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- PDB-8bwf: PTBP1 RRM1 bound to an allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 8bwf
TitlePTBP1 RRM1 bound to an allosteric inhibitor
Components
  • Ligand
  • Polypyrimidine tract-binding protein 1
KeywordsRNA BINDING PROTEIN / RNA binding / protein-peptide interaction / inhibitor
Function / homology
Function and homology information


negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of RNA splicing / pre-mRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of cell differentiation / regulation of RNA splicing ...negative regulation of muscle cell differentiation / poly-pyrimidine tract binding / IRES-dependent viral translational initiation / positive regulation of calcineurin-NFAT signaling cascade / negative regulation of RNA splicing / pre-mRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / regulation of cell differentiation / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / negative regulation of neuron differentiation / positive regulation of protein dephosphorylation / neurogenesis / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
Similarity search - Function
PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain ...PTBP1, RNA recognition motif 1 / PTBP1, RNA recognition motif 3 / HnRNP-L/PTB / PTBP1-like, RNA recognition motif 2 / RRM-like domain / RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
AMINO GROUP / Polypyrimidine tract-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchmeing, S. / Vetter, I. / t Hart, P. / Gasper, R.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Chem Sci / Year: 2023
Title: Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding.
Authors: Schmeing, S. / Amrahova, G. / Bigler, K. / Chang, J.Y. / Openy, J. / Pal, S. / Posada, L. / Gasper, R. / 't Hart, P.
History
DepositionDec 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polypyrimidine tract-binding protein 1
a: Ligand
B: Polypyrimidine tract-binding protein 1
b: Ligand
C: Polypyrimidine tract-binding protein 1
c: Ligand
D: Polypyrimidine tract-binding protein 1
d: Ligand
E: Polypyrimidine tract-binding protein 1
e: Ligand
F: Polypyrimidine tract-binding protein 1
f: Ligand
G: Polypyrimidine tract-binding protein 1
g: Ligand
H: Polypyrimidine tract-binding protein 1
h: Ligand
I: Polypyrimidine tract-binding protein 1
i: Ligand
J: Polypyrimidine tract-binding protein 1
j: Ligand
K: Polypyrimidine tract-binding protein 1
k: Ligand
L: Polypyrimidine tract-binding protein 1
l: Ligand
M: Polypyrimidine tract-binding protein 1
m: Ligand
N: Polypyrimidine tract-binding protein 1
n: Ligand
O: Polypyrimidine tract-binding protein 1
o: Ligand
P: Polypyrimidine tract-binding protein 1
p: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,20170
Polymers178,84732
Non-polymers2,35438
Water0
1
A: Polypyrimidine tract-binding protein 1
a: Ligand
hetero molecules


  • defined by author
  • Evidence: assay for oligomerization, Fluorescence anisotropy measurements, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for ...Evidence: assay for oligomerization, Fluorescence anisotropy measurements, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization, assay for oligomerization
  • 11.7 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)11,6748
Polymers11,1782
Non-polymers4966
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polypyrimidine tract-binding protein 1
b: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1943
Polymers11,1782
Non-polymers161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polypyrimidine tract-binding protein 1
c: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3825
Polymers11,1782
Non-polymers2043
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polypyrimidine tract-binding protein 1
d: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3865
Polymers11,1782
Non-polymers2083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Polypyrimidine tract-binding protein 1
e: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1943
Polymers11,1782
Non-polymers161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Polypyrimidine tract-binding protein 1
f: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4786
Polymers11,1782
Non-polymers3004
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Polypyrimidine tract-binding protein 1
g: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4826
Polymers11,1782
Non-polymers3044
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Polypyrimidine tract-binding protein 1
h: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2904
Polymers11,1782
Non-polymers1122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Polypyrimidine tract-binding protein 1
i: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3785
Polymers11,1782
Non-polymers2003
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Polypyrimidine tract-binding protein 1
j: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1943
Polymers11,1782
Non-polymers161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Polypyrimidine tract-binding protein 1
k: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3865
Polymers11,1782
Non-polymers2083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Polypyrimidine tract-binding protein 1
l: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2904
Polymers11,1782
Non-polymers1122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Polypyrimidine tract-binding protein 1
m: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1943
Polymers11,1782
Non-polymers161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Polypyrimidine tract-binding protein 1
n: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1943
Polymers11,1782
Non-polymers161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Polypyrimidine tract-binding protein 1
o: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2904
Polymers11,1782
Non-polymers1122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Polypyrimidine tract-binding protein 1
p: Ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1943
Polymers11,1782
Non-polymers161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)244.200, 76.630, 94.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Polypyrimidine tract-binding protein 1 / PTB / 57 kDa RNA-binding protein PPTB-1 / Heterogeneous nuclear ribonucleoprotein I / hnRNP I


