1YOV: Amyloid protein-binding protein 1

Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8. Determined by X-ray diffraction at 2.6 Å resolution. Released 8 Mar 2005.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,604
Mol. weight: 220.58 kDa
Ligands: ZN
Released: 8 Mar 2005

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

Secondary structure: helices and β-sheets

1YOV contains 100 α-helices and 70 β-strands across 4 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, 16 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
α-helix	14-30	17
β-strand	32-35	4	1
α-helix	40-50	11
β-strand	56-60	5	1
β-strand	64	1	2
α-helix	67-72	6
α-helix	78-80	3
β-strand	84	1	2
α-helix	85-94	10
β-strand	101	1	1
β-strand	104-105	2	1
α-helix	109-114	6
α-helix	117-122	6
β-strand	125-129	5	1
α-helix	133-146	14
β-strand	150-156	7	1
β-strand	159-165	7	1
β-strand	169-171	3	3
α-helix	179-181	3
α-helix	190-197	8
α-helix	206-209	4
α-helix	214-228	15
α-helix	239-248	10
β-strand	253	1	4
β-strand	259	1	4
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
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	450-468	19
α-helix	476-484	9
α-helix	491-510	20
β-strand	514	1	5
β-strand	519-523	5	1
β-strand	528-532	5	1

Chain B: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	41-48	8
β-strand	51-54	4	6
α-helix	60-68	9
β-strand	75-78	4	6
β-strand	82	1	7
α-helix	85-89	5
α-helix	96-98	3
β-strand	102	1	7
α-helix	103-114	12
β-strand	121-123	3	6
α-helix	127-129	3
β-strand	130	1	8
α-helix	132-135	4
β-strand	140-143	4	6
α-helix	148-160	13
β-strand	164-165	2	9
β-strand	168-169	2	9
α-helix	171-173	3
β-strand	177-183	7	6
β-strand	186-192	7	6
α-helix	200-206	7
α-helix	215-220	6
α-helix	225-231	7
α-helix	232-236	5
α-helix	237-239	3
α-helix	247-249	3
α-helix	254-270	17
α-helix	278-285	8
α-helix	293-312	20
α-helix	316-318	3
β-strand	321-325	5	6
β-strand	328	1	5
β-strand	331-335	5	6
α-helix	337-340	4
α-helix	350	1
β-strand	351	1	10
α-helix	364-367	4
β-strand	381-382	2	11
β-strand	391-392	2	11
α-helix	402-404	3
β-strand	424	1	12
β-strand	427	1	13
β-strand	430	1	13
β-strand	435	1	12
β-strand	436	1	10

Chain C: 29 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	14-30	17
β-strand	32-33	2	14
β-strand	34-35	2	15
α-helix	40-50	11
β-strand	56-58	3	14
β-strand	64	1	16
α-helix	67-72	6
β-strand	84	1	16
α-helix	85-96	12
β-strand	101-103	3	14
α-helix	109-115	7
α-helix	117-122	6
β-strand	126-129	4	15
α-helix	133-145	13
β-strand	150-156	7	15
β-strand	159-165	7	15
β-strand	169-171	3	17
α-helix	179-181	3
α-helix	190-196	7
α-helix	201-203	3
α-helix	206-209	4
α-helix	214-225	12
α-helix	237-248	12
β-strand	253	1	18
β-strand	259	1	18
α-helix	260-261	2
α-helix	263-275	13
α-helix	283-289	7
α-helix	292-295	4
α-helix	303-314	12
α-helix	315-319	5
α-helix	323-325	3
α-helix	336-368	33
α-helix	378-383	6
α-helix	387-389	3
β-strand	391-393	3	17
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	450-468	19
α-helix	477-484	8
α-helix	491-510	20
β-strand	514	1	19
β-strand	520-523	4	15
β-strand	528-531	4	15

Chain D: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	43-46	4
β-strand	51-54	4	20
α-helix	58-68	11
β-strand	74-78	5	20
β-strand	82	1	21
α-helix	85-87	3
β-strand	102	1	21
α-helix	103-114	12
β-strand	119-123	5	20
α-helix	127-129	3
β-strand	130	1	8
α-helix	135-137	3
β-strand	140-143	4	20
α-helix	148-160	13
β-strand	164-165	2	22
β-strand	168-169	2	22
α-helix	171-173	3
β-strand	177-183	7	20
β-strand	186-192	7	20
α-helix	201-203	3
α-helix	215-219	5
α-helix	225-230	6
α-helix	231-236	6
α-helix	237-240	4
α-helix	257-264	8
α-helix	267-270	4
α-helix	278-285	8
α-helix	293-312	20
α-helix	316-318	3
β-strand	322-325	4	20
β-strand	328	1	19
β-strand	331-334	4	20
α-helix	364-370	7
β-strand	380-381	2	23
β-strand	393-394	2	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Amyloid protein-binding protein 1	A, C	protein	537	Homo sapiens	Q13564 (AlphaFold model)
Ubiquitin-activating enzyme E1C	B, D	protein	444	Homo sapiens	Q8TBC4 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1YOV_1 Amyloid protein-binding protein 1 (chains A, C)
MKLMAQLGKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSF
TIIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDP
SFFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPD
NALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTY
KEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINI
TKQTPSFWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAV
GNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMD
NPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDD
YVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL

Sequence of entity 2 (B, D), FASTA

>1YOV_2 Ubiquitin-activating enzyme E1C (chains B, D)
GSMAVDGGCGDTGDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGG
LGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNC
NVVPHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLI
DGGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWP
KEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAV
IAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPS
AKLQEVLDYLTNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLV
DGQELAVADVTTPQTVLFKLHFTS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8. Walden, H., Podgorski, M.S., Schulman, B.A. Nature (2003) 422:330-334. DOI 10.1038/nature01456 · 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…
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…
1R4N 3.6 Å, APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP

Browse structure collections

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