1TT5: Amyloid protein-binding protein 1

Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8. Determined by X-ray diffraction at 2.6 Å resolution. Released 14 Sept 2004.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 6
Atoms: 14,637
Mol. weight: 223.43 kDa
Ligands: ZN
Released: 14 Sept 2004

Explore 1TT5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TT5 contains 110 α-helices and 67 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: 33 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	14-30	17
β-strand	32-36	5	1
α-helix	40-50	11
β-strand	56-60	5	1
α-helix	63	1
β-strand	64	1	2
β-strand	65	1	3
α-helix	66	1
α-helix	67-72	6
α-helix	78-80	3
β-strand	81	1	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	133-145	13
β-strand	150-156	7	1
β-strand	159-165	7	1
β-strand	169-171	3	4
α-helix	179-181	3
α-helix	190-197	8
α-helix	209-211	3
α-helix	214-225	12
α-helix	236-240	5
α-helix	241-249	9
α-helix	262-275	14
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	4
α-helix	395-397	3
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	450-468	19
α-helix	476-484	9
α-helix	491-510	20
β-strand	514	1	5
α-helix	515-517	3
β-strand	520-523	4	1
β-strand	528-531	4	1

Chain B: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	18-25	8
α-helix	41-47	7
β-strand	51-54	4	6
α-helix	59-69	11
β-strand	75-79	5	6
β-strand	82	1	7
α-helix	85-87	3
α-helix	96-98	3
β-strand	102	1	7
α-helix	103-114	12
α-helix	120	1
β-strand	121-124	4	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	1	9
β-strand	169	1	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	209-211	3
α-helix	215-220	6
α-helix	225-231	7
α-helix	232-236	5
α-helix	237-239	3
α-helix	254-270	17
α-helix	278-285	8
α-helix	293-312	20
β-strand	321-325	5	6
β-strand	328	1	5
β-strand	331-335	5	6
α-helix	350	1
β-strand	351	1	10
α-helix	364-370	7
β-strand	382-383	2	10
β-strand	602-603	2	10
β-strand	900-901	2	10
β-strand	1006-1007	2	10

Chain C: 30 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
α-helix	14-30	17
β-strand	32-36	5	11
α-helix	40-50	11
β-strand	56-60	5	11
β-strand	64	1	12
α-helix	67-72	6
β-strand	84	1	12
α-helix	85-93	9
α-helix	94-96	3
β-strand	101-105	5	11
α-helix	109-114	6
α-helix	117-120	4
β-strand	125-129	5	11
α-helix	133-145	13
β-strand	150-156	7	11
β-strand	159-165	7	11
β-strand	169-171	3	13
α-helix	179-181	3
α-helix	190-196	7
α-helix	214-228	15
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	303-314	12
α-helix	315-319	5
α-helix	338-366	29
α-helix	377-385	9
α-helix	387-389	3
β-strand	391-393	3	13
α-helix	395-397	3
α-helix	398-402	5
α-helix	409-415	7
α-helix	423-439	17
α-helix	448-451	4
α-helix	453-468	16
α-helix	476-484	9
α-helix	491-510	20
β-strand	514	1	14
β-strand	520-523	4	11
β-strand	528-531	4	11

Chain D: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
α-helix	40-46	7
β-strand	51-54	4	15
α-helix	58-69	12
β-strand	74-78	5	15
β-strand	82	1	16
α-helix	85-87	3
α-helix	96-98	3
β-strand	102	1	16
α-helix	103-114	12
β-strand	119-123	5	15
α-helix	127-129	3
β-strand	130	1	8
α-helix	132-135	4
β-strand	140-143	4	15
α-helix	148-161	14
β-strand	164-165	2	17
β-strand	168-169	2	17
α-helix	171-173	3
β-strand	177-183	7	15
β-strand	186-192	7	15
α-helix	201-203	3
α-helix	208-211	4
α-helix	215-219	5
α-helix	225-230	6
α-helix	231-236	6
α-helix	237-240	4
α-helix	248-250	3
α-helix	254-268	15
α-helix	278-285	8
α-helix	288-290	3
α-helix	293-312	20
α-helix	316-318	3
β-strand	321-325	5	15
β-strand	328	1	14
β-strand	331-335	5	15
α-helix	336-338	3
α-helix	366-370	5
β-strand	382-383	2	18
β-strand	602-603	2	18
α-helix	702-707	6
β-strand	901	1	18
β-strand	902	1	19
β-strand	1005	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
amyloid protein-binding protein 1	A, C	protein	531	Homo sapiens	Q13564 (AlphaFold model)
ubiquitin-activating enzyme E1C isoform 1	B, D	protein	434	Homo sapiens	Q8TBC4 (AlphaFold model)
Ubiquitin-conjugating enzyme E2 M	E, F	protein	26	Homo sapiens	P61081 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>1TT5_1 amyloid protein-binding protein 1 (chains A, C)
GSMAQLGKLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKNLVLPGIGSFT
IIDGNQVSGEDAGNNFFLQRSSIGKNRAEAAMEFLQELNSDVSGSFVEESPENLLDNDPS
FFCRFTVVVATQLPESTSLRLADVLWNSQIPLLICRTYGLVGYMRIIIKEHPVIESHPDN
ALEDLRLDKPFPELREHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYK
EKEDFRDLIRQGILKPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPS
FWILARALKEFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAK
LLQSIGQAPESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEI
VLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFC
RYGAAEPHTIAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL

Sequence of entity 2 (B, D), FASTA

>1TT5_2 ubiquitin-activating enzyme E1C isoform 1 (chains B, D)
MKLDWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLA
LSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCNVVPHFNKIQ
DFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGN
ARVILPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRMLQWPKEQPFGEGVP
LDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVF
KIATSAYIPLNNYLVFNDVDGLYTYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYL
TNSASLQMKSPAITATLEGKNRTLYLQSVTSIEERTRPNLSKTLKELGLVDGQELAVADV
TTPQTVLFKLHFTS

Sequence of entity 3 (E, F), FASTA

>1TT5_3 Ubiquitin-conjugating enzyme E2 M (chains E, F)
MIKLFSLKQQKKEEESAGGTKGSSKK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8. Huang, D.T., Miller, D.W., Mathew, R. et al. Nat Struct Mol Biol (2004) 11:927-935. DOI 10.1038/nsmb826 · PubMed

Other PDB entries of the same protein (UniProt Q13564 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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

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