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- PDB-1n52: Cap Binding Complex -

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Basic information

Entry
Database: PDB / ID: 1n52
TitleCap Binding Complex
Components
  • 20 kDa nuclear cap binding protein
  • 80 kDa nuclear cap binding protein
KeywordsRNA BINDING PROTEIN / CBP80 / CBP20 / RNP domain / cap binding protein / m7GpppG
Function / homology
Function and homology information


snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding ...snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / positive regulation of RNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated post-transcriptional gene silencing / : / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / mRNA 3'-end processing / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / RNA catabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / regulation of translational initiation / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Signaling by FGFR2 IIIa TM / spliceosomal complex assembly / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / 7-methylguanosine mRNA capping / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 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 / mRNA export from nucleus / 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 / snRNP Assembly / positive regulation of cell growth / defense response to virus / molecular adaptor activity / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) ...Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / 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
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / 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: 2.11 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)112,48421
Polymers109,9882
Non-polymers2,49519
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-21 kcal/mol
Surface area36920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.681, 111.681, 177.588
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#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

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Non-polymers , 5 types, 357 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O18P3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.25
Details: PEG 400, magnesium chloride, 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

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11
SYNCHROTRONCHESS F220.8655
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDJan 17, 2002mirrors
ADSC QUANTUM 42CCDJun 22, 2001mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.86551
ReflectionResolution: 2.12→37.45 Å / Num. all: 135299 / Num. obs: 132887 / % possible obs: 98 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 6 % / Biso Wilson estimate: 14.9 Å2 / Limit h max: 48 / Limit h min: -27 / Limit k max: 55 / Limit k min: -27 / Limit l max: 88 / Limit l min: -88 / Observed criterion F max: 3903632.29 / Observed criterion F min: 0.2 / Rmerge(I) obs: 0.33 / Rsym value: 0.067 / Net I/σ(I): 16
Reflection shellResolution: 2.11→2.17 Å / Mean I/σ(I) obs: 2.4
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 78602 / % possible obs: 99 % / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H6K

1h6k


Resolution: 2.11→24.54 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1.07 / Occupancy min: 1 / Data cutoff high absF: 3917587.28 / Data cutoff high rms absF: 3917587.28 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3949 5 %RANDOM
Rwork0.223 ---
all-142520 --
obs-78216 55.6 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 45.8457 Å2 / ksol: 0.343953 e/Å3
Displacement parametersBiso max: 94.13 Å2 / Biso mean: 49.2 Å2 / Biso min: 15.89 Å2
Baniso -1Baniso -2Baniso -3
1-4.94 Å25.65 Å20 Å2
2--4.94 Å20 Å2
3----9.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.39 Å
Luzzati d res high-2.11
Refinement stepCycle: LAST / Resolution: 2.11→24.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7199 0 162 338 7699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_torsion_deg20.3
X-RAY DIFFRACTIONx_torsion_impr_deg1.12
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.11-2.210.2961110.60.29623200.02817855243113.6
2.21-2.320.3282211.20.32739870.02217839420823.6
2.32-2.470.27935720.27955570.01517824591433.2
2.47-2.660.2634232.40.26380890.01317884851247.6
2.66-2.920.2695833.30.269106740.011178151125763.2
2.92-3.350.2576483.60.257131880.01178081383677.7
3.35-4.210.217814.40.21148530.008178011563487.8
4.21-24.540.1998374.70.199157490.007178391658693
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4dna-rna_new.paramdna-rna_new.top
X-RAY DIFFRACTION5peg400_H_parameter.paramgol_parameter.param
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.12 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.2427 / Rfactor Rwork: 0.2256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / Rfactor Rwork: 0.32

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