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- PDB-4cq1: Crystal structure of the neuronal isoform of PTB -

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Basic information

Entry
Database: PDB / ID: 4cq1
TitleCrystal structure of the neuronal isoform of PTB
ComponentsPOLYPYRIMIDINE TRACT-BINDING PROTEIN 2
KeywordsTRANSLATION / RNA BINDING PROTEIN / NPTB / BRPTB
Function / homology
Function and homology information


regulation of neural precursor cell proliferation / mRNA splice site recognition / negative regulation of RNA splicing / regulation of RNA splicing / spliceosomal complex / mRNA binding / RNA binding / nucleus
Similarity search - Function
PTBP2, RNA recognition motif 3 / PTBP2, RNA recognition motif 4 / PTBP2, RNA recognition motif 1 / 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 ...PTBP2, RNA recognition motif 3 / PTBP2, RNA recognition motif 4 / PTBP2, RNA recognition motif 1 / 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 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.69 Å
AuthorsJoshi, A. / Buckroyd, A.N. / Curry, S.
CitationJournal: Peerj / Year: 2014
Title: Solution and Crystal Structures of a C Terminal Fragment of the Neuronal Isoform of the Polypyrimidine Tract Binding Protein (Nptb)
Authors: Joshi, A. / Esteve, V. / Buckroyd, A.N. / Blatter, M. / Allain, F.H.-T. / Curry, S.
History
DepositionFeb 10, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 19, 2014ID: 4CKO
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Apr 16, 2014Group: Database references
Revision 1.4Jan 13, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
B: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
C: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
D: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
E: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
F: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
G: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
H: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,66128
Polymers175,5938
Non-polymers1,06920
Water14,088782
1
A: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1154
Polymers21,9491
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1815
Polymers21,9491
Non-polymers2324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0503
Polymers21,9491
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9852
Polymers21,9491
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1154
Polymers21,9491
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2166
Polymers21,9491
Non-polymers2675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0503
Polymers21,9491
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: POLYPYRIMIDINE TRACT-BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)21,9491
Polymers21,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.000, 65.810, 99.580
Angle α, β, γ (deg.)89.99, 90.00, 89.99
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
POLYPYRIMIDINE TRACT-BINDING PROTEIN 2 / NEURAL POLYPYRIMIDINE TRACT-BINDING PROTEIN / NEURALLY-ENRICHED HOMOLOG OF PTB / PTB-LIKE PROTEIN / NPTB


Mass: 21949.072 Da / Num. of mol.: 8 / Fragment: RRM3-RRM4, RESIDUES 336-531
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: Q9UKA9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 782 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46 %
Description: INITIAL MAD SOLUTION WAS SOLVED IN P21 FROM AN SE- MET CRYSTAL IN SAME CONDITION. DURING REFINEMENT THE CORRECT SPACE GROUP WAS DETERMINED TO BE P1. SEE METHODS IN JOURNAL ARTICLE.
Crystal growDetails: 0.1 M TRIS (PH 8.0), 2 MM ZNCL2, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 17, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.153
11-h,-k,l20.245
11h,-k,-l30.176
11-H, K, -L40.425
ReflectionResolution: 1.69→44.74 Å / Num. obs: 153732 / % possible obs: 89 % / Observed criterion σ(I): 6 / Redundancy: 1.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.1 / % possible all: 85.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
autoSHARPphasing
PHASERphasing
REFMAC5.8.0049refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.69→40.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.306 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20762 7790 5.1 %RANDOM
Rwork0.17003 ---
obs0.17188 145936 88.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.692 Å2
Baniso -1Baniso -2Baniso -3
1-13.84 Å2-6.47 Å20.53 Å2
2---4.33 Å21.1 Å2
3----9.51 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11595 0 20 782 12397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911819
X-RAY DIFFRACTIONr_bond_other_d00.0211309
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.95116025
X-RAY DIFFRACTIONr_angle_other_deg0.583325854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59251506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59425.079504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.782151963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3711536
X-RAY DIFFRACTIONr_chiral_restr0.0630.21876
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02113568
X-RAY DIFFRACTIONr_gen_planes_other00.022768
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2441.6696072
X-RAY DIFFRACTIONr_mcbond_other3.2441.6696071
X-RAY DIFFRACTIONr_mcangle_it4.1892.4957562
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7811.8815747
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.692→1.736 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 548 -
Rwork0.235 10332 -
obs--85.47 %

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