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- PDB-1h2v: Structure of the human nuclear cap-binding-complex (CBC) -

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Basic information

Entry
Database: PDB / ID: 1h2v
TitleStructure of the human nuclear cap-binding-complex (CBC)
Components
  • 20 KDA NUCLEAR CAP BINDING PROTEIN
  • 80 KDA NUCLEAR CAP BINDING PROTEIN
KeywordsNUCLEAR PROTEIN / CAP-BINDING-COMPLEX / RNP DOMAIN / MIF4G DOMAIN / RNA MATURATION / RNA EXPORT / RNA-BINDING
Function / homology
Function and homology information


positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / positive regulation of RNA export from nucleus / cap-dependent translational initiation / positive regulation of mRNA 3'-end processing / Processing of Intronless Pre-mRNAs ...positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / positive regulation of RNA export from nucleus / cap-dependent translational initiation / positive regulation of mRNA 3'-end processing / Processing of Intronless Pre-mRNAs / RNA cap binding / snRNA binding / regulation of mRNA processing / primary miRNA processing / miRNA-mediated post-transcriptional gene silencing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / alternative mRNA splicing, via spliceosome / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA catabolic process / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of translational initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / Signaling by FGFR2 IIIa TM / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / 7-methylguanosine mRNA capping / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / mRNA export from nucleus / Formation of HIV-1 elongation complex containing HIV-1 Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of HIV elongation complex in the absence of HIV Tat / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / positive regulation of cell growth / snRNP Assembly / defense response to virus / molecular adaptor activity / ciliary basal body / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) ...MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMazza, C. / Segref, A. / Mattaj, I.W. / Cusack, S.
Citation
Journal: Embo J. / Year: 2002
Title: Large-Scale Induced Fit Recognition of an M(7)Gpppg CAP Analogue by the Human Nuclear CAP-Binding Complex
Authors: Mazza, C. / Segref, A. / Mattaj, I.W. / Cusack, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Co-Crystallization of the Human Nuclear CAP-Binding Complex with a M7Gpppg CAP Analogue Using Protein Engineering
Authors: Mazza, C. / Segref, A. / Mattaj, I. / Cusack, S.
History
DepositionAug 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 80 KDA NUCLEAR CAP BINDING PROTEIN
Z: 20 KDA NUCLEAR CAP BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)107,6952
Polymers107,6952
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)264.136, 59.605, 75.430
Angle α, β, γ (deg.)90.00, 99.52, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE COMPLEX IS A HETERODIMER FORMED BY CHAINS CAND Z.

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Components

#1: Protein 80 KDA NUCLEAR CAP BINDING PROTEIN / NCBP 80 KDA SUBUNIT / CBP80


Mass: 89666.742 Da / Num. of mol.: 1 / Fragment: MIF4G DOMAIN, RESIDUES 20-790 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL, ENGINEERED MUTATION ALA 479 SER
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q09161
#2: Protein 20 KDA NUCLEAR CAP BINDING PROTEIN / CBP20 / NCBP 20 KDA SUBUNIT / NCBP INTERACTING PROTEIN 1 / NIP1


Mass: 18028.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRSETA / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P52298
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CAP-BINDING PROTEIN (CBC) COMPLEX IS AN HETERODIMER OF CBP80 AND CBP20. CHAIN C ENGINEERED ...THE CAP-BINDING PROTEIN (CBC) COMPLEX IS AN HETERODIMER OF CBP80 AND CBP20. CHAIN C ENGINEERED DELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL ENGINEERED MUTATION ALA 479 SER CHAIN C

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 53.7 %
Crystal growpH: 6 / Details: 10 % PEG6000, 100 MM MES PH6, pH 6.00
Crystal grow
*PLUS
Temperature: 277 K / pH: 6 / Method: vapor diffusion, hanging drop
Details: Mazza, C., (2002) Acta Crystallogr.,Sect.D, 58, 2194.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %PEG60001reservoir
3100 mMMES1reservoirpH6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 62416 / % possible obs: 79.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 18.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.65 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.23 / % possible all: 58.8
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 59304

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H6K

1h6k


Resolution: 2→19.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3899332.92 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 20 - 29, 528 - 537 AND 664 - FROM CHAIN C ARE DISORDERED, RESIDUES 1 - 32 AND 126 - 156 FROM CHAIN Z ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3112 5 %RANDOM
Rwork0.212 ---
obs0.212 62416 79.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.7568 Å2 / ksol: 0.367254 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1-14.53 Å20 Å26.17 Å2
2---0.55 Å20 Å2
3----13.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6667 0 0 294 6961
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.061.5
X-RAY DIFFRACTIONc_mcangle_it4.022
X-RAY DIFFRACTIONc_scbond_it3.523
X-RAY DIFFRACTIONc_scangle_it4.844
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 382 5 %
Rwork0.356 7255 -
obs--59.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA-MULTI-ENDO.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Num. reflection obs: 59304 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0057
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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