PDBsum entry 1h2v

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Nuclear protein PDB id
Protein chains
722 a.a. *
93 a.a. *
Waters ×294
* Residue conservation analysis
PDB id:
Name: Nuclear protein
Title: Structure of the human nuclear cap-binding-complex (cbc)
Structure: 80 kda nuclear cap binding protein. Chain: c. Fragment: mif4g domain, residues 20-790. Synonym: ncbp 80 kda subunit, cbp80. Engineered: yes. Mutation: yes. Other_details: deletion of the first 19 residues in n-terminal, engineered mutation ala 479 ser. 20 kda nuclear cap binding protein.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Expression_system_cell_line: high five. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
2.0Å     R-factor:   0.212     R-free:   0.247
Authors: C.Mazza,A.Segref,I.W.Mattaj,S.Cusack
Key ref:
C.Mazza et al. (2002). Large-scale induced fit recognition of an m(7)GpppG cap analogue by the human nuclear cap-binding complex. EMBO J, 21, 5548-5557. PubMed id: 12374755 DOI: 10.1093/emboj/cdf538
16-Aug-02     Release date:   17-Oct-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q09161  (NCBP1_HUMAN) -  Nuclear cap-binding protein subunit 1
790 a.a.
722 a.a.*
Protein chain
Pfam   ArchSchema ?
P52298  (NCBP2_HUMAN) -  Nuclear cap-binding protein subunit 2
156 a.a.
93 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribonucleoprotein complex   8 terms 
  Biological process     viral reproduction   28 terms 
  Biochemical function     protein binding     7 terms  


DOI no: 10.1093/emboj/cdf538 EMBO J 21:5548-5557 (2002)
PubMed id: 12374755  
Large-scale induced fit recognition of an m(7)GpppG cap analogue by the human nuclear cap-binding complex.
C.Mazza, A.Segref, I.W.Mattaj, S.Cusack.
The heterodimeric nuclear cap-binding complex (CBC) binds to the 5' cap structure of RNAs in the nucleus and plays a central role in their diverse maturation steps. We describe the crystal structure at 2.1 A resolution of human CBC bound to an m(7)GpppG cap analogue. Comparison with the structure of uncomplexed CBC shows that cap binding induces co-operative folding around the dinucleotide of some 50 residues from the N- and C-terminal extensions to the central RNP domain of the small subunit CBP20. The cap-bound conformation of CBP20 is stabilized by an intricate network of interactions both to the ligand and within the subunit, as well as new interactions of the CBP20 N-terminal tail with the large subunit CBP80. Although the structure is very different from that of other known cap-binding proteins, such as the cytoplasmic cap-binding protein eIF4E, specificity for the methylated guanosine again is achieved by sandwiching the base between two aromatic residues, in this case two conserved tyrosines. Implications for the transfer of capped mRNAs to eIF4E, required for translation initiation, are discussed.
  Selected figure(s)  
Figure 1.
Figure 1 (A) Time course of limited proteolysis. A 42 g aliquot of CBC was incubated at room temperature with 210 ng of trypsin in the absence or presence of 10 mM cap analogue m^7GpppG in a total volume of 60 l. Aliquots of 10 l were taken off every 0, 5, 10, 20, 40 and 60 min, denatured by 3 l of denaturing buffer (125 mM Tris pH 6.8, 260 mM DTT, 30% glycerol, 10% SDS and 0.025% Coomassie Blue) and loaded onto a 13.5% Tricine SDS−polyacrylamide gel. (B) Cap-binding activity of CBP80 653−701. [^35S]Methionine-labelled wild-type or mutant CBP80 was incubated for 30 min at room temperature in the absence (−) or presence of either 1.7 M (high) or 53 nM (low) m^7GpppG-capped (m7) or ApppG-capped (A) unlabelled U1 Sm RNAs. The samples were fractionated by native 6% PAGE followed by fluorography. Free CBP80, CBC and the CBC−RNA complex are indicated. In the lanes indicated by an asterisk, the corresponding CBP80 proteins were loaded without CBP20. (C) Shuttling activity of CBP80 NLS 653−701 in Xenopus oocytes. [^35S]methionine-labelled CBP80 NLS2 or CBP80 NLS2 653−701 were injected together with [^35S]methionine-labelled GST−M10 into Xenopus oocyte nuclei either (1) alone (lanes 1 and 2, and 7 and 8), (2) together with m7GpppG-capped unlabelled U1 Sm RNAs (lanes 3 and 4, and 9 and 10) or (3) together with ApppG-capped U1 Sm RNAs (lanes 5 and 6, and 11 and12). Oocytes were dissected either immediately (lanes 1 and 2, and 7 and 8) or 5 h after injection (lanes 3−6 and 9−12) and the proteins analysed by SDS−PAGE followed by fluorography. GST−M10 is a mutant of HIV Rev with a non-functional nuclear export signal used as a negative control. See Ohno et al. (2000) or Segref et al. (2001) for more details.
