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- PDB-1h6k: nuclear Cap Binding Complex -

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Basic information

Entry
Database: PDB / ID: 1h6k
Titlenuclear Cap Binding Complex
Components
  • 20 KDA NUCLEAR CAP BINDING PROTEIN
  • CBP80
KeywordsNUCLEAR PROTEIN / M7G CAP / CAP-BINDING-COMPLEX / RNP DOMAIN / MIF4G DOMAIN / RNA MATURATION / RNA EXPORT
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 mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / 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 mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / alternative mRNA splicing, via spliceosome / RNA cap binding / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulation of mRNA processing / 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 / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / RNA catabolic process / mRNA cis splicing, via spliceosome / Abortive elongation of HIV-1 transcript in the absence of Tat / Transport of Mature mRNA derived from an Intron-Containing Transcript / regulation of translational initiation / positive regulation of mRNA splicing, via spliceosome / FGFR2 alternative splicing / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Signaling by FGFR2 IIIa TM / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 7-methylguanosine mRNA capping / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / RNA-binding domain superfamily / 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 / MAD / Resolution: 2 Å
AuthorsMazza, C. / Ohno, M. / Segref, A. / Mattaj, I.W. / Cusack, S.
CitationJournal: Mol.Cell / Year: 2001
Title: Crystal Structure of the Human Nuclear CAP Binding Complex
Authors: Mazza, C. / Ohno, M. / Segref, A. / Mattaj, I.W. / Cusack, S.
History
DepositionJun 18, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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
A: CBP80
B: CBP80
C: CBP80
X: 20 KDA NUCLEAR CAP BINDING PROTEIN
Y: 20 KDA NUCLEAR CAP BINDING PROTEIN
Z: 20 KDA NUCLEAR CAP BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)298,3356
Polymers298,3356
Non-polymers00
Water30,8061710
1
A: CBP80
X: 20 KDA NUCLEAR CAP BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)99,4452
Polymers99,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CBP80
Y: 20 KDA NUCLEAR CAP BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)99,4452
Polymers99,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: CBP80
Z: 20 KDA NUCLEAR CAP BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)99,4452
Polymers99,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.527, 161.480, 303.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999969, -0.004966, 0.00601), (-0.007794, -0.654022, 0.756435), (0.000174, -0.756459, -0.654041)25.145, 73.829, 39.572
2given(0.999969, -0.004966, 0.00601), (-0.007794, -0.654022, 0.756435), (0.000174, -0.756459, -0.654041)25.145, 73.829, 39.572
3given(0.999927, -0.006696, 0.010008), (-0.006708, 0.380447, 0.924778), (-0.01, -0.924778, 0.380374)12.824, 25.168, 46.259
4given(0.999927, -0.006696, 0.010008), (-0.006708, 0.380447, 0.924778), (-0.01, -0.924778, 0.380374)12.824, 25.168, 46.259

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Components

#1: Protein CBP80 / NCBP 80 KDA SUBUNIT / CBP80


Mass: 87942.930 Da / Num. of mol.: 3 / Fragment: MIF4G DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: EXPRESSION IN INSECT CELLS / 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


Mass: 11501.983 Da / Num. of mol.: 3 / Fragment: RNP DOMAIN
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.: 1710 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C ENGINEERED MUTATION ALA479SER BINDS TO 5'CAPPED MRNA. AND INVOLVED IN MEDIATING U ...CHAIN A, B, C ENGINEERED MUTATION ALA479SER BINDS TO 5'CAPPED MRNA. AND INVOLVED IN MEDIATING U SNRNA EXPORT FROM THE NUCLEUS.
Sequence detailsRESIDUES 1-19 AND 671-684 FROM CBP80 (CHAINS A,B,C) HAVE BEEN REMOVED BY TRYPSIN RESIDUES 1-21, 78 ...RESIDUES 1-19 AND 671-684 FROM CBP80 (CHAINS A,B,C) HAVE BEEN REMOVED BY TRYPSIN RESIDUES 1-21, 78 AND 121-156 FROM CBP20 (CHAINS X,Y,Z) HAVE BEEN REMOVED BY TRYPSIN

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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: 59.8 %
Crystal growpH: 7.5 / Details: SEE REFERENCES, pH 7.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250-100 mMmagnesium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 208094 / % possible obs: 83.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.058
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.363 / % possible all: 40.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 730893
Reflection shell
*PLUS
% possible obs: 40.7 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.815 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2157 1 %RANDOM
Rwork0.203 ---
obs0.203 205458 83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19805 0 0 1710 21515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02120304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.0451.94827512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0770.23053
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215305
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.211296
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.51844
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.526
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.581.512161
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.124219785
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63338143
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7744.57727
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 90
Rwork0.265 7488
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d1.071
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.051 Å / Num. reflection obs: 7488

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