Structure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP. Determined by electron microscopy at 3.43 Å resolution. Released 17 Jan 2024.
Explore 8PMP in 3D Show helices and sheets RCSB PDB PDBe
8PMP contains 54 α-helices and 15 β-strands across 3 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 26-37 | 12 | |
| α-helix | 46-59 | 14 | |
| α-helix | 61-63 | 3 | |
| α-helix | 65-78 | 14 | |
| 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 | 142-154 | 13 | |
| α-helix | 155-157 | 3 | |
| α-helix | 163-203 | 41 | |
| α-helix | 211-214 | 4 | |
| β-strand | 217 | 1 | 2 |
| β-strand | 227 | 1 | 3 |
| α-helix | 228-241 | 14 | |
| α-helix | 252-254 | 3 | |
| α-helix | 257-261 | 5 | |
| β-strand | 266 | 1 | 1 |
| α-helix | 268-271 | 4 | |
| 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 | 309-324 | 16 | |
| α-helix | 329-337 | 9 | |
| α-helix | 347-360 | 14 | |
| α-helix | 369-382 | 14 | |
| α-helix | 387-400 | 14 | |
| β-strand | 405 | 1 | 2 |
| α-helix | 407-423 | 17 | |
| α-helix | 430-433 | 4 | |
| α-helix | 435-438 | 4 | |
| α-helix | 444-458 | 15 | |
| α-helix | 462-468 | 7 | |
| α-helix | 471-476 | 6 | |
| α-helix | 478-480 | 3 | |
| α-helix | 498-509 | 12 | |
| α-helix | 514-522 | 9 | |
| α-helix | 541-554 | 14 | |
| α-helix | 559-568 | 10 | |
| α-helix | 570-576 | 7 | |
| α-helix | 580-593 | 14 | |
| α-helix | 598-610 | 13 | |
| α-helix | 616-621 | 6 | |
| α-helix | 629-631 | 3 | |
| α-helix | 635-675 | 41 | |
| α-helix | 687-731 | 45 | |
| α-helix | 738-764 | 27 | |
| α-helix | 765-769 | 5 | |
| α-helix | 776-788 | 13 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 7-10 | 4 | |
| α-helix | 29-38 | 10 | |
| β-strand | 41-45 | 5 | 4 |
| α-helix | 53-62 | 10 | |
| β-strand | 66-73 | 8 | 4 |
| β-strand | 79 | 1 | 5 |
| β-strand | 80-88 | 9 | 4 |
| α-helix | 91-100 | 10 | |
| β-strand | 105-106 | 2 | 6 |
| β-strand | 109-110 | 2 | 6 |
| β-strand | 112-116 | 5 | 4 |
| β-strand | 125 | 1 | 4 |
| α-helix | 134-138 | 5 | |
| α-helix | 144-146 | 3 | |
| α-helix | 151-154 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 855-857 | 3 | |
| β-strand | 858 | 1 | 5 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Nuclear cap-binding protein subunit 1 | A | protein | 772 | Homo sapiens | Q09161 (AlphaFold model) |
| Nuclear cap-binding protein subunit 2 | B | protein | 156 | Homo sapiens | P52298 (AlphaFold model) |
| Serrate RNA effector molecule homolog | D | protein | 729 | Homo sapiens | Q9BXP5 (AlphaFold model) |
>8PMP_1 Nuclear cap-binding protein subunit 1 (chains A) MKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARL LPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCH VIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFAN TESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDS ILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENL HCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIE LCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDCLS QDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPANPTCIYKYGDESSNSLPGH SVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFNPLKIEVFVQTLLHLAAKS FSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAA VANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELEEAKEKLARQHKRRSDDDD RSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTP WYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQA
>8PMP_2 Nuclear cap-binding protein subunit 2 (chains B) MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK EGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ
>8PMP_3 Serrate RNA effector molecule homolog (chains D) VMKTFKEFLLSLDDSVDETEAVKRYNDYKLDFRRQQMQDFFLAHKDEEWFRSKYHPDEVG KRRQEARGALQNRLRVFLSLMETGWFDNLLLDIDKADAIVKMLDAAVIKMEGGTENDLRI LEQEEEEEQAGKPGEPSKKEEGRAGAGLGDGERKTNDKDEKKEDGKQAENDSSNDDKTKK SEGDGDKEEKKEDSEKEAKKSSKKRNRKHSGDDSFDEGSVSESESESESGQAEEEKEEAE EALKEKEKPKEEEWEKPKDAAGLECKPRPLHKTCSLFMRNIAPNISRAEIISLCKRYPGF MRVALSEPQPERRFFRRGWVTFDRSVNIKEICWNLQNIRLRECELSPGVNRDLTRRVRNI NGITQHKQIVRNDIKLAAKLIHTLDDRTQLWASEPGTPPLPTSLPSQNPILKNITDYLIE EVSAEEEELLGSSGGAPPEEPPKEGNPAEINVERDEKLIKVLDKLLLYLRIVHSLDYYNT CEYPNEDEMPNRCGIIHVRGPMPPNRISHGEVLEWQKTFEEKLTPLLSVRESLSEEEAQK MGRKDPEQEVEKFVTSNTQELGKDKWLCPLSGKKFKGPEFVRKHIFNKHAEKIEEVKKEV AFFNNFLTDAKRPALPEIKPAQPPGPAQILPPGLTPGLPYPHQTPQGLMPYGQPRPPILG YGAGAVRPAVPTGGPPYPHAPYGAGRGNYDAFRGQGGYPGKPRNRMVRGDPRAIVEYRDL DAPDDVDFF
| ID | Name | Formula | Copies |
|---|---|---|---|
| MGT | 7N-methyl-8-hydroguanosine-5'-triphosphate | C11 H20 N5 O14 P3 | 1 |
Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. Dubiez, E., Pellegrini, E., Finderup Brask, M. et al. Cell Rep (2024) 43:113639-113639. DOI 10.1016/j.celrep.2023.113639 · PubMed
Other PDB entries of the same protein (UniProt Q09161 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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