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- PDB-7weg: Complex structure of PDZD7 and FCHSD2 -

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Basic information

Entry
Database: PDB / ID: 7weg
TitleComplex structure of PDZD7 and FCHSD2
Components
  • FCHSD2
  • PDZ domain-containing protein 7
KeywordsLIPID BINDING PROTEIN / PDZD7 / HHD domain / membrane-targeting
Function / homology
Function and homology information


USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / stereocilium / auditory receptor cell stereocilium organization / establishment of localization in cell ...USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / stereocilium / auditory receptor cell stereocilium organization / establishment of localization in cell / sensory perception of sound / establishment of protein localization / cilium / nucleoplasm / identical protein binding / nucleus / plasma membrane
Similarity search - Function
PDZD7, Harmonin N-like domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
PDZ domain-containing protein 7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, H. / Lin, L. / Lu, Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.J. / Year: 2022
Title: Deafness-related protein PDZD7 forms complex with the C-terminal tail of FCHSD2.
Authors: Wang, H. / Zhao, D. / Du, H. / Zhai, X. / Wu, S. / Lin, L. / Xu, Z. / Lu, Q.
History
DepositionDec 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PDZ domain-containing protein 7
B: PDZ domain-containing protein 7
C: FCHSD2
D: FCHSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9748
Polymers26,7134
Non-polymers2624
Water2,378132
1
A: PDZ domain-containing protein 7
D: FCHSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4874
Polymers13,3562
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-64 kcal/mol
Surface area5890 Å2
MethodPISA
2
B: PDZ domain-containing protein 7
C: FCHSD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4874
Polymers13,3562
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-65 kcal/mol
Surface area5770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.603, 62.918, 46.030
Angle α, β, γ (deg.)90.000, 95.190, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 14 through 84 or (resid 85...
12chain C
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA851 - 946
211(chain B and (resid 14 through 84 or (resid 85...B14 - 84
221(chain B and (resid 14 through 84 or (resid 85...B85 - 86
231(chain B and (resid 14 through 84 or (resid 85...B851 - 946
241(chain B and (resid 14 through 84 or (resid 85...B851 - 946
251(chain B and (resid 14 through 84 or (resid 85...B851 - 946
261(chain B and (resid 14 through 84 or (resid 85...B851 - 946
112chain CC734 - 740
212chain DD734 - 740

NCS ensembles :
ID
1
2

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Components

#1: Protein PDZ domain-containing protein 7


Mass: 11650.431 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdzd7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9Q9W7
#2: Protein/peptide FCHSD2 /


Mass: 1705.901 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.05M Zinc acetate dehydrate, 20% w/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97846 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97846 Å / Relative weight: 1
ReflectionResolution: 2→19.68 Å / Num. obs: 15785 / % possible obs: 98.6 % / Redundancy: 6.747 % / Biso Wilson estimate: 30.513 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.136 / Χ2: 0.856 / Net I/σ(I): 10.01 / Num. measured all: 106495 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.066.7270.71537534117311200.9150.77495.5
2.06-2.116.3290.5693.517196115811370.950.6298.2
2.11-2.176.8960.4884.087655112511100.9610.52898.7
2.17-2.246.5320.3585.26800105810410.970.38998.4
2.24-2.316.8850.3854.977284107310580.9720.41798.6
2.31-2.397.0820.3056.0269409939800.9830.32998.7
2.39-2.486.9470.3016.2868439979850.9810.32598.8
2.48-2.596.8860.2317.1464529489370.990.2598.8
2.59-2.76.4590.1998.0358399139040.9880.21699
2.7-2.836.9290.1719.2658488528440.9930.18599.1
2.83-2.996.6360.13411.2655288418330.9930.14599
2.99-3.177.1010.1213.5154617737690.9930.1399.5
3.17-3.397.0340.10415.2451287347290.9960.11299.3
3.39-3.666.7210.08517.6345846846820.9960.09299.7
3.66-4.016.4210.07619.0740266316270.9960.08399.4
4.01-4.486.4790.06222.2137455825780.9970.06799.3
4.48-5.176.9310.06523.1735285125090.9980.0799.4
5.17-6.336.6890.06922.0128364244240.9960.075100
6.33-8.966.2180.0623.3221393463440.9970.06599.4
8.96-19.686.4890.05526.9511291941740.9970.05989.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VRF

