1N52: Cap Binding Complex

Cap Binding Complex. Determined by X-ray diffraction at 2.11 Å resolution. Released 18 Feb 2003.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,699
Mol. weight: 112.48 kDa
Ligands: MG, GTG
Released: 18 Feb 2003

Explore 1N52 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1N52 contains 56 α-helices and 15 β-strands across 2 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: 49 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	27-39	13
α-helix	46-60	15
α-helix	65-78	14
α-helix	80-82	3
α-helix	83-94	12
α-helix	98-117	20
α-helix	121-134	14
α-helix	135-137	3
β-strand	140	1	1
α-helix	142-153	12
α-helix	154-156	3
α-helix	163-174	12
α-helix	191-203	13
α-helix	211-214	4
β-strand	217	1	2
β-strand	227	1	3
α-helix	228-240	13
α-helix	252-254	3
α-helix	257-261	5
β-strand	266	1	1
α-helix	274-276	3
α-helix	283-285	3
β-strand	287	1	3
α-helix	294-296	3
α-helix	303-305	3
α-helix	309-325	17
α-helix	329-337	9
α-helix	347-359	13
α-helix	370-382	13
α-helix	387-400	14
α-helix	402-404	3
β-strand	405	1	2
α-helix	407-421	15
α-helix	430-438	9
α-helix	444-458	15
α-helix	462-468	7
α-helix	471-476	6
α-helix	478-480	3
α-helix	498-508	11
α-helix	514-522	9
α-helix	541-553	13
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	626-628	3
α-helix	635-663	29
α-helix	688-731	44
α-helix	738-758	21
α-helix	759-761	3
α-helix	762-764	3
α-helix	765-769	5
α-helix	776-786	11
α-helix	787-789	3

Chain B: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
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	80-88	9	4
α-helix	91-100	10
β-strand	105-106	2	5
β-strand	109-110	2	5
β-strand	112-115	4	4
β-strand	125	1	4
α-helix	135-138	4
β-strand	143	1	6
β-strand	148	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
80 kDa nuclear cap binding protein	A	protein	790	Homo sapiens	Q09161 (AlphaFold model)
20 kDa nuclear cap binding protein	B	protein	156	Homo sapiens	P52298 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1N52_1 80 kDa nuclear cap binding protein (chains A)
MSRRRHSDENDGGQPHKRRKTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEAD
LPNYKSKILRLLCTVARLLPEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANN
YNEAVYLVRFLSDLVNCHVIAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWV
GKELYEKKDAEMDRIFANTESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLK
KDRWQERHILRPYLAFDSILCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEG
PVMPGSHSVERFVIEENLHCIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELF
QLPAPPHIDVMYTTLLIELCKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHH
LSNFQFRWSWEDWSDCLSQDPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPAN
PTCIYKYGDESSNSLPGHSVALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFN
PLKIEVFVQTLLHLAAKSFSHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQM
IAVLVDKMIRTQIVDCAAVANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVLKIQKELE
EAKEKLARQHKRRSDDDDRSSDRKDGVLEEQIERLQEKVESAQSEQKNLFLVIFQRFIMI
LTEHLVRCETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILA
VFQQFCALQA

Sequence of entity 2 (B), FASTA

>1N52_2 20 kDa nuclear cap binding protein (chains B)
MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK
EGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
GTG	7-methyl-guanosine-5'-triphosphate-5'-guanosine	C21 H30 N10 O18 P3	1

Water and common crystallization additives (PG4, GOL) are not listed.

Primary citation

Structural basis of m7GpppG binding to the nuclear cap-binding protein complex. Calero, G., Wilson, K., Ly, T. et al. Nat Struct Biol (2002) 9:912-917. DOI 10.1038/nsb874 · 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…
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…
8SRR 3.22 Å, Cryo-EM structure of the CBC-ALYREF complex

Browse structure collections

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