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- PDB-1n54: Cap Binding Complex m7GpppG free -

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Basic information

Entry
Database: PDB / ID: 1n54
TitleCap Binding Complex m7GpppG free
Components
  • 20 kDa nuclear cap binding protein
  • 80 kDa nuclear cap binding protein
KeywordsRNA BINDING PROTEIN / CBP80 / CBBP20 / Nuclear cap binding complex / m7GpppG / RNP domain
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: 2.72 Å
AuthorsCalero, G. / Wilson, K. / Ly, T. / Rios-Steiner, J. / Clardy, J. / Cerione, R.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structural basis of m7GpppG binding to the nuclear cap-binding protein complex.
Authors: Calero, G. / Wilson, K. / Ly, T. / Rios-Steiner, J. / Clardy, J. / Cerione, R.
History
DepositionNov 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 80 kDa nuclear cap binding protein
B: 20 kDa nuclear cap binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6339
Polymers109,9882
Non-polymers6457
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-6 kcal/mol
Surface area37940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.770, 111.770, 175.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 80 kDa nuclear cap binding protein / NCBP 80 kDa subunit / Cap Binding Protein 80 / CBP80


Mass: 91960.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBP80 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09161
#2: Protein 20 kDa nuclear cap binding protein / NCBP 20 kDa subunit / Cap Binding Protein 20 / CBP20 / 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) / Gene: CBP20 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P52298
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: Peg 400, Magnesium chloride, glycerol, Tris, glycine, ethylene glycol, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
222 %(w/v)PEG4001reservoir
3100 mMTris-HCl1reservoirpH7.25
4125 mM1reservoirMgCl2
510 %(v/v)glycerol1reservoir
62 mMdithiothreitol1reservoir
710 mMglycine1reservoir
83 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.943 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 2.59→48.49 Å / Num. all: 39454 / Num. obs: 33886 / Observed criterion σ(I): 3 / Redundancy: 11 % / Biso Wilson estimate: 30.3 Å2 / Rsym value: 0.079 / Net I/σ(I): 20
Reflection shellResolution: 2.69→2.85 Å / Mean I/σ(I) obs: 2.3
Reflection
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 40 Å / Num. obs: 39454 / % possible obs: 100 % / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N52

1n52


Resolution: 2.72→24.41 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 3238611.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
Details: Data set had 15% twinning. Used CNS twinning refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2312 9.1 %RANDOM
Rwork0.263 ---
all-33675 --
obs-25307 72.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.25 Å2 / ksol: 0.26 e/Å3
Displacement parametersBiso mean: 72.7 Å2
Baniso -1Baniso -2Baniso -3
1--8.27 Å222.33 Å20 Å2
2---8.27 Å20 Å2
3---16.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 2.72→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6995 0 42 255 7292
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 2.72→2.84 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 114 2.7 %
Rwork0.404 936 -
obs--24.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GOL_PARAMETER.PARAMGOL_TOPOLOGY.PARAM
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM
Refinement
*PLUS
Highest resolution: 2.75 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.43 / Rfactor Rwork: 0.39

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