Figure 2.
Figure 2 (A) Structure of CBP20 in the CBC NLS complex. Ribbon representation of the cap-free conformation of CBP20 showing residues 30−125 (grey). Residues involved in cap binding are shown in yellow (already in their cap-bound conformation) and blue (undergo a conformational change to interact with the cap) (compare with B). Phe49 (light green) changes conformation to help stabilize the C-terminal domain (compare with B). Salt bridges and hydrogen bonds are indicated by dashed lines. (B) Stabilization of the N- and C-terminal extensions of CBP20 upon cap binding. Ribbon representation of cap-bound CBP20 showing residues 32−125 (already ordered in the cap-free form) in grey and the N- and C-terminal extensions that fold upon cap binding in green and orange, respectively. Yellow residues stabilize the folded conformation of these two extensions through interactions with the cap. This stabilization is reinforced by protein−protein interactions involving the light green residues. D116, R123 and R127 take part to both kinds of contacts. CBP80 residues interacting with residues 5−13 from CBP20 are depicted in pink. Hydrogen bonds and salt bridges are represented as dashed lines, and the hydrophobic contacts as dashed bars. (C and D) Two views of CBC bound to the cap analogue m^7GpppG. The three MIF4G domains of CBP80 are represented in pink, yellow and green for domains 1, 2 and 3, respectively. CBP20 is depicted in red, and the cap analogue m^7GpppG in cyan. (A), (B) and (C) were generated with Molscript (Kraulis, 1991) and Render (Merritt and Murphy, 1994).
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 5548-5557) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21399644 A.Cléry, S.Jayne, N.Benderska, C.Dominguez, S.Stamm, and F.H.Allain (2011).
Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-β1.
  Nat Struct Mol Biol, 18, 443-450.
PDB code: 2kxn
21419778 D.Anunciado, A.Dhar, M.Gruebele, and A.M.Baranger (2011).
Multistep kinetics of the U1A-SL2 RNA complex dissociation.
  J Mol Biol, 408, 896-908.  
20535623 K.Ruszczyńska-Bartnik, M.Maciejczyk, and R.Stolarski (2011).
Dynamical insight into Caenorhabditis elegans eIF4E recognition specificity for mono-and trimethylated structures of mRNA 5' cap.
  J Mol Model, 17, 727-737.  
21075799 S.Lahudkar, A.Shukla, P.Bajwa, G.Durairaj, N.Stanojevic, and S.R.Bhaumik (2011).
The mRNA cap-binding complex stimulates the formation of pre-initiation complex at the promoter via its interaction with Mot1p in vivo.
  Nucleic Acids Res, 39, 2188-2209.  
20430857 A.Mourão, A.Varrot, C.D.Mackereth, S.Cusack, and M.Sattler (2010).
Structure and RNA recognition by the snRNA and snoRNA transport factor PHAX.
  RNA, 16, 1205-1216.
PDB codes: 2w4s 2xc7
20360394 J.Chang, B.Schwer, and S.Shuman (2010).
Mutational analyses of trimethylguanosine synthase (Tgs1) and Mud2: proteins implicated in pre-mRNA splicing.
  RNA, 16, 1018-1031.  
  21326824 M.Pabis, N.Neufeld, Y.Shav-Tal, and K.M.Neugebauer (2010).
Binding properties and dynamic localization of an alternative isoform of the cap-binding complex subunit CBP20.
  Nucleus, 1, 412-421.  
  21326945 S.M.Dias, R.A.Cerione, and K.F.Wilson (2010).
Unloading RNAs in the cytoplasm: An "importin" task.
  Nucleus, 1, 139-143.  
19203580 A.Marintchev, K.A.Edmonds, B.Marintcheva, E.Hendrickson, M.Oberer, C.Suzuki, B.Herdy, N.Sonenberg, and G.Wagner (2009).
Topology and regulation of the human eIF4A/4G/4H helicase complex in translation initiation.
  Cell, 136, 447-460.  
19101564 B.J.Geiss, A.A.Thompson, A.J.Andrews, R.L.Sons, H.H.Gari, S.M.Keenan, and O.B.Peersen (2009).
Analysis of flavivirus NS5 methyltransferase cap binding.
  J Mol Biol, 385, 1643-1654.
