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- PDB-6d0y: X-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP8... -

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Basic information

Entry
Database: PDB / ID: 6d0y
TitleX-ray Crystal Structure of PGC-1beta C-terminus bound to the CBP80-CBP20 Cap Binding Complex
Components
  • (Nuclear cap-binding protein subunit ...) x 2
  • Peroxisome proliferator-activated receptor gamma coactivator 1-beta
KeywordsTRANSCRIPTION / Cap-binding / m7GpppA / mRNA
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 / AF-2 domain binding / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / bone trabecula formation ...positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / AF-2 domain binding / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / bone trabecula formation / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / mitochondrial transcription / 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 / regulation of mRNA processing / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / mediator complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / positive regulation of osteoclast differentiation / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / RNA catabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / regulation of translational initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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) / positive regulation of bone resorption / 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 / positive regulation of phosphorylation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of RNA Pol II elongation complex / energy homeostasis / estrogen receptor signaling pathway / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / ossification / RNA splicing / actin filament organization / nuclear estrogen receptor binding / cellular response to reactive oxygen species / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / Regulation of RUNX2 expression and activity / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / snRNP Assembly / positive regulation of cell growth / molecular adaptor activity / defense response to virus / transcription coactivator activity / ciliary basal body / ribonucleoprotein complex / negative regulation of DNA-templated transcription / mRNA binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
PPARGC1B, RNA recognition motif / 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 / PGC-1 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 ...PPARGC1B, RNA recognition motif / 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 / PGC-1 / 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
Chem-GTA / Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1 / Peroxisome proliferator-activated receptor gamma coactivator 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.676 Å
AuthorsGleghorn, M.L. / Maquat, L.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM59514 United States
CitationJournal: Genes Dev. / Year: 2018
Title: Transcriptional coactivator PGC-1 alpha contains a novel CBP80-binding motif that orchestrates efficient target gene expression.
Authors: Cho, H. / Rambout, X. / Gleghorn, M.L. / Nguyen, P.Q.T. / Phipps, C.R. / Miyoshi, K. / Myers, J.R. / Kataoka, N. / Fasan, R. / Maquat, L.E.
History
DepositionApr 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Nuclear cap-binding protein subunit 1
A: Nuclear cap-binding protein subunit 2
B: Peroxisome proliferator-activated receptor gamma coactivator 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,4555
Polymers114,6433
Non-polymers8122
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-30 kcal/mol
Surface area39150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.106, 111.897, 124.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Nuclear cap-binding protein subunit ... , 2 types, 2 molecules CA

#1: Protein Nuclear cap-binding protein subunit 1 / 80 kDa nuclear cap-binding protein / NCBP 80 kDa subunit


Mass: 91129.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP1, CBP80, NCBP / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q09161
#2: Protein Nuclear cap-binding protein subunit 2 / 20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa ...20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa subunit / CBP20 / NCBP-interacting protein 1 / NIP1


Mass: 20047.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP2, CBP20, PIG55 / Production host: Escherichia coli (E. coli) / References: UniProt: P52298

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Protein/peptide , 1 types, 1 molecules B

#3: Protein/peptide Peroxisome proliferator-activated receptor gamma coactivator 1-beta / PPARGC-1-beta / PGC-1-related estrogen receptor alpha coactivator


Mass: 3466.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YN6

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Non-polymers , 3 types, 276 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GTA / P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / 7-METHYL-GPPPA


Mass: 787.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride, 0.1 M Tris (pH 7.0), 10% [w/v] polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9553 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9553 Å / Relative weight: 1
ReflectionResolution: 2.67→39.05 Å / Num. obs: 30950 / % possible obs: 97.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 40.21 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.1 / Rrim(I) all: 0.234 / Net I/σ(I): 5.9 / Num. measured all: 167278 / Scaling rejects: 70
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.67-2.84.91.1881749235540.3490.6021.3382.186.2
8.87-39.055.10.06749039610.9910.0320.07410.598.5

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Processing

Software
NameVersionClassification
Aimless0.5.4data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementResolution: 2.676→39.053 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2401 2000 6.5 %
Rwork0.1812 28784 -
obs0.185 30784 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.15 Å2 / Biso mean: 54.8244 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 2.676→39.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7318 0 79 274 7671
Biso mean--85.72 39.78 -
Num. residues----902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047546
X-RAY DIFFRACTIONf_angle_d0.55210226
X-RAY DIFFRACTIONf_chiral_restr0.0361121
X-RAY DIFFRACTIONf_plane_restr0.0031299
X-RAY DIFFRACTIONf_dihedral_angle_d15.9594520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6764-2.74330.33351040.27371492159673
2.7433-2.81750.36991440.241420752219100
2.8175-2.90040.27811450.232720822227100
2.9004-2.9940.33591430.216220652208100
2.994-3.10090.2531420.21242056219899
3.1009-3.2250.33561430.21562043218699
3.225-3.37170.24651460.189521052251100
3.3717-3.54940.25551450.178420812226100
3.5494-3.77160.21051460.172421042250100
3.7716-4.06250.19641450.154920812226100
4.0625-4.47080.21591460.14432105225199
4.4708-5.11650.21031460.1512102224899
5.1165-6.44160.22821500.184221572307100
6.4416-39.05710.20381550.17332236239199

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