1R4M: Amyloid beta precursor protein-binding protein 1
APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 23 Dec 2003.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organism
- Homo sapiens
- Chains
- 12
- Atoms
- 31,620
- Mol. weight
- 467.45 kDa
- Ligands
- ZN
- Released
- 23 Dec 2003
Explore 1R4M in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1R4M contains 228 α-helices and 167 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: 30 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| 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 | 65 | 1 | |
| α-helix | 67-72 | 6 | |
| 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 | 133-146 | 14 | |
| 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 | 236-240 | 5 | |
| α-helix | 241-248 | 8 | |
| 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 | 336-366 | 31 | |
| α-helix | 377-385 | 9 | |
| α-helix | 387-389 | 3 | |
| 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 | 447-467 | 21 | |
| α-helix | 476-485 | 10 | |
| α-helix | 491-510 | 20 | |
| β-strand | 514 | 1 | 4 |
| α-helix | 515-516 | 2 | |
| β-strand | 520-523 | 4 | 1 |
| β-strand | 528-531 | 4 | 1 |
Chains B, F and H: 24 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-25 | 8 | |
| α-helix | 41-48 | 8 | |
| β-strand | 51-54 | 4 | 5 |
| α-helix | 59-68 | 10 | |
| β-strand | 75-78 | 4 | 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 | 132-136 | 5 | |
| β-strand | 140-143 | 4 | 5 |
| α-helix | 148-160 | 13 | |
| β-strand | 163-165 | 3 | 8 |
| β-strand | 168-170 | 3 | 8 |
| α-helix | 171-173 | 3 | |
| β-strand | 177-183 | 7 | 5 |
| β-strand | 186-192 | 7 | 5 |
| α-helix | 204-206 | 3 | |
| α-helix | 208-210 | 3 | |
| α-helix | 215 | 1 | |
| α-helix | 216-220 | 5 | |
| α-helix | 225-234 | 10 | |
| α-helix | 236-239 | 4 | |
| α-helix | 247-249 | 3 | |
| 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 | 1 | 9 |
| α-helix | 365-370 | 6 | |
| β-strand | 381-382 | 2 | 10 |
| β-strand | 391 | 1 | 10 |
| α-helix | 601-606 | 6 | |
| α-helix | 703-706 | 4 | |
| β-strand | 903-904 | 2 | 10 |
| β-strand | 914 | 1 | 10 |
| β-strand | 916 | 1 | 9 |
Chain C: 30 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| α-helix | 14-30 | 17 | |
| β-strand | 32-35 | 4 | 14 |
| α-helix | 40-50 | 11 | |
| β-strand | 56-60 | 5 | 14 |
| β-strand | 64 | 1 | 15 |
| α-helix | 65 | 1 | |
| α-helix | 67-72 | 6 | |
| α-helix | 78-80 | 3 | |
| β-strand | 84 | 1 | 15 |
| α-helix | 85-94 | 10 | |
| β-strand | 101-105 | 5 | 14 |
| α-helix | 109-115 | 7 | |
| α-helix | 117-122 | 6 | |
| β-strand | 125-129 | 5 | 14 |
| α-helix | 133-146 | 14 | |
| 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 | 236-240 | 5 | |
| α-helix | 241-248 | 8 | |
| 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 | 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 |
| α-helix | 515-516 | 2 | |
| β-strand | 520-523 | 4 | 14 |
| β-strand | 528-531 | 4 | 14 |
Chain D: 24 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 18-25 | 8 | |
| α-helix | 41-48 | 8 | |
| β-strand | 50-54 | 5 | 18 |
| α-helix | 59-68 | 10 | |
| 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 | 121-123 | 3 | 18 |
| α-helix | 127-129 | 3 | |
| β-strand | 130 | 1 | 7 |
| α-helix | 132-136 | 5 | |
| β-strand | 140-143 | 4 | 18 |
| α-helix | 148-160 | 13 | |
| β-strand | 163-165 | 3 | 20 |
| β-strand | 168-170 | 3 | 20 |
| α-helix | 171-173 | 3 | |
| β-strand | 177-183 | 7 | 18 |
| β-strand | 186-192 | 7 | 18 |
| α-helix | 204-206 | 3 | |
| α-helix | 208-210 | 3 | |
| α-helix | 215 | 1 | |
| α-helix | 216-220 | 5 | |
| α-helix | 225-234 | 10 | |
| α-helix | 236-239 | 4 | |
| α-helix | 247-249 | 3 | |
| 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 | 331-334 | 4 | 18 |
| β-strand | 351 | 1 | 21 |
| α-helix | 365-370 | 6 | |
| β-strand | 381-382 | 2 | 22 |
| β-strand | 391 | 1 | 22 |
| α-helix | 601-606 | 6 | |
| α-helix | 703-706 | 4 | |
| β-strand | 903-904 | 2 | 22 |
| β-strand | 914 | 1 | 22 |
| β-strand | 916 | 1 | 21 |
Chains E and G: 30 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-12 | 4 | |
| α-helix | 14-30 | 17 | |
| 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 | 85-94 | 10 | |
| β-strand | 101-105 | 5 | 26 |
| α-helix | 109-115 | 7 | |
| α-helix | 117-122 | 6 | |
| β-strand | 125-129 | 5 | 26 |
| α-helix | 133-146 | 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 | 236-240 | 5 | |
| α-helix | 241-248 | 8 | |
| 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 | 336-366 | 31 | |
| α-helix | 377-386 | 10 | |
| α-helix | 387-389 | 3 | |
| β-strand | 391-393 | 3 | 28 |
| 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 | 29 |
| α-helix | 515-516 | 2 | |
| β-strand | 520-523 | 4 | 26 |
| β-strand | 528-531 | 4 | 26 |
Chains I, J and L: 3 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 102-106 | 5 | 11 |
| β-strand | 113-116 | 4 | 11 |
| β-strand | 122 | 1 | 12 |
| α-helix | 123-134 | 12 | |
| α-helix | 138-140 | 3 | |
| β-strand | 143-144 | 2 | 11 |
| β-strand | 145 | 1 | 13 |
| β-strand | 148 | 1 | 13 |
| β-strand | 155 | 1 | 12 |
| α-helix | 157-159 | 3 | |
| β-strand | 166-169 | 4 | 11 |
| β-strand | 175 | 1 | 5 |
Chain K: 3 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 102-106 | 5 | 36 |
| β-strand | 113-116 | 4 | 36 |
| β-strand | 122 | 1 | 37 |
| α-helix | 123-134 | 12 | |
| α-helix | 138-140 | 3 | |
| β-strand | 143-145 | 3 | 36 |
| β-strand | 148-149 | 2 | 36 |
| β-strand | 155 | 1 | 37 |
| α-helix | 157-159 | 3 | |
| β-strand | 166-169 | 4 | 36 |
| β-strand | 175 | 1 | 30 |
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
>1R4M_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
>1R4M_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
>1R4M_3 Ubiquitin-like protein NEDD8 (chains I, J, K, L)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ZN | Zinc ion | Zn | 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…
- 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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