13
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	263-275	13
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
α-helix	387-389	3
β-strand	391-393	3	28
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	449-467	19
α-helix	477-485	9
α-helix	491-506	16
α-helix	507-511	5
β-strand	514	1	29
β-strand	520-523	4	26
β-strand	528-531	4	26

Chain F: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
α-helix	41-48	8
β-strand	51-54	4	30
α-helix	59-70	12
β-strand	74-78	5	30
β-strand	82	1	31
α-helix	85-87	3
α-helix	96-98	3
β-strand	102	1	31
α-helix	103-114	12
β-strand	119-123	5	30
α-helix	127-129	3
β-strand	130	1	32
α-helix	132-135	4
β-strand	140-143	4	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	186-192	7	30
β-strand	194	1	34
β-strand	197	1	34
α-helix	204-206	3
α-helix	208-210	3
α-helix	215-219	5
α-helix	225-234	10
α-helix	236-239	4
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	30
β-strand	328	1	29
β-strand	331	1	30
β-strand	351	1	35
α-helix	365-370	6
β-strand	380-383	4	36
β-strand	390-394	5	36
α-helix	601-604	4
α-helix	703-706	4
β-strand	903-904	2	36
β-strand	914	1	36
β-strand	916	1	35

Chain G: 28 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	14-28	15
β-strand	33-35	3	39
α-helix	40-50	11
β-strand	56-60	5	39
β-strand	64	1	40
α-helix	67-70	4
α-helix	78-80	3
β-strand	84	1	40
α-helix	85-96	12
β-strand	101-105	5	39
α-helix	109-115	7
α-helix	117-122	6
β-strand	125-129	5	39
α-helix	133-145	13
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	214-227	14
α-helix	239-248	10
α-helix	263-275	13
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
α-helix	387-389	3
β-strand	391-393	3	41
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	449-468	20
α-helix	477-485	9
α-helix	491-506	16
α-helix	507-511	5
β-strand	514	1	42
α-helix	515-516	2
β-strand	520-523	4	39
β-strand	528-531	4	39

Chain H: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	18-24	7
α-helix	41-48	8
β-strand	51-54	4	43
α-helix	59-70	12
β-strand	74-78	5	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	119-123	5	43
α-helix	127-129	3
β-strand	130	1	32
α-helix	132-135	4
β-strand	140-143	4	43
α-helix	148-160	13
β-strand	164-165	2	45
β-strand	168-169	2	45
α-helix	171-173	3
β-strand	177-183	7	43
β-strand	186-192	7	43
β-strand	194	1	46
β-strand	197	1	46
α-helix	202-206	5
α-helix	208-210	3
α-helix	215-219	5
α-helix	225-234	10
α-helix	236-239	4
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	43
β-strand	328	1	42
β-strand	331	1	43
β-strand	351	1	47
α-helix	365-370	6
β-strand	380-383	4	48
β-strand	390-394	5	48
α-helix	601-604	4
α-helix	703-706	4
β-strand	903-904	2	48
β-strand	914	1	48
β-strand	916	1	47

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
amyloid beta precursor protein-binding protein 1	A, C, E, G	protein	529	Homo sapiens	Q13564 (AlphaFold model)
ubiquitin-activating enzyme E1C	B, D, F, H	protein	431	Homo sapiens	Q8TBC4 (AlphaFold model)
Ubiquitin-like protein NEDD8	I, J, K, L	protein	76	Homo sapiens	Q15843 (AlphaFold model)

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

>1R4N_1 amyloid beta precursor protein-binding protein 1 (chains A, C, E, G)
MAQLGKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFTII
DGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPSFF
CRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDNAL
EDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEK
EDFRDLIRQGILKPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFW
ILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLL
QSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVL
YLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRY
GAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL

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

>1R4N_2 ubiquitin-activating enzyme E1C (chains B, D, F, H)
DWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSG
FRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQDFN
DTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARV
ILPGMTACIECTLELYPPQVNFPMATIASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDG
DDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIA
TSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNS
ASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADVTTP
QTVLFKLHFTS

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

>1R4N_3 Ubiquitin-like protein NEDD8 (chains I, J, K, L)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	4

Primary citation

The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Walden, H., Podgorski, M.S., Huang, D.T. et al. Mol Cell (2003) 12:1427-1437. DOI 10.1016/S1097-2765(03)00452-0 · 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
3DBR 3.05 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…

Browse structure collections

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