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- PDB-5yi7: Crystal structure of drosophila Numb PTB domain and Pon peptide c... -

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Basic information

Entry
Database: PDB / ID: 5yi7
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 / positive regulation of neurogenesis / negative regulation of neuroblast proliferation / negative regulation of Notch signaling pathway / positive regulation of endocytosis / regulation of neurogenesis / neuroblast proliferation / 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
Protein numb / Partner of numb
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Protein numb
D: Pon peptide from Partner of numb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0426
Polymers39,8584
Non-polymers1842
Water2,792155
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)40,0426
Polymers39,8584
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+1/31
Buried area4170 Å2
ΔGint-33 kcal/mol
Surface area14270 Å2
MethodPISA
2
C: Protein numb
D: Pon peptide from Partner of numb
hetero molecules

C: Protein numb
D: Pon peptide from Partner of numb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0426
Polymers39,8584
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_775-y+2,-x+2,-z+2/31
Buried area4130 Å2
ΔGint-35 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.593, 65.593, 143.879
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 118 through 123 or (resid 124...
21(chain D and (resid 118 through 135 or resid 137...
12(chain A and (resid 72 or (resid 73 and (name...
22(chain C and (resid 72 through 103 or (resid 104...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLEULEU(chain B and (resid 118 through 123 or (resid 124...BB118 - 1237 - 12
121ARGARGARGARG(chain B and (resid 118 through 123 or (resid 124...BB12413
131ASNASNASNASN(chain B and (resid 118 through 123 or (resid 124...BB118 - 1437 - 32
141ASNASNASNASN(chain B and (resid 118 through 123 or (resid 124...BB118 - 1437 - 32
151ASNASNASNASN(chain B and (resid 118 through 123 or (resid 124...BB118 - 1437 - 32
161ASNASNASNASN(chain B and (resid 118 through 123 or (resid 124...BB118 - 1437 - 32
171ASNASNASNASN(chain B and (resid 118 through 123 or (resid 124...BB118 - 1437 - 32
181ASNASNASNASN(chain B and (resid 118 through 123 or (resid 124...BB118 - 1437 - 32
191ASNASNASNASN(chain B and (resid 118 through 123 or (resid 124...BB118 - 1437 - 32
1101ASNASNASNASN(chain B and (resid 118 through 123 or (resid 124...BB118 - 1437 - 32
211ASNASNALAALA(chain D and (resid 118 through 135 or resid 137...DD118 - 1357 - 24
221PHEPHEPHEPHE(chain D and (resid 118 through 135 or resid 137...DD13726
231GLUGLUGLUGLU(chain D and (resid 118 through 135 or resid 137...DD13827
241ASNASNASNASN(chain D and (resid 118 through 135 or resid 137...DD118 - 1437 - 32
251ASNASNASNASN(chain D and (resid 118 through 135 or resid 137...DD118 - 1437 - 32
261ASNASNASNASN(chain D and (resid 118 through 135 or resid 137...DD118 - 1437 - 32
271ASNASNASNASN(chain D and (resid 118 through 135 or resid 137...DD118 - 1437 - 32
281ASNASNASNASN(chain D and (resid 118 through 135 or resid 137...DD118 - 1437 - 32
291ASNASNASNASN(chain D and (resid 118 through 135 or resid 137...DD118 - 1437 - 32
112ASPASPASPASP(chain A and (resid 72 or (resid 73 and (name...AA7210
122GLUGLUGLUGLU(chain A and (resid 72 or (resid 73 and (name...AA7311
132ASPASPARGARG(chain A and (resid 72 or (resid 73 and (name...AA72 - 20110 - 139
142ASPASPARGARG(chain A and (resid 72 or (resid 73 and (name...AA72 - 20110 - 139
152ASPASPARGARG(chain A and (resid 72 or (resid 73 and (name...AA72 - 20110 - 139
162ASPASPARGARG(chain A and (resid 72 or (resid 73 and (name...AA72 - 20110 - 139
172ASPASPARGARG(chain A and (resid 72 or (resid 73 and (name...AA72 - 20110 - 139
212ASPASPGLUGLU(chain C and (resid 72 through 103 or (resid 104...CC72 - 10310 - 41
222GLUGLUALAALA(chain C and (resid 72 through 103 or (resid 104...CC104 - 10542 - 43
232TRPTRPARGARG(chain C and (resid 72 through 103 or (resid 104...CC69 - 2017 - 139
242TRPTRPARGARG(chain C and (resid 72 through 103 or (resid 104...CC69 - 2017 - 139
252TRPTRPARGARG(chain C and (resid 72 through 103 or (resid 104...CC69 - 2017 - 139
262TRPTRPARGARG(chain C and (resid 72 through 103 or (resid 104...CC69 - 2017 - 139