PDB codes: 3eva 3evb 3evc 3evd 3eve 3evf 3evg
19884259 H.Sato, and L.E.Maquat (2009).
Remodeling of the pioneer translation initiation complex involves translation and the karyopherin importin beta.
  Genes Dev, 23, 2537-2550.  
19033360 M.A.Brooks, A.Dziembowski, S.Quevillon-Cheruel, V.Henriot, C.Faux, H.van Tilbeurgh, and B.Séraphin (2009).
Structure of the yeast Pml1 splicing factor and its integration into the RES complex.
  Nucleic Acids Res, 37, 129-143.
PDB code: 2jkd
19668212 S.M.Dias, K.F.Wilson, K.S.Rojas, A.L.Ambrosio, and R.A.Cerione (2009).
The molecular basis for the regulation of the cap-binding complex by the importins.
  Nat Struct Mol Biol, 16, 930-937.
PDB codes: 3fex 3fey
19750007 S.S.Bradrick, and M.Gromeier (2009).
Identification of gemin5 as a novel 7-methylguanosine cap-binding protein.
  PLoS One, 4, e7030.  
19386620 T.Monecke, A.Dickmanns, and R.Ficner (2009).
Structural basis for m7G-cap hypermethylation of small nuclear, small nucleolar and telomerase RNA by the dimethyltransferase TGS1.
  Nucleic Acids Res, 37, 3865-3877.
PDB code: 3gdh
18515081 A.Cléry, M.Blatter, and F.H.Allain (2008).
RNA recognition motifs: boring? Not quite.
  Curr Opin Struct Biol, 18, 290-298.  
18454157 D.Guilligay, F.Tarendeau, P.Resa-Infante, R.Coloma, T.Crepin, P.Sehr, J.Lewis, R.W.Ruigrok, J.Ortin, D.J.Hart, and S.Cusack (2008).
The structural basis for cap binding by influenza virus polymerase subunit PB2.
  Nat Struct Mol Biol, 15, 500-506.
PDB code: 2vqz
18824697 J.Song, J.V.McGivern, K.W.Nichols, J.L.Markley, and M.D.Sheets (2008).
Structural basis for RNA recognition by a type II poly(A)-binding protein.
  Proc Natl Acad Sci U S A, 105, 15317-15322.
PDB code: 2jwn
18280238 M.V.Deshmukh, B.N.Jones, D.U.Quang-Dang, J.Flinders, S.N.Floor, C.Kim, J.Jemielity, M.Kalek, E.Darzynkiewicz, and J.D.Gross (2008).
mRNA decapping is promoted by an RNA-binding channel in Dcp2.
  Mol Cell, 29, 324-336.
PDB code: 2jvb
18186485 R.Worch, and R.Stolarski (2008).
Stacking efficiency and flexibility analysis of aromatic amino acids in cap-binding proteins.
  Proteins, 71, 2026-2037.  
18641416 T.Nagata, S.Suzuki, R.Endo, M.Shirouzu, T.Terada, M.Inoue, T.Kigawa, N.Kobayashi, P.Güntert, A.Tanaka, Y.Hayashizaki, Y.Muto, and S.Yokoyama (2008).
The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.
  Nucleic Acids Res, 36, 4754-4767.
PDB code: 2rok
18426921 V.Shen, H.Liu, S.W.Liu, X.Jiao, and M.Kiledjian (2008).
DcpS scavenger decapping enzyme can modulate pre-mRNA splicing.
  RNA, 14, 1132-1142.  
17426384 A.Pal, P.Chakrabarti, R.Bahadur, F.Rodier, and J.Janin (2007).
Peptide segments in protein-protein interfaces.
  J Biosci, 32, 101-111.  
17268778 B.Kierdaszuk, and J.Włodarczyk (2007).
Interpretation of fluorescence decay kinetics in 3-methylbenzimidazolyl(5'-5')guanosine dinucleotides: exponential dependence on the number of phosphates in the polyphosphate bridge.
  Eur Biophys J, 36, 253-259.  
17473849 B.M.Lunde, C.Moore, and G.Varani (2007).
RNA-binding proteins: modular design for efficient function.
  Nat Rev Mol Cell Biol, 8, 479-490.  
17636014 C.M.Wong, H.Qiu, C.Hu, J.Dong, and A.G.Hinnebusch (2007).
Yeast cap binding complex impedes recruitment of cleavage factor IA to weak termination sites.
  Mol Cell Biol, 27, 6520-6531.  
17507471 J.Qiu, F.Cheng, and D.Pintel (2007).
Distance-dependent processing of adeno-associated virus type 5 RNA is controlled by 5' exon definition.
  J Virol, 81, 7974-7984.  
