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- PDB-3r0h: Structure of INAD PDZ45 in complex with NG2 peptide -

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Basic information

Entry
Database: PDB / ID: 3r0h
TitleStructure of INAD PDZ45 in complex with NG2 peptide
Components
  • Inactivation-no-after-potential D protein
  • NG2
KeywordsPEPTIDE BINDING PROTEIN / protein-protein complex / PDZ domain
Function / homology
Function and homology information


myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of opsin-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / rhabdomere / cellular response to light stimulus / myosin binding / photoreceptor activity / phototransduction ...myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of opsin-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / rhabdomere / cellular response to light stimulus / myosin binding / photoreceptor activity / phototransduction / visual perception / sensory perception of sound / protein localization / signaling receptor complex adaptor activity / calmodulin binding
Similarity search - Function
: / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Inactivation-no-after-potential D protein
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsWei, Z. / Liu, W. / Zhang, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: The INAD scaffold is a dynamic, redox-regulated modulator of signaling in the Drosophila eye
Authors: Liu, W. / Wen, W. / Wei, Z. / Yu, J. / Ye, F. / Liu, C.-H. / Hardie, R.C. / Zhang, M.
History
DepositionMar 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inactivation-no-after-potential D protein
a: NG2
B: Inactivation-no-after-potential D protein
b: NG2
C: Inactivation-no-after-potential D protein
c: NG2
D: Inactivation-no-after-potential D protein
d: NG2
E: Inactivation-no-after-potential D protein
e: NG2
F: Inactivation-no-after-potential D protein
f: NG2
G: Inactivation-no-after-potential D protein
g: NG2
H: Inactivation-no-after-potential D protein
h: NG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,16726
Polymers188,91516
Non-polymers1,25210
Water2,792155
1
A: Inactivation-no-after-potential D protein
a: NG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7693
Polymers23,6142
Non-polymers1541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-5 kcal/mol
Surface area10330 Å2
MethodPISA
2
B: Inactivation-no-after-potential D protein
b: NG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9234
Polymers23,6142
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-4 kcal/mol
Surface area10110 Å2
MethodPISA
3
C: Inactivation-no-after-potential D protein
c: NG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7103
Polymers23,6142
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-4 kcal/mol
Surface area10370 Å2
MethodPISA
4
D: Inactivation-no-after-potential D protein
d: NG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9234
Polymers23,6142
Non-polymers3092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-4 kcal/mol
Surface area10520 Å2
MethodPISA
5
E: Inactivation-no-after-potential D protein
e: NG2


Theoretical massNumber of molelcules
Total (without water)23,6142
Polymers23,6142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-5 kcal/mol
Surface area10590 Å2
MethodPISA
6
F: Inactivation-no-after-potential D protein
f: NG2


Theoretical massNumber of molelcules
Total (without water)23,6142
Polymers23,6142
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-5 kcal/mol
Surface area10240 Å2
MethodPISA
7
G: Inactivation-no-after-potential D protein
g: NG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8074
Polymers23,6142
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area10210 Å2
MethodPISA
8
H: Inactivation-no-after-potential D protein
h: NG2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8074
Polymers23,6142
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-5 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.079, 134.988, 215.986
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 16 molecules ABCDEFGHabcdefgh

#1: Protein
Inactivation-no-after-potential D protein / INAD


Mass: 22507.174 Da / Num. of mol.: 8 / Fragment: UNP residues 473-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3504, inaD / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q24008
#2: Protein/peptide
NG2


Mass: 1107.242 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: Ng2 peptide is synthesized by a company

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Non-polymers , 4 types, 165 molecules

#3: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: 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: 2