2vrf


Resolution: 2→19.68 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1577 10.01 %
Rwork0.2088 14172 -
obs0.2136 15749 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.03 Å2 / Biso mean: 32.6645 Å2 / Biso min: 15.66 Å2
Refinement stepCycle: final / Resolution: 2→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 4 132 1700
Biso mean--49.22 37.63 -
Num. residues----206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A582X-RAY DIFFRACTION7.225TORSIONAL
12B582X-RAY DIFFRACTION7.225TORSIONAL
21C38X-RAY DIFFRACTION7.225TORSIONAL
22D38X-RAY DIFFRACTION7.225TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.070.36841380.30111234137296
2.07-2.140.32251430.25761277142098
2.14-2.230.29311410.2291279142098
2.23-2.330.271430.21221289143298
2.33-2.450.26691420.19931278142099
2.45-2.60.21951440.21041291143598
2.6-2.80.2531430.19831276141999
2.8-3.090.2361440.19951305144999
3.09-3.530.26531440.17981293143799
3.53-4.440.21161450.18841311145699
4.44-19.680.26481500.222313391489100
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)
10.1480.0553-0.07240.0821-0.00910.09920.5845-0.17410.12050.2084-0.2295-0.5680.46590.1686-0.00240.2043-0.0177-0.06040.2914-0.02820.2905-27.87675.4215-14.6592
20.3413-0.1789-0.12850.28050.22480.07490.0125-0.03860.0333-0.06060.01490.1961-0.10520.0104-0.00030.3258-0.0003-0.07720.18690.01430.3078-16.08553.12221.7576
30.56660.04120.21280.324-0.14420.53510.0743-0.0896-0.1809-0.0433-0.20020.36360.0306-0.1828-0.00890.2326-0.0305-0.07260.22560.01040.306-27.9754-7.875-2.0867
41.53990.34090.54330.58280.17740.67520.5615-0.10290.9968-0.26480.1435-0.03380.15730.410.25290.03980.12680.24280.2212-0.22860.1262-20.31087.09698.289
50.0278-0.01670.06380.0116-0.02550.5618-0.1110.11070.2065-0.49440.03170.48360.00820.134-0.00440.3799-0.0267-0.17670.2197-0.00920.489-23.35566.9394-2.0355
60.4687-0.06190.08830.49550.78421.32490.09750.1451-0.31340.03780.31780.1243-0.59030.03960.1120.1955-0.0176-0.0180.1920.02660.3089-19.1649-3.0953-6.6321
70.09690.26910.26421.37980.72581.2440.06290.417-0.3545-0.0278-0.0129-0.5066-0.09540.30370.24920.38190.0165-0.15620.21680.02080.3852-16.3115-8.9283-7.0184
82.12651.19450.13250.66740.10440.22170.487-0.7581-1.01910.1429-0.4199-0.60160.74150.252-0.0260.38370.0171-0.22170.17540.00780.2884-14.4834-8.17853.2549
90.11980.151-0.05650.1519-0.08310.6474-0.19540.4657-0.0295-0.17430.11880.0482-0.20960.3045-0.00040.3389-0.0174-0.1680.2145-0.00460.3752-12.85181.7349-3.7433
10-0.1197-0.08290.32460.2640.03960.38180.1961-0.0091-0.190.1233-0.0252-0.10730.21590.0484-0.00070.303-0.0214-0.07440.20330.04750.25390.4325-2.8714-20.6328
110.0872-0.0167-0.25040.1410.02030.555-0.05620.10850.288-0.30810.1404-0.15150.02550.1463-0.00250.3429-0.0148-0.10240.1863-0.01020.30081.46678.5402-30.3344
120.17060.3277-0.08690.8881-0.2420.34380.2904-0.4374-0.5139-0.28480.01780.04040.2839-0.35280.00140.37840.0256-0.13480.2145-0.01860.29832.8831-3.8948-23.2348
130.2886-0.1077-0.18290.23020.18420.1480.31730.01980.03490.25-0.21540.1902-0.53550.15340.00020.3623-0.0045-0.09780.2134-0.03840.296-5.65949.5437-19.9319
14-0.0091-0.12880.2340.3574-0.73971.3108-0.1412-0.28130.40270.5999-0.0983-0.1024-0.95550.2334-0.00460.2845-0.0252-0.04420.2158-0.00850.25853.70828.9349-16.1153
150.41291.26590.84224.05662.91272.2085-0.1006-0.48190.0247-0.3628-0.38330.9218-0.209-0.3137-0.2820.1584-0.01810.12140.33660.03760.17460.0278-1.0499-7.0685
160.3825-0.00740.27120.0124-0.01790.59510.2801-0.1982-0.3985-0.4299-0.0680.901-0.1925-0.80290.05820.4210.0194-0.14520.3103-0.04150.3248-5.4556-1.2011-22.5989
170.06430.05670.05720.09840.17620.28370.04960.01290.14070.1622-0.28030.0928-0.5452-0.0521-0.00340.3814-0.0545-0.12670.28090.03420.39397.9929.8986-27.0556
180.0868-0.0969-0.01910.1074-0.01440.03830.1738-0.3944-0.37890.1322-0.1412-0.03560.3886-0.192900.2431-0.0233-0.07680.26550.00780.2872-26.1042-9.21074.9187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 851 through 855 )A851 - 855
2X-RAY DIFFRACTION2chain 'A' and (resid 856 through 873 )A856 - 873
3X-RAY DIFFRACTION3chain 'A' and (resid 874 through 889 )A874 - 889
4X-RAY DIFFRACTION4chain 'A' and (resid 890 through 897 )A890 - 897
5X-RAY DIFFRACTION5chain 'A' and (resid 898 through 905 )A898 - 905
6X-RAY DIFFRACTION6chain 'A' and (resid 906 through 910 )A906 - 910
7X-RAY DIFFRACTION7chain 'A' and (resid 911 through 919 )A911 - 919
8X-RAY DIFFRACTION8chain 'A' and (resid 920 through 932 )A920 - 932
9X-RAY DIFFRACTION9chain 'A' and (resid 933 through 946 )A933 - 946
10X-RAY DIFFRACTION10chain 'B' and (resid 851 through 873 )B851 - 873
11X-RAY DIFFRACTION11chain 'B' and (resid 874 through 889 )B874 - 889
12X-RAY DIFFRACTION12chain 'B' and (resid 890 through 910 )B890 - 910
13X-RAY DIFFRACTION13chain 'B' and (resid 911 through 919 )B911 - 919
14X-RAY DIFFRACTION14chain 'B' and (resid 920 through 932 )B920 - 932
15X-RAY DIFFRACTION15chain 'B' and (resid 933 through 938 )B933 - 938
16X-RAY DIFFRACTION16chain 'B' and (resid 939 through 946 )B939 - 946
17X-RAY DIFFRACTION17chain 'C' and (resid 734 through 740 )C734 - 740
18X-RAY DIFFRACTION18chain 'D' and (resid 734 through 740 )D734 - 740

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