8SRR: CBC-ALYREF complex

Cryo-EM structure of the CBC-ALYREF complex. Determined by electron microscopy at 3.22 Å resolution. Released 25 Sept 2024.

Method: Electron microscopy
Resolution: 3.22 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 7,975
Mol. weight: 127.99 kDa
Ligands: M7G
Released: 25 Sept 2024

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

Secondary structure: helices and β-sheets

8SRR contains 58 α-helices and 19 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: 50 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	30-36	7
α-helix	46-59	14
α-helix	61-78	18
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	163-175	13
α-helix	177-187	11
α-helix	189-204	16
β-strand	227	1	2
α-helix	228-241	14
α-helix	252-254	3
α-helix	257-261	5
α-helix	263-265	3
β-strand	266	1	1
α-helix	267-269	3
α-helix	273-276	4
α-helix	283-285	3
β-strand	287	1	2
α-helix	294-296	3
α-helix	303-305	3
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
α-helix	402-404	3
α-helix	407-422	16
α-helix	430-436	7
α-helix	444-457	14
α-helix	462-468	7
α-helix	471-476	6
α-helix	478-480	3
α-helix	498-509	12
α-helix	514-521	8
α-helix	525-526	2
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	635-675	41
α-helix	682-731	50
α-helix	738-753	16
α-helix	755-758	4
α-helix	759-761	3
α-helix	762-764	3
α-helix	765-769	5
α-helix	776-789	14

Chain B: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	17-18	2
α-helix	29-37	9
β-strand	41-45	5	3
α-helix	53-61	9
β-strand	66-73	8	3
β-strand	80-88	9	3
α-helix	91-100	10
β-strand	105	1	4
β-strand	110	1	4
β-strand	112-116	5	3
β-strand	125	1	3
α-helix	134-138	5
β-strand	143	1	5
β-strand	148	1	5

Chain C: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	75-80	6	6
α-helix	88-94	7
β-strand	101-108	8	6
β-strand	114-122	9	6
α-helix	125-135	11
β-strand	139-140	2	7
β-strand	143-144	2	7
β-strand	146-149	4	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear cap-binding protein subunit 1	A	protein	790	Homo sapiens	Q09161 (AlphaFold model)
Nuclear cap-binding protein subunit 2	B	protein	156	Homo sapiens	P52298 (AlphaFold model)
RNA and export factor binding protein 2	C	protein	160	Mus musculus	Q9JJW6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8SRR_1 Nuclear cap-binding protein subunit 1 (chains A)
MSRRRHSDENDGGQPHKRRKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEAD
LPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANN
YNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWV
GKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLK
KDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEG
PVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELF
QLPAPPHIDVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHH
LSNFQFRWSWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPAN
PTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFN
PLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQM
IAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELE
EAKEKLARQHKRRSDDDDRSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMI
LTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILA
VFQQFCALQA

Sequence of entity 2 (B), FASTA

>8SRR_2 Nuclear cap-binding protein subunit 2 (chains B)
MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK
EGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

Sequence of entity 3 (C), FASTA

>8SRR_3 RNA and export factor binding protein 2 (chains C)
GAMGSMADKMDMSLDDIIKLNRNQRRVNRGGGPRRNRPAIARGGRNRPAPYSRPKPLPDK
WQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL
GTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVTSQID

Ligands and cofactors

ID	Name	Formula	Copies
M7G	7N-methyl-8-hydroguanosine-5'-diphosphate	C11 H18 N5 O11 P2	1

Primary citation

Cryo-EM structure of the CBC-ALYREF complex. Clarke, B.P., Angelos, A.E., Mei, M. et al. Elife (2024) 12. DOI 10.7554/eLife.91432 · 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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