Mass: 9612.091 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Details: GPPSRVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQAFIEMNTEEAANTMVNYYTSVTPVLRGQPIYIQFSNHKELKTDS
Source: (gene. exp.) Homo sapiens (human) / Gene: PTBP1, PTB / Production host: Escherichia coli (E. coli) / References: UniProt: P26599
#2: Protein/peptide
Ligand /


Mass: 1565.877 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NH2 / AMINO GROUP / Amine


Mass: 16.023 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: NH2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.86 / Details: 1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999876 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999876 Å / Relative weight: 1
ReflectionResolution: 2.9→46.21 Å / Num. obs: 39834 / % possible obs: 99.4 % / Redundancy: 4.56 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.074 / Net I/σ(I): 14.58
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.9-2.981.61529070.5331.8121
2.98-3.061.24528290.6111.3971
3.06-3.151.00627260.6871.131
3.15-3.240.65526880.8470.7371
3.24-3.350.4426080.9290.4951
3.35-3.470.29625130.9620.3341
3.47-3.60.21324230.980.2411
3.6-3.740.15123470.9880.1731
3.74-3.910.10922510.9930.1241
3.91-4.10.08321410.9960.0941
4.1-4.320.06720640.9970.0751
4.32-4.590.04919440.9980.0551
4.59-4.90.04618430.9980.0521
4.9-5.290.04517320.9990.0511
5.29-5.80.04815930.9980.0541
5.8-6.480.04314450.9980.0491
6.48-7.490.03112950.9990.0361
7.49-9.170.02211010.9990.0251
9.17-12.970.01988210.0211
12.97-46.210.0185020.9990.0211

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.21 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3403 1992 5 %
Rwork0.2432 --
obs0.2478 39816 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11548 0 130 0 11678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01211818
X-RAY DIFFRACTIONf_angle_d1.38416015
X-RAY DIFFRACTIONf_dihedral_angle_d8.9831783
X-RAY DIFFRACTIONf_chiral_restr0.0671837
X-RAY DIFFRACTIONf_plane_restr0.0112006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.44281400.37732665X-RAY DIFFRACTION99
2.97-3.050.45421400.37662665X-RAY DIFFRACTION99
3.05-3.140.50191390.36892631X-RAY DIFFRACTION99
3.14-3.240.41121410.32822669X-RAY DIFFRACTION99
3.24-3.360.39591410.28352682X-RAY DIFFRACTION99
3.36-3.490.33851410.25242679X-RAY DIFFRACTION99
3.49-3.650.32251410.25582674X-RAY DIFFRACTION100
3.65-3.850.39081400.25732675X-RAY DIFFRACTION99
3.85-4.090.40791420.24382679X-RAY DIFFRACTION99
4.09-4.40.32951410.23542686X-RAY DIFFRACTION100
4.4-4.840.33541440.2122734X-RAY DIFFRACTION100
4.84-5.540.30691440.24072739X-RAY DIFFRACTION99
5.54-6.980.32291450.27072762X-RAY DIFFRACTION99
6.98-46.210.29421530.19392884X-RAY DIFFRACTION99

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