NCS ensembles :
ID
1
2

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Components

#1: Protein Protein numb


Mass: 15905.161 Da / Num. of mol.: 2 / 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: 4023.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9W4I7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.46 Å3/Da / Density % sol: 45.13 % / Mosaicity: 0.396 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 4.3 / Details: 0,2M MgCl2.6H2O,25% PEG 3350,0.1M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 39132 / % possible obs: 99.3 % / Redundancy: 9.8 % / Biso Wilson estimate: 24.29 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.018 / Rrim(I) all: 0.059 / Χ2: 1.736 / Net I/σ(I): 12.7 / Num. measured all: 384771
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.739.40.79519160.8750.260.8381.36197.7
1.73-1.769.70.69418880.870.2240.731.24497.5
1.76-1.799.60.52818980.9190.1710.5561.2797.9
1.79-1.839.40.45319500.9230.1490.4781.28298.5
1.83-1.879.60.41319300.9570.1350.4351.31398.6
1.87-1.919.40.38719140.9630.1290.4091.72299.2
1.91-1.969.40.28519460.9670.0960.3021.68499.5
1.96-2.029.60.19319360.9890.0640.2031.37599.8
2.02-2.079.40.19519550.9850.0660.2061.8399.6
2.07-2.149.70.13419520.9940.0440.1411.542100
2.14-2.229.90.11219690.9950.0370.1181.494100
2.22-2.319.70.10119550.9980.0340.1071.88199.9
2.31-2.4110.10.08719820.9970.0280.0911.72799.9
2.41-2.5410.20.08619770.9970.0280.0912.064100
2.54-2.7100.08219430.9970.0270.0872.53999.9
2.7-2.91100.06819850.9980.0230.0722.598100
2.91-3.29.90.0619850.9980.020.0632.952100
3.2-3.6610.40.04420110.9990.0140.0462.278100
3.66-4.6110.70.02919970.9990.0090.031.344100
4.61-5010.60.02620430.9990.0090.0281.197.7

