5OOB: Nuclear cap-binding protein subunit 1
Complex of human nuclear cap-binding complex with M7GTP and nelf-E C-terminal peptide. Determined by X-ray diffraction at 2.79 Å resolution. Released 15 Nov 2017.
- Method
- X-ray diffraction
- Resolution
- 2.79 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 29,296
- Mol. weight
- 441.43 kDa
- Ligands
- MGT
- Released
- 15 Nov 2017
Explore 5OOB in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5OOB contains 236 α-helices and 54 β-strands across 11 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: 50 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 27-37 | 11 | |
| α-helix | 46-59 | 14 | |
| α-helix | 61-78 | 18 | |
| α-helix | 80-82 | 3 | |
| α-helix | 83-96 | 14 | |
| α-helix | 98-117 | 20 | |
| α-helix | 121-136 | 16 | |
| β-strand | 140 | 1 | 1 |
| α-helix | 142-153 | 12 | |
| α-helix | 154-157 | 4 | |
| α-helix | 163-174 | 12 | |
| α-helix | 177-187 | 11 | |
| α-helix | 189-204 | 16 | |
| α-helix | 211-214 | 4 | |
| β-strand | 217 | 1 | 2 |
| β-strand | 227 | 1 | 3 |
| α-helix | 228-241 | 14 | |
| α-helix | 252-256 | 5 | |
| α-helix | 257-261 | 5 | |
| α-helix | 264-265 | 2 | |
| β-strand | 266 | 1 | 1 |
| α-helix | 268-270 | 3 | |
| α-helix | 273-276 | 4 | |
| α-helix | 283-285 | 3 | |
| β-strand | 287 | 1 | 3 |
| α-helix | 294-296 | 3 | |
| α-helix | 302-305 | 4 | |
| α-helix | 309-325 | 17 | |
| α-helix | 329-337 | 9 | |
| α-helix | 347-359 | 13 | |
| α-helix | 369-382 | 14 | |
| α-helix | 387-400 | 14 | |
| α-helix | 402-404 | 3 | |
| β-strand | 405 | 1 | 2 |
| α-helix | 407-422 | 16 | |
| α-helix | 430-436 | 7 | |
| α-helix | 444-459 | 16 | |
| α-helix | 462-467 | 6 | |
| α-helix | 471-475 | 5 | |
| α-helix | 478-480 | 3 | |
| α-helix | 498-509 | 12 | |
| α-helix | 514-521 | 8 | |
| α-helix | 541-554 | 14 | |
| α-helix | 559-568 | 10 | |
| α-helix | 570-576 | 7 | |
| α-helix | 580-594 | 15 | |
| α-helix | 598-610 | 13 | |
| α-helix | 616-623 | 8 | |
| α-helix | 626-631 | 6 | |
| α-helix | 635-667 | 33 | |
| α-helix | 689-731 | 43 | |
| α-helix | 738-758 | 21 | |
| α-helix | 759-761 | 3 | |
| α-helix | 762-764 | 3 | |
| α-helix | 765-769 | 5 | |
| α-helix | 776-787 | 12 | |
Chain B: 9 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 13-15 | 3 | |
| α-helix | 29-36 | 8 | |
| β-strand | 41-45 | 5 | 4 |
| α-helix | 53-60 | 8 | |
| α-helix | 61-63 | 3 | |
| β-strand | 66-73 | 8 | 4 |
| β-strand | 79 | 1 | 5 |
| β-strand | 80-88 | 9 | 4 |
| α-helix | 91-100 | 10 | |
| β-strand | 105 | 1 | 6 |
| β-strand | 110 | 1 | 6 |
| β-strand | 112-115 | 4 | 4 |
| β-strand | 125 | 1 | 4 |
| α-helix | 135-138 | 4 | |
| α-helix | 144-146 | 3 | |
| α-helix | 151-154 | 4 | |
Chain C: 50 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 24-37 | 14 | |
| α-helix | 46-59 | 14 | |
| α-helix | 61-78 | 18 | |
| α-helix | 80-82 | 3 | |
| α-helix | 83-96 | 14 | |
| α-helix | 98-117 | 20 | |
| α-helix | 121-136 | 16 | |
| β-strand | 140 | 1 | 7 |
| α-helix | 142-153 | 12 | |
| α-helix | 154-157 | 4 | |
| α-helix | 163-174 | 12 | |
| α-helix | 177-187 | 11 | |
| α-helix | 189-204 | 16 | |
| α-helix | 211-214 | 4 | |
| β-strand | 217 | 1 | 8 |
| β-strand | 227 | 1 | 9 |
| α-helix | 228-241 | 14 | |
| α-helix | 252-256 | 5 | |
| α-helix | 257-261 | 5 | |
| α-helix | 264-265 | 2 | |
| β-strand | 266 | 1 | 7 |
| α-helix | 268-270 | 3 | |
| α-helix | 273-276 | 4 | |
| α-helix | 283-285 | 3 | |
| β-strand | 287 | 1 | 9 |
| α-helix | 294-296 | 3 | |
| α-helix | 302-305 | 4 | |
| α-helix | 309-325 | 17 | |
| α-helix | 329-337 | 9 | |
| α-helix | 347-359 | 13 | |
| α-helix | 369-382 | 14 | |
| α-helix | 387-400 | 14 | |
| α-helix | 402-404 | 3 | |
| β-strand | 405 | 1 | 8 |
| α-helix | 407-422 | 16 | |
| α-helix | 430-436 | 7 | |
