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- PDB-7pc5: The third PDZ domain of PDZD7 complexed with the PDZ-binding moti... -

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Basic information

Entry
Database: PDB / ID: 7pc5
TitleThe third PDZ domain of PDZD7 complexed with the PDZ-binding motif of EXOC4
Components
  • Exocyst complex component 4Exocyst
  • PDZ domain-containing protein 7,Annexin A2
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone
Function / homology
Function and homology information


vesicle tethering involved in exocytosis / paraxial mesoderm formation / USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / exocyst / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex ...vesicle tethering involved in exocytosis / paraxial mesoderm formation / USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / exocyst / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / protein localization to ciliary membrane / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / stereocilium tip / PCSK9-AnxA2 complex / growth cone membrane / : / VxPx cargo-targeting to cilium / myelin sheath abaxonal region / myelin sheath adaxonal region / auditory receptor cell development / detection of mechanical stimulus involved in sensory perception of sound / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / Golgi to plasma membrane transport / vesicle budding from membrane / stereocilium / cornified envelope / vesicle docking involved in exocytosis / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Flemming body / collagen fibril organization / auditory receptor cell stereocilium organization / S100 protein binding / Dissolution of Fibrin Clot / virion binding / osteoclast development / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / Insulin processing / exocytosis / positive regulation of exocytosis / microvillus / cilium assembly / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / regulation of macroautophagy / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoskeletal protein binding / lipid droplet / cell-matrix adhesion / response to activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / establishment of localization in cell / PDZ domain binding / sensory perception of sound / adherens junction / lung development / sarcolemma / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / establishment of protein localization / calcium channel activity / cilium / small GTPase binding / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / protein transport / late endosome membrane / midbody / chemical synaptic transmission / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / early endosome / endosome / lysosomal membrane / synapse / calcium ion binding / Neutrophil degranulation / cell surface / positive regulation of transcription by RNA polymerase II
Similarity search - Function
PDZD7, Harmonin N-like domain / Exocyst complex component Sec8, N-terminal / Exocyst complex component Sec8/EXOC4 / Exocyst complex component Sec8 N-terminal / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats ...PDZD7, Harmonin N-like domain / Exocyst complex component Sec8, N-terminal / Exocyst complex component Sec8/EXOC4 / Exocyst complex component Sec8 N-terminal / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Annexin A2 / Exocyst complex component 4 / PDZ domain-containing protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCousido-Siah, A. / Trave, G. / Gogl, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: A scalable strategy to solve structures of PDZ domains and their complexes.
Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G.
History
DepositionAug 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: PDZ domain-containing protein 7,Annexin A2
B: Exocyst complex component 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7899
Polymers48,4042
Non-polymers3857
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-55 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.110, 60.350, 181.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein PDZ domain-containing protein 7,Annexin A2 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / ...Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy chain / Chromobindin-8 / Lipocortin II / Placental anticoagulant protein IV / PAP-IV / Protein I / p36


Mass: 47297.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDZD7, PDZK7, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H5P4, UniProt: P07355
#2: Protein/peptide Exocyst complex component 4 / Exocyst / Exocyst complex component Sec8


Mass: 1107.320 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: N-terminal biotin-ado-ado (amino-dodecanoic acid) label
Source: (synth.) Homo sapiens (human) / References: UniProt: Q96A65
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium sulfate, 15% PEG 4000, 0.1M TRIS pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→42.748 Å / Num. obs: 64942 / % possible obs: 97.6 % / Redundancy: 13.64 % / CC1/2: 0.999 / Rrim(I) all: 0.1 / Net I/σ(I): 16.64
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 1.83 / Num. unique obs: 4670 / CC1/2: 0.715 / Rrim(I) all: 1.561

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N7D, 3LNY

5n7d

3lny


Resolution: 1.7→42.748 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1882 3246 5 %
Rwork0.1661 61639 -
obs0.1672 64885 97.6 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.68 Å2 / Biso mean: 40.7018 Å2 / Biso min: 13.93 Å2
Refinement stepCycle: final / Resolution: 1.7→42.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3273 0 17 504 3794
Biso mean--36.44 43.59 -
Num. residues----411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72530.27911360.2555258195
1.7253-1.75220.261370.2461259997
1.7522-1.78090.24391370.2389259296
1.7809-1.81170.3081380.214263397
1.8117-1.84460.2511390.2121262796
1.8446-1.88010.19951370.1995261497
1.8801-1.91850.20121380.1977262097
1.9185-1.96020.22011390.1878263897
1.9602-2.00580.18511400.1823265397
2.0058-2.05590.19881370.1679260798
2.0559-2.11150.20351410.168267198
2.1115-2.17360.19731410.1615267897
2.1736-2.24380.18791400.1519265197
2.2438-2.3240.17551390.1554265698
2.324-2.4170.19341410.1547268198
2.417-2.5270.19591430.1612270598
2.527-2.66020.18791410.164267899
2.6602-2.82690.17851440.1665273099
2.8269-3.04510.18551430.1613273098
3.0451-3.35140.19941450.1511275299
3.3514-3.83610.17161450.1537277099
3.8361-4.8320.14421480.1404280899
4.832-42.7480.19491570.1855296599
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)
11.81662.2931.87073.46851.84542.8466-0.29120.5224-1.2634-0.4037-0.29780.74841.2051-0.74690.55360.905-0.16170.10540.693-0.32631.02812.8532-16.658411.4362
20.60190.0484-0.09190.7909-0.57051.77510.01130.0228-0.03950.0222-0.0389-0.024-0.10780.1870.02920.1345-0.01940.02950.1566-0.02690.181515.34450.953934.3464
35.7379-0.6108-0.44234.8373-3.9013.3006-0.54020.54870.1013-0.4219-0.73121.23131.3074-1.99291.26110.9406-0.049-0.2061.4349-0.61121.0584-3.2031-12.93251.6715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 859 through 964 )A859 - 964
2X-RAY DIFFRACTION2chain 'A' and (resid 965 through 1272 )A965 - 1272
3X-RAY DIFFRACTION3chain 'B' and (resid 31 through 36 )B31 - 36

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