8PNT: Human nuclear cap-binding complex

Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA. Determined by electron microscopy at 3.46 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 3.46 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,609
Mol. weight: 197.29 kDa
Ligands: MGT
Released: 17 Jan 2024

Explore 8PNT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PNT contains 54 α-helices and 13 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.

Chain A: 46 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	27-37	11
α-helix	46-59	14
α-helix	65-78	14
α-helix	80-82	3
α-helix	83-96	14
α-helix	98-118	21
α-helix	121-135	15
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	257-260	4
α-helix	264-265	2
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	347-359	13
α-helix	369-382	14
α-helix	387-400	14
β-strand	405	1	2
α-helix	407-423	17
α-helix	430-437	8
α-helix	444-458	15
α-helix	462-468	7
α-helix	471-476	6
α-helix	490-494	5
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	580-593	14
α-helix	598-610	13
α-helix	616-623	8
α-helix	626-628	3
α-helix	635-674	40
α-helix	684-731	48
α-helix	738-753	16
α-helix	755-764	10
α-helix	765-769	5
α-helix	776-788	13

Chain B: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	29-36	8
β-strand	41-45	5	4
α-helix	53-60	8
β-strand	66-73	8	4
β-strand	80-88	9	4
α-helix	91-96	6
α-helix	97-101	5
β-strand	105-106	2	5
β-strand	109-110	2	5
β-strand	112-116	5	4
β-strand	125	1	4
α-helix	134-138	5
α-helix	144-146	3

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	117-131	15

Molecules and chains

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)
Phosphorylated adapter RNA export protein	C, D	protein	394	Homo sapiens	Q9H814 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PNT_1 Nuclear cap-binding protein subunit 1 (chains A)
MKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARL
LPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCH
VIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFAN
TESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDS
ILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENL
HCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIE
LCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDCLS
QDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPANPTCIYKYGDESSNSLPGH
SVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFNPLKIEVFVQTLLHLAAKS
FSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAA
VANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELEEAKEKLARQHKRRSDDDD
RSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTP
WYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQA

Sequence of entity 2 (B), FASTA

>8PNT_2 Nuclear cap-binding protein subunit 2 (chains B)
MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK
EGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

Sequence of entity 3 (C, D), FASTA

>8PNT_3 Phosphorylated adapter RNA export protein (chains C, D)
MALEVGDMEDGQLSDSDSDMTVAPSDRPLQLPKVLGGDSAMRAFQNTATACAPVSHYRAV
ESVDSSEESFSDSDDDSCLWKRKRQKCFNPPPKPEPFQFGQSSQKPPVAGGKKINNIWGA
VLQEQNQDAVATELGILGMEGTIDRSRQSETYNYLLAKKLRKESQEHTKDLDKELDEYMH
GGKKMGSKEEENGQGHLKRKRPVKDRLGNRPEMNYKGRYEITAEDSQEKVADEISFRLQE
PKKDLIARVVRIIGNKKAIELLMETAEVEQNGGLFIMNGSRRRTPGGVFLNLLKNTPSIS
EEQIKDIFYIENQKEYENKKAARKRRTQVLGKKMKQAIKSLNFQEDDDTSRETFASDTNE
ALASLDESQEGHAEAKLEAEEAIEVDHSHDLDIF

Ligands and cofactors

ID	Name	Formula	Copies
MGT	7N-methyl-8-hydroguanosine-5'-triphosphate	C11 H20 N5 O14 P3	1

Primary citation

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:

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
5OOB 2.79 Å, Complex of human nuclear cap-binding complex with M7GTP and nelf-E C-terminal peptide
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…

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