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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: 1.7→27.865 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2176 1949 4.99 %
Rwork0.1938 --
obs0.1949 39041 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.52 Å2 / Biso mean: 29.3111 Å2 / Biso min: 16.17 Å2
Refinement stepCycle: final / Resolution: 1.7→27.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 12 155 2322
Biso mean--38.18 32.91 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112210
X-RAY DIFFRACTIONf_angle_d1.1382979
X-RAY DIFFRACTIONf_chiral_restr0.075342
X-RAY DIFFRACTIONf_plane_restr0.008381
X-RAY DIFFRACTIONf_dihedral_angle_d3.1091737
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B130X-RAY DIFFRACTION0.844TORSIONAL
12D130X-RAY DIFFRACTION0.844TORSIONAL
21A1092X-RAY DIFFRACTION0.844TORSIONAL
22C1092X-RAY DIFFRACTION0.844TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.74260.30341340.24612566270097
1.7426-1.78970.27271300.21552596272698
1.7897-1.84240.27321470.21342588273598
1.8424-1.90180.23431360.21652609274599
1.9018-1.96980.23591260.20322658278499
1.9698-2.04860.22261320.192226782810100
2.0486-2.14180.23631460.185426062752100
2.1418-2.25470.23021510.188326642815100
2.2547-2.39590.21721330.183226552788100
2.3959-2.58080.24341480.20126542802100
2.5808-2.84030.19961620.209626572819100
2.8403-3.25070.19961490.196826822831100
3.2507-4.09350.21091370.181827192856100
4.0935-27.86860.20071180.18842760287898
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)
14.94965.0719-4.81036.4768-3.29156.7281-0.49520.07530.01650.21850.38060.17740.2436-1.0462-0.6510.27080.1369-0.13790.50430.12530.26271.990164.022437.8649
22.99044.90931.52718.96770.36397.62980.06940.3728-0.7124-0.6441-0.0822-1.00781.02030.58180.02310.38870.12180.01150.31770.02780.352421.761178.235731.6673
32.4349-1.44730.37844.50851.44934.36360.05640.1712-0.1167-0.2775-0.09170.10110.16450.05610.06550.0701-0.00230.03980.1383-0.01730.144318.750250.973431.1044
45.8222-5.9385.49086.4552-6.03845.7920.17940.56040.29670.0298-0.6249-0.707-0.18150.77640.38730.24970.02740.04680.25310.00410.279524.844851.964926.0979
54.2323-0.8809-1.96945.3132-0.85078.0630.05850.15640.22240.1244-0.00450.0531-0.3883-0.1011-0.07850.13620.01680.00570.1642-0.02610.215712.891157.576538.8598
68.1262-4.68230.53872.7232-0.19372.81310.11820.25330.0234-0.1267-0.12660.5938-0.20550.00930.01510.18690.02070.0050.2235-0.02780.22417.862758.05737.1633
74.7744-0.51020.07364.52910.77732.30930.05140.05480.2623-0.0971-0.0194-0.39640.05080.2403-0.02580.18070.04110.03470.1567-0.03390.192324.01149.290935.3788
80.8914-1.0185-1.83945.34920.06754.7799-0.10140.1108-0.2424-0.1915-0.05140.5485-0.0005-0.66580.19120.17420.01940.03220.2319-0.04750.245114.246245.596431.2571
96.77763.30433.67695.19765.75577.52670.0629-0.00320.0797-0.3639-0.0888-0.1487-0.2205-0.19260.05720.15970.02410.01510.1805-0.01050.239419.074253.403633.3663
105.47880.81-0.67685.3717-2.51976.028-0.0964-0.4144-0.09240.44610.3358-0.08290.5010.23-0.17990.25090.08660.00060.1736-0.04350.163320.059946.844246.1943
118.56645.4767-0.99526.7411-4.62998.18730.0025-0.4025-0.50920.6055-0.4643-0.8984-0.8051.15920.27430.3818-0.1221-0.09350.40570.02440.25455.66954.959122.847
123.64410.50780.2480.5328-1.46055.4480.42720.24960.0332-0.3109-0.2774-0.1183-0.79880.6462-1.21440.4455-0.00610.04420.1237-0.19980.288240.733948.749234.037
138.46822.4725-1.92455.9191-0.85937.4721-0.062-0.54280.05010.70770.29970.62220.7920.1792-0.18570.36330.05070.04010.1883-0.00510.273819.466739.322140.4308
141.7064-0.96340.55753.1666-1.40025.84930.0273-0.0181-0.0049-0.04970.05470.21880.3232-0.014-0.07920.21-0.0206-0.04070.15840.01430.266310.283283.55436.5378
151.5672-0.86640.62113.9873-0.92112.3880.0825-0.04080.0464-0.0155-0.07410.08490.00540.0577-0.00750.1470.0127-0.01510.12850.02370.183512.483887.114634.4604
166.9993-3.3728-7.20787.09930.40199.391-0.5650.8112-1.1437-0.45380.050.5090.8759-1.08780.30140.29-0.088-0.00860.5207-0.05110.2755-9.844555.005449.121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 123 through 136 )D123 - 136
2X-RAY DIFFRACTION2chain 'D' and (resid 137 through 143 )D137 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 98 )A82 - 98
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 111 )A99 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 132 )A112 - 132
6X-RAY DIFFRACTION6chain 'A' and (resid 133 through 143 )A133 - 143
7X-RAY DIFFRACTION7chain 'A' and (resid 144 through 158 )A144 - 158
8X-RAY DIFFRACTION8chain 'A' and (resid 159 through 170 )A159 - 170
9X-RAY DIFFRACTION9chain 'A' and (resid 171 through 183 )A171 - 183
10X-RAY DIFFRACTION10chain 'A' and (resid 184 through 201 )A184 - 201
11X-RAY DIFFRACTION11chain 'B' and (resid 118 through 122 )B118 - 122
12X-RAY DIFFRACTION12chain 'B' and (resid 123 through 136 )B123 - 136
13X-RAY DIFFRACTION13chain 'B' and (resid 137 through 143 )B137 - 143
14X-RAY DIFFRACTION14chain 'C' and (resid 69 through 111 )C69 - 111
15X-RAY DIFFRACTION15chain 'C' and (resid 112 through 201 )C112 - 201
16X-RAY DIFFRACTION16chain 'D' and (resid 118 through 122 )D118 - 122

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