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.38 % / Mosaicity: 0.268 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.4M ammonium sulfate, Bicine buffer, pH 9.0, vapor diffusion, hanging drop, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONCHESS A110.9789
SYNCHROTRONCHESS A120.9789
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMar 22, 2009
ADSC QUANTUM 2102CCDMar 22, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 66155 / % possible obs: 99.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.084 / Χ2: 1.061 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.6450.57132401.0381,299.3
2.64-2.6950.50232710.9641,299.3
2.69-2.7450.43632540.9741,299.3
2.74-2.85.10.37833001.0011,299.5
2.8-2.8650.32132261.011,299.5
2.86-2.935.10.26633391.0531,299.4
2.93-350.21732501.0481,299.4
3-3.0850.18233051.0981,299.6
3.08-3.175.10.15132841.1691,299.7
3.17-3.2850.11832871.1491,299.5
3.28-3.3950.10133001.1681,299.7
3.39-3.5350.08933031.1081,299.7
3.53-3.6950.07433361.1411,299.7
3.69-3.8850.06633111.1751,299.7
3.88-4.1350.06133311.0471,299.6
4.13-4.4550.05433290.9931,299.5
4.45-4.8950.05333631.041,299.2
4.89-5.64.90.05433581.0941,298.7
5.6-7.054.90.05433490.9291,298
7.05-504.70.05234191.0211,294.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.53 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.094 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3349 5.1 %RANDOM
Rwork0.1984 ---
obs0.2016 66008 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.78 Å2 / Biso mean: 49.512 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12657 0 65 155 12877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212957
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.98117548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50251630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.25125.128509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91152298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2541548
X-RAY DIFFRACTIONr_chiral_restr0.0860.22040
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219504
X-RAY DIFFRACTIONr_mcbond_it1.74828186
X-RAY DIFFRACTIONr_mcangle_it3.044313276
X-RAY DIFFRACTIONr_scbond_it4.9844771
X-RAY DIFFRACTIONr_scangle_it7.10564272
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 239 -
Rwork0.301 4507 -
all-4746 -
obs--99.23 %
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)
12.4797-0.94810.94633.1494-1.58743.13140.25940.0867-0.2001-0.54910.38581.02170.135-0.2541-0.64520.1257-0.0464-0.22650.09610.11550.6347-30.68695.0299-13.671
22.05491.048-0.63981.9666-1.48432.7660.2456-0.17030.14730.37070.22440.7611-0.0151-0.2179-0.470.12050.05110.16740.16190.10040.5734-30.5351-6.202313.2088
31.80710.65340.0445.9812-1.07982.6628-0.03430.17260.0488-0.0313-0.1279-0.2756-0.26480.28340.16230.0327-0.0444-0.01040.13340.01370.03141.918314.7305-4.8655
41.9793-0.95550.07135.5978-1.03732.24990.0451-0.1257-0.17780.082-0.1108-0.21290.15630.2680.06570.01970.0245-0.00780.13960.00750.04733.2295-12.81055.2325
53.5434-1.39070.9132.1171-0.91123.0230.20870.1205-0.2034-0.0858-0.0441-0.0407-0.36350.1288-0.16470.18480.0442-0.06480.1661-0.05540.0881-29.43736.2055-36.4198
63.37441.8363-0.70982.5998-0.98523.34970.1954-0.24240.12390.1382-0.0443-0.09810.39650.1226-0.15110.225-0.00930.08320.241-0.03740.1123-27.4223-37.225436.1547
71.8474-0.70730.36651.7884-1.30595.75440.0264-0.0877-0.1774-0.07240.03180.06130.81890.2892-0.05820.29410.17430.08980.20980.01860.1128-0.9445-38.910632.9296
82.14790.73930.27911.9796-0.78654.5965-0.04750.08250.08140.0288-0.02520.0796-0.68070.03460.07270.2728-0.104-0.10040.1745-0.02380.106-3.229440.2517-33.2355
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A475 - 672
2X-RAY DIFFRACTION1a1 - 9
3X-RAY DIFFRACTION2B476 - 671
4X-RAY DIFFRACTION2b1 - 9
5X-RAY DIFFRACTION3C476 - 673
6X-RAY DIFFRACTION3c1 - 9
7X-RAY DIFFRACTION4D475 - 673
8X-RAY DIFFRACTION4d1 - 9
9X-RAY DIFFRACTION5E474 - 672
10X-RAY DIFFRACTION5e1 - 9
11X-RAY DIFFRACTION6F475 - 672
12X-RAY DIFFRACTION6f1 - 9
13X-RAY DIFFRACTION7G479 - 671
14X-RAY DIFFRACTION7g1 - 9
15X-RAY DIFFRACTION8H479 - 671
16X-RAY DIFFRACTION8h1 - 9

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