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- PDB-5yi8: Crystal structure of drosophila Numb PTB domain and Pon peptide c... -

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Basic information

Entry
Database: PDB / ID: 5yi8
TitleCrystal structure of drosophila Numb PTB domain and Pon peptide complex
Components
  • Pon peptide from Partner of numb
  • Protein numb
KeywordsCELL CYCLE / Numb PTB domain and Pon complex
Function / homology
Function and homology information


pericardial nephrocyte differentiation / enteroendocrine cell differentiation / Malpighian tubule tip cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation ...pericardial nephrocyte differentiation / enteroendocrine cell differentiation / Malpighian tubule tip cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation / negative regulation of receptor recycling / glial cell migration / asymmetric neuroblast division / basal part of cell / embryonic heart tube development / Notch binding / centrosome localization / negative regulation of neuroblast proliferation / negative regulation of Notch signaling pathway / positive regulation of endocytosis / neuroblast proliferation / regulation of neurogenesis / protein localization / cell cortex / negative regulation of gene expression / ATP binding / nucleus / cytoplasm
Similarity search - Function
NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / Protein numb / Partner of numb
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
Model detailsDrosophila Numb PTB recognizes repeating motifs in the N terminus of Pon
AuthorsShan, Z. / Wen, W.
CitationJournal: Nat Commun / Year: 2018
Title: Basal condensation of Numb and Pon complex via phase transition during Drosophila neuroblast asymmetric division.
Authors: Shan, Z. / Tu, Y. / Yang, Y. / Liu, Z. / Zeng, M. / Xu, H. / Long, J. / Zhang, M. / Cai, Y. / Wen, W.
History
DepositionOct 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein numb
B: Pon peptide from Partner of numb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8603
Polymers19,8142
Non-polymers461
Water95553
1
A: Protein numb
B: Pon peptide from Partner of numb
hetero molecules

A: Protein numb
B: Pon peptide from Partner of numb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7196
Polymers39,6274
Non-polymers922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area5020 Å2
ΔGint-32 kcal/mol
Surface area16620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.392, 43.392, 181.304
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein numb


Mass: 15905.161 Da / Num. of mol.: 1 / Fragment: PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: numb, CG3779 / Plasmid: pETM3C / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P16554
#2: Protein/peptide Pon peptide from Partner of numb / RE65495p


Mass: 3908.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W4I7
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.57 Å3/Da / Density % sol: 52.15 % / Mosaicity: 0.468 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 7 / Details: 0.1M sodium formate, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9754 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14087 / % possible obs: 98.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.34 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.025 / Rrim(I) all: 0.058 / Χ2: 0.912 / Net I/σ(I): 10.3 / Num. measured all: 67717
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.30.7626710.7350.4070.870.79596.7
2.03-2.074.50.5256670.8560.2720.5940.72996
2.07-2.114.50.4736750.8130.250.5390.899
2.11-2.154.20.4096950.8770.2180.4660.74999.4
2.15-2.24.40.46810.8540.2070.4530.7897.6
2.2-2.254.60.3726830.8510.1940.4221.45399
2.25-2.314.70.2686990.9540.1350.3020.99799.1
2.31-2.374.70.2117020.9620.1070.2380.85799.9
2.37-2.444.70.1676890.9660.0850.1880.83799.6
2.44-2.524.80.1427130.9740.0720.160.764100
2.52-2.614.70.1156900.9850.0580.130.836100
2.61-2.714.70.0947260.9850.0480.1060.843100
2.71-2.844.60.0756780.9870.0380.0840.86199.6
2.84-2.9950.0617040.9940.030.0680.89498.7
2.99-3.175.30.057130.9940.0240.0560.93399.6
3.17-3.425.20.0447240.9960.0210.0490.99299.3
3.42-3.765.20.0397070.9960.0180.0431.10397
3.76-4.315.10.0337250.9970.0150.0371.03198
4.31-5.435.60.0347540.9980.0160.0381.01398.8
5.43-505.10.037910.9980.0140.0340.84995.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F0W

