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- PDB-1h2u: Structure of the human nuclear cap-binding-complex (CBC) in compl... -

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Basic information

Entry
Database: PDB / ID: 1h2u
TitleStructure of the human nuclear cap-binding-complex (CBC) in complex with a cap analogue m7GpppG
Components
  • 20 KDA NUCLEAR CAP BINDING PROTEIN
  • 80 KDA NUCLEAR CAP BINDING PROTEIN
KeywordsNUCLEAR PROTEIN / M7GCAP / 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 / positive regulation of mRNA 3'-end processing / 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 RNA export from nucleus / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / 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 / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / 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 / Abortive elongation of HIV-1 transcript in the absence of Tat / regulation of translational initiation / 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) / Formation of HIV-1 elongation complex containing HIV-1 Tat / mRNA export from nucleus / Formation of HIV elongation complex in the absence of HIV Tat / 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 / Regulation of expression of SLITs and ROBOs / mRNA splicing, via spliceosome / snRNP Assembly / positive regulation of cell growth / molecular adaptor activity / defense response to virus / ciliary basal body / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
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
7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / 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: 2.4 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 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.4Apr 3, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 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
A: 80 KDA NUCLEAR CAP BINDING PROTEIN
B: 80 KDA NUCLEAR CAP BINDING PROTEIN
X: 20 KDA NUCLEAR CAP BINDING PROTEIN
Y: 20 KDA NUCLEAR CAP BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,3728
Polymers203,7274
Non-polymers1,6454
Water23,7261317
1
A: 80 KDA NUCLEAR CAP BINDING PROTEIN
X: 20 KDA NUCLEAR CAP BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6864
Polymers101,8632
Non-polymers8222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 80 KDA NUCLEAR CAP BINDING PROTEIN
Y: 20 KDA NUCLEAR CAP BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,6864
Polymers101,8632
Non-polymers8222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.838, 125.720, 188.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999313, 0.020211, 0.031048), (0.014045, -0.982198, 0.18732), (0.034281, -0.186756, -0.981808)
Vector: -57.651, 3.043, 89.424)
DetailsONE DIMER IS FORMED BY A HETERODIMERIC ASSOCIATIONOF CHAIN A AND CHAIN XONE DIMER IS FORMED BY A HETERODIMERIC ASSOCIATIONOF CHAIN B AND CHAIN Y

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Components

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


Mass: 83835.242 Da / Num. of mol.: 2 / Fragment: MIF4G DOMAIN, RESIDUES 20-652,701-790 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL AND DELETION OF RESIDUES 653-701 REPLACED BY A GLYCINE, 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.: 2
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: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-7MG / 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 379.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1317 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CAP-BINDING PROTEIN (CBC) COMPLEX IS AN HETERODIMER OF CBP80 AND CBP20. CHAIN A, B ENGINEERED ...THE CAP-BINDING PROTEIN (CBC) COMPLEX IS AN HETERODIMER OF CBP80 AND CBP20. CHAIN A, B ENGINEERED DELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL AND DELETION OF RESIDUES 653-701 REPLACED BY A GLYCINE ENGINEERED MUTATION ALA 479 SER CHAINS A AND B
Sequence detailsDELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL AND DELETION OF RESIDUES 653-701 REPLACED BY A ...DELETION OF THE FIRST 19 RESIDUES IN N-TERMINAL AND DELETION OF RESIDUES 653-701 REPLACED BY A GLYCINE FOR CHAIN A,B

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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: 3.3 Å3/Da / Density % sol: 62.6 %
Crystal growpH: 6
Details: 0.25 TO 1 % PEG 4000, 100 MM MES PH6, 75 TO 100 MM MAGNESIUM FORMATE, 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: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 105598 / % possible obs: 89.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 5.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.6 / % possible all: 65.4
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 91470

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Processing

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

1h6k


Resolution: 2.4→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2384394.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 20 - 26 FROM CHAIN A AND B AR DISORDERED RESIDUES, 528 - 538 FROM CHAIN A ARE DISORDERED, RESIDUES 528 - 537 FROM CHAIN B ARE DISORDERED, RESIDUES 1-3 AND 153 - 156 FROM CHAIN X ARE ...Details: RESIDUES 20 - 26 FROM CHAIN A AND B AR DISORDERED RESIDUES, 528 - 538 FROM CHAIN A ARE DISORDERED, RESIDUES 528 - 537 FROM CHAIN B ARE DISORDERED, RESIDUES 1-3 AND 153 - 156 FROM CHAIN X ARE DISORDERED, RESIDUES 1 - 4 AND 152 - 156 FROM CHAIN Y ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4794 5 %RANDOM
Rwork0.194 ---
obs0.194 96264 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4005 Å2 / ksol: 0.339272 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.44 Å20 Å20 Å2
2--14.56 Å20 Å2
3----9.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13943 0 104 1317 15364
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_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.691.5
X-RAY DIFFRACTIONc_mcangle_it32
X-RAY DIFFRACTIONc_scbond_it4.013
X-RAY DIFFRACTIONc_scangle_it5.684.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 647 5.4 %
Rwork0.269 11419 -
obs--70.2 %
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
X-RAY DIFFRACTION5ATP_GTP.PARATP_GTP.TOP
Refinement
*PLUS
Num. reflection obs: 91470 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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