| α-helix | 444-459 | 16 | |
| α-helix | 462-467 | 6 | |
| α-helix | 471-475 | 5 | |
| α-helix | 478-480 | 3 | |
| α-helix | 498-509 | 12 | |
| α-helix | 514-521 | 8 | |
| α-helix | 541-554 | 14 | |
| α-helix | 559-568 | 10 | |
| α-helix | 570-576 | 7 | |
| α-helix | 580-594 | 15 | |
| α-helix | 598-610 | 13 | |
| α-helix | 616-623 | 8 | |
| α-helix | 626-631 | 6 | |
| α-helix | 635-663 | 29 | |
| α-helix | 692-731 | 40 | |
| α-helix | 738-758 | 21 | |
| α-helix | 759-761 | 3 | |
| α-helix | 762-764 | 3 | |
| α-helix | 765-769 | 5 | |
| α-helix | 776-787 | 12 | |
Chains D, G and J: 8 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-10 | 4 | |
| α-helix | 13-15 | 3 | |
| α-helix | 29-36 | 8 | |
| β-strand | 41-45 | 5 | 10 |
| α-helix | 53-60 | 8 | |
| α-helix | 61-63 | 3 | |
| β-strand | 66-73 | 8 | 10 |
| β-strand | 80-88 | 9 | 10 |
| α-helix | 91-100 | 10 | |
| β-strand | 105 | 1 | 11 |
| β-strand | 110 | 1 | 11 |
| β-strand | 112-115 | 4 | 10 |
| β-strand | 125 | 1 | 10 |
| α-helix | 135-138 | 4 | |
| α-helix | 144-146 | 3 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 362-367 | 6 | |
Chain F: 50 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-37 | 13 | |
| α-helix | 46-59 | 14 | |
| α-helix | 61-78 | 18 | |
| α-helix | 80-82 | 3 | |
| α-helix | 83-96 | 14 | |
| α-helix | 98-117 | 20 | |
| α-helix | 121-136 | 16 | |
| β-strand | 140 | 1 | 12 |
| α-helix | 142-153 | 12 | |
| α-helix | 154-157 | 4 | |
| α-helix | 163-174 | 12 | |
| α-helix | 177-187 | 11 | |
| α-helix | 189-204 | 16 | |
| α-helix | 211-214 | 4 | |
| β-strand | 217 | 1 | 13 |
| β-strand | 227 | 1 | 14 |
| α-helix | 228-241 | 14 | |
| α-helix | 252-256 | 5 | |
| α-helix | 257-261 | 5 | |
| α-helix | 264-265 | 2 | |
| β-strand | 266 | 1 | 12 |
| α-helix | 268-270 | 3 | |
| α-helix | 273-276 | 4 | |
| α-helix | 283-285 | 3 | |
| β-strand | 287 | 1 | 14 |
| α-helix | 294-296 | 3 | |
| α-helix | 302-305 | 4 | |
| α-helix | 309-325 | 17 | |
| α-helix | 329-337 | 9 | |
| α-helix | 347-359 | 13 | |
| α-helix | 369-382 | 14 | |
| α-helix | 387-400 | 14 | |
| α-helix | 402-404 | 3 | |
| β-strand | 405 | 1 | 13 |
| α-helix | 407-422 | 16 | |
| α-helix | 430-436 | 7 | |
| α-helix | 444-459 | 16 | |
| α-helix | 462-467 | 6 | |
| α-helix | 471-475 | 5 | |
| α-helix | 478-480 | 3 | |
| α-helix | 499-509 | 11 | |
| α-helix | 514-521 | 8 | |
| α-helix | 541-554 | 14 | |
| α-helix | 559-568 | 10 | |
| α-helix | 570-576 | 7 | |
| α-helix | 580-594 | 15 | |
| α-helix | 598-610 | 13 | |
| α-helix | 616-623 | 8 | |
| α-helix | 626-631 | 6 | |
| α-helix | 635-664 | 30 | |
| α-helix | 689-731 | 43 | |
| α-helix | 738-758 | 21 | |
| α-helix | 759-761 | 3 | |
| α-helix | 762-764 | 3 | |
| α-helix | 765-769 | 5 | |
| α-helix | 776-787 | 12 | |
Chain I: 49 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-37 | 9 | |
| α-helix | 46-78 | 33 | |
| α-helix | 80-82 | 3 | |
| α-helix | 83-96 | 14 | |
| α-helix | 98-117 | 20 | |
| α-helix | 121-136 | 16 | |
| β-strand | 140 | 1 | 17 |
| α-helix | 142-153 | 12 | |
| α-helix | 154-157 | 4 | |
| α-helix | 163-174 | 12 | |
| α-helix | 177-187 | 11 | |
| α-helix | 189-204 | 16 | |
| α-helix | 211-214 | 4 | |
| β-strand | 217 | 1 | 18 |
| β-strand | 227 | 1 | 19 |
| α-helix | 228-241 | 14 | |
| α-helix | 252-256 | 5 | |
| α-helix | 257-261 | 5 | |
| α-helix | 264-265 | 2 | |
| β-strand | 266 | 1 | 17 |
| α-helix | 268-270 | 3 | |
| α-helix | 273-276 | 4 | |
| α-helix | 283-285 | 3 | |
| β-strand | 287 | 1 | 19 |
| α-helix | 294-296 | 3 | |
| α-helix | 302-305 | 4 | |
| α-helix | 309-325 | 17 | |
| α-helix | 329-337 | 9 | |
| α-helix | 347-359 | 13 | |
| α-helix | 369-382 | 14 | |
| α-helix | 387-400 | 14 | |
| α-helix | 402-404 | 3 | |
| β-strand | 405 | 1 | 18 |
| α-helix | 407-422 | 16 | |
