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- PDB-3zzz: Crystal structure of a Raver1 PRI4 peptide in complex with polypy... -

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Basic information

Entry
Database: PDB / ID: 3zzz
TitleCrystal structure of a Raver1 PRI4 peptide in complex with polypyrimidine tract binding protein RRM2
Components
  • POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
  • RIBONUCLEOPROTEIN PTB-BINDING 1
KeywordsPROTEIN BINDING / PEPTIDE BINDING / RNA RECOGNITION MOTIF
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 / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / negative regulation of neuron differentiation / regulation of alternative mRNA splicing, via spliceosome / 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 / pre-mRNA binding / negative regulation of RNA splicing / FGFR2 alternative splicing / negative regulation of neuron differentiation / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / negative regulation of mRNA splicing, via spliceosome / regulation of cell differentiation / Processing of Capped Intron-Containing Pre-mRNA / neurogenesis / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA binding / nucleolus / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytoplasm
Similarity search - Function
Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 / 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) / RRM (RNA recognition motif) domain / RNA recognition motif ...Ribonucleoprotein PTB-binding 1, RNA recognition motif 1 / 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) / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Polypyrimidine tract-binding protein 1 / Ribonucleoprotein PTB-binding 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsJoshi, A. / Kotik-Kogan, O. / Curry, S.
CitationJournal: Structure / Year: 2011
Title: Crystallographic Analysis of Polypyrimidine Tract-Binding Protein-Raver1 Interactions Involved in Regulation of Alternative Splicing.
Authors: Joshi, A. / Coelho, M.B. / Kotik-Kogan, O. / Simpson, P.J. / Matthews, S.J. / Smith, C.W. / Curry, S.
History
DepositionSep 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
B: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
C: RIBONUCLEOPROTEIN PTB-BINDING 1
D: RIBONUCLEOPROTEIN PTB-BINDING 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7729
Polymers31,1374
Non-polymers6355
Water2,378132
1
A: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
C: RIBONUCLEOPROTEIN PTB-BINDING 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0766
Polymers15,5692
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-6.9 kcal/mol
Surface area6180 Å2
MethodPISA
2
B: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
D: RIBONUCLEOPROTEIN PTB-BINDING 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6963
Polymers15,5692
Non-polymers1271
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-6.4 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.480, 60.380, 61.060
Angle α, β, γ (deg.)90.00, 107.86, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1983, 0.03711, 0.9794), (-0.04978, -0.9984, 0.02775), (0.9789, -0.04325, 0.1999)
Vector: -47.41, -9.589, 17.22)

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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: 14169.072 Da / Num. of mol.: 2 / Fragment: RNA RECOGNITION MOTIF 2, RESIDUES 156-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P26599
#2: Protein/peptide RIBONUCLEOPROTEIN PTB-BINDING 1 / RAVER1 / PROTEIN RAVER-1


Mass: 1399.572 Da / Num. of mol.: 2 / Fragment: MOTIF PRI4, RESIDUES 680-692
Source method: isolated from a genetically manipulated source
Details: THIS FRAGMENT IS ACTUALLY FUSED TO THE N-TERMINUS OF MOLECULE 1, SEE REMARK 999
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9CW46
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST 3 RESIDUES (GAM) ARE VECTOR DERIVED. RESIDUES 4 - 16 CORRESPOND TO RESIDUES 680-692 OF RAVER1 ...FIRST 3 RESIDUES (GAM) ARE VECTOR DERIVED. RESIDUES 4 - 16 CORRESPOND TO RESIDUES 680-692 OF RAVER1 (PRI4 MOTIF). THESE 16 RESIDUES ARE FUSED GENETICALLY TO PTB RRM2 ( RECORDED AS CHAINS A AND B). BECAUSE OF LINKER DISORDER WE CANNOT DETERMINE WHICH RRM DOMAIN (CHAINS A, B) IS COVALENTLY LINKED TO WHICH RAVER1 PEPTIDE (CHAINS C,D). METHIONINE 1 IN RAVER1 IS AN INITIATOR MET AND IS REMOVED.

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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: 2.01 Å3/Da / Density % sol: 38.94 % / Description: NONE
Crystal growpH: 6.5 / Details: SEE PAPER., pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.55→35.49 Å / Num. obs: 36184 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3 / % possible all: 96.5

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Processing

Software
NameVersionClassification
CNS1.2refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASER1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZZY

3zzy


Resolution: 1.55→20.07 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1123728.72 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: BULK SOLVENT MODEL USED. THE CRYSTALLISED PROTEIN HAS A RAVER1 PEPTIDE GENETICALLY FUSED AS AN N-TERMINAL EXTENSION OF PTB RRM3. OWING TO LINKER DISORDER WE CANNOT DETERMINE WHICH RRM DOMAIN ...Details: BULK SOLVENT MODEL USED. THE CRYSTALLISED PROTEIN HAS A RAVER1 PEPTIDE GENETICALLY FUSED AS AN N-TERMINAL EXTENSION OF PTB RRM3. OWING TO LINKER DISORDER WE CANNOT DETERMINE WHICH RRM DOMAIN (CHAINS A, B) IS COVALENTLY LINKED TO WHICH RAVER1 PEPTIDE (CHAINS C,D).
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1789 4.9 %RANDOM
Rwork0.217 ---
obs0.217 36156 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.8846 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å2-3.8 Å2
2---4.84 Å20 Å2
3---3.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.55→20.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 5 132 1860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 293 4.9 %
Rwork0.316 5685 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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