17369309 J.Zuberek, D.Kubacka, A.Jablonowska, J.Jemielity, J.Stepinski, N.Sonenberg, and E.Darzynkiewicz (2007).
Weak binding affinity of human 4EHP for mRNA cap analogs.
  RNA, 13, 691-697.  
17785461 P.Nilsson, N.Henriksson, A.Niedzwiecka, N.A.Balatsos, K.Kokkoris, J.Eriksson, and A.Virtanen (2007).
A multifunctional RNA recognition motif in poly(A)-specific ribonuclease with cap and poly(A) binding properties.
  J Biol Chem, 282, 32902-32911.  
16729021 H.Hernández, A.Dziembowski, T.Taverner, B.Séraphin, and C.V.Robinson (2006).
Subunit architecture of multimeric complexes isolated directly from cells.
  EMBO Rep, 7, 605-610.  
16317009 N.A.Balatsos, P.Nilsson, C.Mazza, S.Cusack, and A.Virtanen (2006).
Inhibition of mRNA deadenylation by the nuclear cap binding complex (CBC).
  J Biol Chem, 281, 4517-4522.  
16982642 S.D.Auweter, F.C.Oberstrass, and F.H.Allain (2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
  Nucleic Acids Res, 34, 4943-4959.  
16278830 Y.Zhao, B.L.Kormos, D.L.Beveridge, and A.M.Baranger (2006).
Molecular dynamics simulation studies of a protein-RNA complex with a selectively modified binding interface.
  Biopolymers, 81, 256-269.  
15920472 A.Strasser, A.Dickmanns, R.Lührmann, and R.Ficner (2005).
Structural basis for m3G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1.
  EMBO J, 24, 2235-2243.
PDB code: 1xk5
16131589 B.Westman, L.Beeren, E.Grudzien, J.Stepinski, R.Worch, J.Zuberek, J.Jemielity, R.Stolarski, E.Darzynkiewicz, R.E.Rhoads, and T.Preiss (2005).
The antiviral drug ribavirin does not mimic the 7-methylguanosine moiety of the mRNA cap structure in vitro.
  RNA, 11, 1505-1513.  
15853797 C.Maris, C.Dominguez, and F.H.Allain (2005).
The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression.
  FEBS J, 272, 2118-2131.  
15743819 H.Li, and C.Tschudi (2005).
Novel and essential subunits in the 300-kilodalton nuclear cap binding complex of Trypanosoma brucei.
  Mol Cell Biol, 25, 2216-2226.  
15643449 R.Stefl, L.Skrisovska, and F.H.Allain (2005).
RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle.
  EMBO Rep, 6, 33-38.  
16043498 R.Worch, A.Niedzwiecka, J.Stepinski, C.Mazza, M.Jankowska-Anyszka, E.Darzynkiewicz, S.Cusack, and R.Stolarski (2005).
Specificity of recognition of mRNA 5' cap by human nuclear cap-binding complex.
  RNA, 11, 1355-1363.  
15004547 J.Kadlec, E.Izaurralde, and S.Cusack (2004).
The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3.
  Nat Struct Mol Biol, 11, 330-337.
PDB code: 1uw4
15274918 O.Weichenrieder, K.Repanas, and A.Perrakis (2004).
Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.
  Structure, 12, 975-986.
PDB code: 1vyb
14517230 B.F.Eichman, E.J.O'Rourke, J.P.Radicella, and T.Ellenberger (2003).
Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases.
  EMBO J, 22, 4898-4909.
PDB codes: 1pu6 1pu7 1pu8
12756324 J.Baron-Benhamou, P.Fortes, T.Inada, T.Preiss, and M.W.Hentze (2003).
The interaction of the cap-binding complex (CBC) with eIF4G is dispensable for translation in yeast.
  RNA, 9, 654-662.  
12944262 K.Ruszczynska, K.Kamienska-Trela, J.Wojcik, J.Stepinski, E.Darzynkiewicz, and R.Stolarski (2003).
Charge distribution in 7-methylguanine regarding cation-pi interaction with protein factor eIF4E.
  Biophys J, 85, 1450-1456.  
12646557 P.Fechter, L.Mingay, J.Sharps, A.Chambers, E.Fodor, and G.G.Brownlee (2003).
Two aromatic residues in the PB2 subunit of influenza A RNA polymerase are crucial for cap binding.
  J Biol Chem, 278, 20381-20388.  
12730685 S.Fribourg, D.Gatfield, E.Izaurralde, and E.Conti (2003).
A novel mode of RBD-protein recognition in the Y14-Mago complex.
  Nat Struct Biol, 10, 433-439.
PDB code: 1hl6
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