| α-helix | 430-436 | 7 | |
| α-helix | 444-459 | 16 | |
| α-helix | 462-467 | 6 | |
| α-helix | 471-475 | 5 | |
| α-helix | 478-480 | 3 | |
| α-helix | 498-509 | 12 | |
| α-helix | 514-521 | 8 | |
| α-helix | 541-554 | 14 | |
| α-helix | 559-568 | 10 | |
| α-helix | 570-576 | 7 | |
| α-helix | 580-594 | 15 | |
| α-helix | 598-610 | 13 | |
| α-helix | 616-623 | 8 | |
| α-helix | 626-631 | 6 | |
| α-helix | 635-664 | 30 | |
| α-helix | 689-731 | 43 | |
| α-helix | 738-758 | 21 | |
| α-helix | 759-761 | 3 | |
| α-helix | 762-764 | 3 | |
| α-helix | 765-769 | 5 | |
| α-helix | 776-787 | 12 | |
Chain K: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 362-368 | 7 | |
1 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 |
|---|
| Nuclear cap-binding protein subunit 1 | A, C, F, I | protein | 772 | Homo sapiens | Q09161 (AlphaFold model) |
| Nuclear cap-binding protein subunit 2 | B, D, G, J | protein | 158 | Homo sapiens | P52298 (AlphaFold model) |
| Negative elongation factor E | E, K, Z | protein | 21 | Homo sapiens | P18615 (AlphaFold model) |
Sequence of entity 1 (A, C, F, I), FASTA
>5OOB_1 Nuclear cap-binding protein subunit 1 (chains A, C, F, I)
MKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARL
LPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCH
VIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFAN
TESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDS
ILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENL
HCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIE
LCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDCLS
QDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPANPTCIYKYGDESSNSLPGH
SVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFNPLKIEVFVQTLLHLAAKS
FSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAA
VANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELEEAKEKLARQHKRRSDDDD
RSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTP
WYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQA
Sequence of entity 2 (B, D, G, J), FASTA
>5OOB_2 Nuclear cap-binding protein subunit 2 (chains B, D, G, J)
GAMSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYE
LFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG
FKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ
Sequence of entity 3 (E, K, Z), FASTA
>5OOB_3 Negative elongation factor E (chains E, K, Z)
DKRTQIVYSDDVYKENLVDGF
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MGT | 7N-methyl-8-hydroguanosine-5'-triphosphate | C11 H20 N5 O14 P3 | 4 |
Primary citation
Structural basis for mutually exclusive co-transcriptional nuclear cap-binding complexes with either NELF-E or ARS2. Schulze, W.M., Cusack, S. Nat Commun (2017) 8:1302-1302. DOI 10.1038/s41467-017-01402-w · PubMed
Other PDB entries of the same protein (UniProt Q09161 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1H2V 2.0 Å, Structure of the human nuclear cap-binding-complex (CBC)
- 1H6K 2.0 Å, nuclear Cap Binding Complex
- 1H2T 2.1 Å, Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue…
- 1N52 2.11 Å, Cap Binding Complex
- 3FEY 2.2 Å, Crystal structure of the CBC-importin alpha complex.
- 1H2U 2.4 Å, Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue…
- 9HFL 2.62 Å, Cryo-EM structure of the human snRNA export complex comprising CBC-PHAX-CRM1-RanGTP and…
- 6D0Y 2.68 Å, X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding…
- 1N54 2.72 Å, Cap Binding Complex m7GpppG free
- 5OO6 2.8 Å, Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide
- 8BY6 3.19 Å, Structure of the human nuclear cap-binding complex bound to NCBP3(560-620) and…
- 8SRR 3.22 Å, Cryo-EM structure of the CBC-ALYREF complex
Browse structure collections
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