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- PDB-3zzy: Crystal structure of a Raver1 PRI3 peptide in complex with polypy... -

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Basic information

Entry
Database: PDB / ID: 3zzy
TitleCrystal structure of a Raver1 PRI3 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 / regulation of cell differentiation / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome ...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 / regulation of cell differentiation / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / positive regulation of protein dephosphorylation / mRNA Splicing - Major Pathway / RNA splicing / mRNA processing / mRNA binding / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / 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 / 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
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: 1.4 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 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 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: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
B: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
C: RIBONUCLEOPROTEIN PTB-BINDING 1
D: RIBONUCLEOPROTEIN PTB-BINDING 1


Theoretical massNumber of molelcules
Total (without water)31,2744
Polymers31,2744
Non-polymers00
Water3,441191
1
A: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
C: RIBONUCLEOPROTEIN PTB-BINDING 1


Theoretical massNumber of molelcules
Total (without water)15,6372
Polymers15,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-6.5 kcal/mol
Surface area6260 Å2
MethodPISA
2
B: POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
D: RIBONUCLEOPROTEIN PTB-BINDING 1


Theoretical massNumber of molelcules
Total (without water)15,6372
Polymers15,6372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-6.5 kcal/mol
Surface area6130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.233, 60.606, 60.842
Angle α, β, γ (deg.)90.00, 107.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.2051, 0.0424, 0.9778), (-0.02532, -0.999, 0.038), (0.9784, -0.01697, 0.2059)
Vector: -47.02, -10.24, 16.62)

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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 172-301
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: 1467.710 Da / Num. of mol.: 2 / Fragment: MOTIF PRI3, RESIDUES 496-507 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THIS FRAGMENT IS ACTUALLY FUSED TO 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN C AND D FIRST 4 RESIDUES (GAMG) ARE VECTOR DERIVED. RESIDUES 5 - 16 CORRESPOND TO RAVER1 PRI3 ...CHAIN C AND D FIRST 4 RESIDUES (GAMG) ARE VECTOR DERIVED. RESIDUES 5 - 16 CORRESPOND TO RAVER1 PRI3 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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2008 / Details: MIRROR
RadiationMonochromator: GEMANIUM CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.4→30.32 Å / Num. obs: 50129 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.3 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASER1.3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SJR

1sjr


Resolution: 1.4→29.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 839936.87 / 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 RRM2. 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 RRM2. 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
Rfree0.234 2506 5 %RANDOM
Rwork0.224 ---
obs0.224 50129 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.17 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.22 Å20 Å2-5.57 Å2
2---5.39 Å20 Å2
3---3.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.4→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 191 1932
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
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
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
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 411 5 %
Rwork0.325 7750 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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