3f0w


Resolution: 2.001→36.796 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 699 5.03 %
Rwork0.1911 13198 -
obs0.1929 13897 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.09 Å2 / Biso mean: 30.8975 Å2 / Biso min: 13.29 Å2
Refinement stepCycle: final / Resolution: 2.001→36.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 3 53 1278
Biso mean--41.56 31.58 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011246
X-RAY DIFFRACTIONf_angle_d0.9511676
X-RAY DIFFRACTIONf_chiral_restr0.06184
X-RAY DIFFRACTIONf_plane_restr0.006218
X-RAY DIFFRACTIONf_dihedral_angle_d9.825743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0005-2.1550.29371270.20812454258193
2.155-2.37180.26871480.20352568271698
2.3718-2.71490.24231510.196826702821100
2.7149-3.42010.21341430.196926672810100
3.4201-36.80270.20111300.17922839296998
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.39491.78642.99152.3947-1.38532.81150.05360.2185-0.1696-0.58360.2239-0.1014-0.07740.6414-0.25330.329-0.1368-0.00510.4183-0.03950.236116.7455-11.4557-31.5564
21.89450.643-0.69691.8614-0.31981.7413-0.03080.36020.1409-0.07540.1238-0.1354-0.24110.196-0.08460.1306-0.0808-0.04830.19410.02310.169717.506-6.382-13.8373
34.64480.91620.10575.94152.47875.8599-0.0650.1194-0.0709-0.16130.09940.42260.1116-0.3803-0.03320.1651-0.0619-0.01880.11830.05110.20258.7056-15.7161-7.1504
40.5084-0.81790.57182.5898-1.71261.2265-0.02370.1127-0.0050.18450.05080.0041-0.77850.2138-0.05860.1962-0.1213-0.0310.21040.00940.236817.0348-1.2835-10.7826
54.0601-2.2320.57788.5951.94633.49260.0433-0.07380.4471-0.00470.065-0.7634-0.48910.7087-0.14720.2547-0.1528-0.02980.4952-0.00930.393424.9759-2.7434-13.141
63.71880.03870.14433.48520.69233.5258-0.0230.20710.11340.15830.120.41430.1068-0.1899-0.06440.1281-0.0438-0.00920.18580.05390.173911.6166-13.8706-14.965
73.7350.1614-0.13013.60050.14024.9437-0.06070.2285-0.1696-0.07250.0493-0.22490.19620.38130.00110.1326-0.0697-0.02920.21140.00650.187217.7006-13.0386-16.1303
86.98370.43941.42395.5269-2.98718.449-0.0965-0.7354-1.0465-0.24090.33480.90360.6837-1.3716-0.16730.329-0.1739-0.06340.42490.02340.40293.5004-18.2346-19.674
96.1878-4.45915.67735.7457-3.61945.92060.1386-0.2271-0.2928-0.076-0.084-0.60660.59250.7918-0.10670.22090.0809-0.050.3556-0.02250.337521.1501-22.6926-16.6648
103.67622.1215-0.45984.28430.37660.9223-0.13180.37360.0553-0.29590.26840.56860.0423-0.16890.18870.2673-0.1544-0.07360.20490.09670.268647.9901-26.5321-2.1772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 64 through 77 )A64 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 93 )A78 - 93
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 111 )A94 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 124 )A112 - 124
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 143 )A125 - 143
6X-RAY DIFFRACTION6chain 'A' and (resid 144 through 158 )A144 - 158
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 201 )A159 - 201
8X-RAY DIFFRACTION8chain 'B' and (resid 131 through 135 )B131 - 135
9X-RAY DIFFRACTION9chain 'B' and (resid 136 through 145 )B136 - 145
10X-RAY DIFFRACTION10chain 'B' and (resid 149 through 159 )B149 - 159

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