1H2U: Human nuclear cap-binding-complex

Structure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG. Determined by X-ray diffraction at 2.4 Å resolution. Released 17 Oct 2002.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 15,364
Mol. weight: 205.37 kDa
Ligands: 7MG, GDP
Released: 17 Oct 2002

Explore 1H2U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1H2U contains 114 α-helices and 30 β-strands across 4 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	28-37	10
α-helix	46-59	14
α-helix	61-78	18
α-helix	80-82	3
α-helix	83-96	14
α-helix	98-117	20
α-helix	121-133	13
β-strand	140	1	1
α-helix	142-153	12
α-helix	154-157	4
α-helix	163-174	12
α-helix	177-205	29
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	257-260	4
α-helix	264-265	2
β-strand	266	1	1
α-helix	268-271	4
α-helix	273-276	4
α-helix	282-285	4
β-strand	287	1	3
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	2
α-helix	407-421	15
α-helix	430-438	9
α-helix	444-459	16
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	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	616-623	8
α-helix	626-628	3
α-helix	635-649	15
α-helix	703-730	28
α-helix	738-753	16
α-helix	755-758	4
α-helix	759-761	3
α-helix	762-768	7
α-helix	776-786	11

Chain B: 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	4
α-helix	142-154	13
α-helix	155-157	3
α-helix	163-174	12
α-helix	177-187	11
α-helix	189-204	16
α-helix	211-214	4
β-strand	217	1	5
β-strand	227	1	6
α-helix	228-241	14
α-helix	252-256	5
α-helix	257-261	5
α-helix	264-265	2
β-strand	266	1	4
α-helix	267-270	4
α-helix	283-285	3
β-strand	287	1	6
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	370-382	13
α-helix	387-400	14
α-helix	402-404	3
β-strand	405	1	5
α-helix	407-421	15
α-helix	430-438	9
α-helix	444-459	16
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	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	616-623	8
α-helix	626-628	3
α-helix	635-650	16
α-helix	703-731	29
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 X: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	13-15	3
α-helix	29-36	8
β-strand	41-45	5	7
α-helix	53-60	8
α-helix	61-63	3
β-strand	66-73	8	7
β-strand	80-88	9	7
α-helix	91-100	10
β-strand	105-106	2	8
β-strand	109-110	2	8
β-strand	112-115	4	7
β-strand	125	1	7
α-helix	134-137	4
β-strand	143	1	9
α-helix	144-146	3
β-strand	148	1	9

Chain Y: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	13-15	3
α-helix	29-36	8
β-strand	41-45	5	10
α-helix	53-60	8
α-helix	61-63	3
β-strand	66-73	8	10
β-strand	80-88	9	10
α-helix	91-100	10
β-strand	105-106	2	11
β-strand	109-110	2	11
β-strand	112-115	4	10
β-strand	125	1	10
α-helix	135-138	4
β-strand	142-143	2	12
α-helix	144-146	3
β-strand	148-149	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
80 kda nuclear cap binding protein	A, B	protein	723	HOMO SAPIENS	Q09161 (AlphaFold model)
20 kda nuclear cap binding protein	X, Y	protein	156	HOMO SAPIENS	P52298 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1H2U_1 80 KDA NUCLEAR CAP BINDING PROTEIN (chains A, B)
KTSDANETEDHLESLICKVGEKSACSLESNLEGLAGVLEADLPNYKSKILRLLCTVARLL
PEKLTIYTTLVGLLNARNYNFGGEFVEAMIRQLKESLKANNYNEAVYLVRFLSDLVNCHV
IAAPSMVAMFENFVSVTQEEDVPQVRRDWYVYAFLSSLPWVGKELYEKKDAEMDRIFANT
ESYLKRRQKTHVPMLQVWTADKPHPQEEYLDCLWAQIQKLKKDRWQERHILRPYLAFDSI
LCEALQHNLPPFTPPPHTEDSVYPMPRVIFRMFDYTDDPEGPVMPGSHSVERFVIEENLH
CIIKSHWKERKTCAAQLVSYPGKNKIPLNYHIVEVIFAELFQLPAPPHIDVMYTTLLIEL
CKLQPGSLPQVLAQATEMLYMRLDTMNTTCVDRFINWFSHHLSNFQFRWSWEDWSDCLSQ
DPESPKPKFVREVLEKCMRLSYHQRILDIVPPTFSALCPSNPTCIYKYGDESSNSLPGHS
VALCLAVAFKSKATNDEIFSILKDVPNPNQDDDDDEGFSFNPLKIEVFVQTLLHLAAKSF
SHSFSALAKFHEVFKTLAESDEGKLHVLRVMFEVWRNHPQMIAVLVDKMIRTQIVDCAAV
ANWIFSSELSRDFTRLFVWEILHSTIRKMNKHVGAQSEQKNLFLVIFQRFIMILTEHLVR
CETDGTSVLTPWYKNCIERLQQIFLQHHQIIQQYMVTLENLLFTAELDPHILAVFQQFCA
LQA

Sequence of entity 2 (X, Y), FASTA

>1H2U_2 20 KDA NUCLEAR CAP BINDING PROTEIN (chains X, Y)
MSGGLLKALRSDSYVELSQYRDQHFRGDNEEQEKLLKKSCTLYVGNLSFYTTEEQIYELF
SKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYINGTRLDDRIIRTDWDAGFK
EGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQNQ

Ligands and cofactors

ID	Name	Formula	Copies
7MG	7N-methyl-8-hydroguanosine-5'-monophosphate	C11 H18 N5 O8 P	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

Large-Scale Induced Fit Recognition of an M(7)Gpppg CAP Analogue by the Human Nuclear CAP-Binding Complex. Mazza, C., Segref, A., Mattaj, I.W. et al. EMBO J (2002) 21:5548. DOI 10.1093/EMBOJ/CDF538 · 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.
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

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