5OO6: Nuclear cap-binding protein subunit 1

Complex of human nuclear cap-binding complex with ARS2 C-terminal peptide. Determined by X-ray diffraction at 2.8 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 24
Atoms: 58,743
Mol. weight: 911.12 kDa
Ligands: MGT
Released: 15 Nov 2017

Explore 5OO6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OO6 contains 447 α-helices and 136 β-strands across 24 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.

Chains A and V: 49 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	28-37	10
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	1
α-helix	142-153	12
α-helix	154-156	3
α-helix	163-174	12
α-helix	177-187	11
α-helix	189-205	17
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	267-270	4
α-helix	272-276	5
α-helix	283-285	3
β-strand	287	1	3
α-helix	294-296	3
α-helix	301-305	5
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	462-468	7
α-helix	478-480	3
α-helix	498-509	12
α-helix	514-520	7
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	616-624	9
α-helix	626-628	3
α-helix	635-669	35
α-helix	688-731	44
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	776-787	12

Chains B, E, H, K, N, Q, T and W: 7 helices, 10 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
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
β-strand	143	1	7
α-helix	144-146	3
β-strand	148	1	7

Chains C, F, I, L, O, R, U and X: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	858	1	5

Chains D, G, J, M and P: 49 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	28-37	10
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	8
α-helix	142-153	12
α-helix	154-156	3
α-helix	163-174	12
α-helix	177-187	11
α-helix	189-205	17
α-helix	211-214	4
β-strand	217	1	9
β-strand	227	1	10
α-helix	228-241	14
α-helix	252-256	5
α-helix	257-261	5
α-helix	264-265	2
β-strand	266	1	8
α-helix	267-270	4
α-helix	272-276	5
α-helix	283-285	3
β-strand	287	1	10
α-helix	294-296	3
α-helix	301-305	5
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	9
α-helix	407-422	16
α-helix	430-436	7
α-helix	444-459	16
α-helix	462-468	7
α-helix	478-480	3
α-helix	498-509	12
α-helix	514-520	7
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	616-624	9
α-helix	626-628	3
α-helix	635-669	35
α-helix	685-731	47
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	776-787	12

Chain S: 48 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	28-37	10
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	43
α-helix	142-153	12
α-helix	154-156	3
α-helix	163-174	12
α-helix	177-187	11
α-helix	189-205	17
α-helix	211-214	4
β-strand	217	1	44
β-strand	227	1	45
α-helix	228-241	14
α-helix	252-256	5
α-helix	257-261	5
α-helix	264-265	2
β-strand	266	1	43
α-helix	267-270	4
α-helix	272-276	5
α-helix	283-285	3
β-strand	287	1	45
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	44
α-helix	407-422	16
α-helix	430-436	7
α-helix	444-459	16
α-helix	462-468	7
α-helix	498-509	12
α-helix	514-520	7
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	616-624	9
α-helix	626-628	3
α-helix	635-669	35
α-helix	688-731	44
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	776-787	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nuclear cap-binding protein subunit 1	A, D, G, J, M, P, S, V	protein	772	Homo sapiens	Q09161 (AlphaFold model)
Nuclear cap-binding protein subunit 2	B, E, H, K, N, Q, T, W	protein	158	Homo sapiens	P52298 (AlphaFold model)
Serrate RNA effector molecule homolog	C, F, I, L, O, R, U, X	protein	48	Homo sapiens	Q9BXP5 (AlphaFold model)

Sequence of entity 1 (A, D, G, J, M, P, S, V), FASTA

>5OO6_1 Nuclear cap-binding protein subunit 1 (chains A, D, G, J, M, P, S, V)
MKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARL
LPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCH
VIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFAN
TESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDS
ILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENL
HCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIE
LCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDCLS
QDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPVNPTCIYKYGDESSNSLPGH
SVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFNPLKIEVFVQTLLHLAAKS
FSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAA
VANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELEEAKEKLARQHKRRSDDDD
RSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMILTEHLVRCETDGTSVLTP
WYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCALQA

Sequence of entity 2 (B, E, H, K, N, Q, T, W), FASTA

>5OO6_2 Nuclear cap-binding protein subunit 2 (chains B, E, H, K, N, Q, T, W)
GAMSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYE
LFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAG
FKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

Sequence of entity 3 (C, F, I, L, O, R, U, X), FASTA

>5OO6_3 Serrate RNA effector molecule homolog (chains C, F, I, L, O, R, U, X)
GAMGRGNYDAFRGQGGYPGKPRNRMVRGDPRAIVEYRDLDAPDDVDFF

Ligands and cofactors

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

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