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- PDB-7qqn: The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding... -

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Basic information

Entry
Database: PDB / ID: 7qqn
TitleThe PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of TRPV3
Components
  • Gamma-1-syntrophin,Annexin A2
  • Transient receptor potential cation channel subfamily V member 3
KeywordsPEPTIDE BINDING PROTEIN / PDZ / linear motif / crystallization chaperone
Function / homology
Function and homology information


syntrophin complex / positive regulation of low-density lipoprotein particle receptor binding / PCSK9-AnxA2 complex / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / dystrophin-associated glycoprotein complex / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity ...syntrophin complex / positive regulation of low-density lipoprotein particle receptor binding / PCSK9-AnxA2 complex / AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / dystrophin-associated glycoprotein complex / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / negative regulation of hair cycle / 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 / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / cell communication / Schmidt-Lanterman incisure / cornified envelope / vesicle budding from membrane / negative regulation of receptor internalization / plasma membrane protein complex / osteoclast development / calcium-dependent phospholipid binding / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / TRP channels / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / response to temperature stimulus / positive regulation of receptor recycling / positive regulation of calcium ion import / phosphatidylserine binding / positive regulation of exocytosis / regulation of neurogenesis / basement membrane / Smooth Muscle Contraction / phosphatidylinositol-4,5-bisphosphate binding / fibrinolysis / cytoskeletal protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cell-matrix adhesion / lipid droplet / response to activity / adherens junction / lung development / calcium ion transmembrane transport / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / calcium channel activity / sarcolemma / ruffle membrane / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / actin binding / midbody / basolateral plasma membrane / protease binding / angiogenesis / collagen-containing extracellular matrix / vesicle / lysosome / early endosome / cytoskeleton / receptor complex / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / structural molecule activity / cell surface / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Syntrophin / Syntrophin C-terminal PH domain / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily ...Syntrophin / Syntrophin C-terminal PH domain / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Transient receptor potential cation channel subfamily V member 1-4 / Transient receptor potential cation channel subfamily V / Ankyrin repeat / PH domain profile. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Annexin A2 / Transient receptor potential cation channel subfamily V member 3 / Gamma-1-syntrophin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
DepositionJan 10, 2022Deposition 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

Downloads & links

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Assembly

Deposited unit
A: Gamma-1-syntrophin,Annexin A2
C: Gamma-1-syntrophin,Annexin A2
B: Transient receptor potential cation channel subfamily V member 3
D: Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,32414
Polymers95,8714
Non-polymers45310
Water3,855214
1
A: Gamma-1-syntrophin,Annexin A2
B: Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0966
Polymers47,9362
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-41 kcal/mol
Surface area21050 Å2
MethodPISA
2
C: Gamma-1-syntrophin,Annexin A2
D: Transient receptor potential cation channel subfamily V member 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2288
Polymers47,9362
Non-polymers2926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-50 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.830, 132.440, 63.660
Angle α, β, γ (deg.)90.000, 100.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gamma-1-syntrophin,Annexin A2 / G1SYN / Syntrophin-4 / SYN4 / Annexin II / Annexin-2 / Calpactin I heavy chain / Calpactin-1 heavy ...G1SYN / Syntrophin-4 / SYN4 / 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: 46770.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNTG1, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSN8, UniProt: P07355
#2: Protein/peptide Transient receptor potential cation channel subfamily V member 3 / TrpV3 / Vanilloid receptor-like 3 / VRL-3


Mass: 1165.202 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-terminal biotin-ado-ado linker (amino-dodecanoic acid)
Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NET8
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Lithium sulfate 0.05 M Magnesium chloride hexahydrate 0.1 M HEPES 7.8 20 % v/v PEG Smear High

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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: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→45.467 Å / Num. obs: 35752 / % possible obs: 99.8 % / Redundancy: 6.66 % / CC1/2: 0.996 / Rrim(I) all: 0.222 / Net I/σ(I): 8.22
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 6.66 % / Mean I/σ(I) obs: 1.18 / Num. unique obs: 2621 / CC1/2: 0.529 / Rrim(I) all: 2.042 / % possible all: 99.6

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Processing

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

5n7d


Resolution: 2.45→45.467 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 1788 5.01 %
Rwork0.2199 33917 -
obs0.2221 35705 99.86 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.44 Å2 / Biso mean: 63.1659 Å2 / Biso min: 22.5 Å2
Refinement stepCycle: final / Resolution: 2.45→45.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 0 15 214 6870
Biso mean--66.38 47.23 -
Num. residues----838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.45-2.51630.39511360.33152590
2.5163-2.59030.3761380.32332617
2.5903-2.67390.34981350.30592567
2.6739-2.76950.36951380.3152617
2.7695-2.88030.38391370.2842600
2.8803-3.01140.32161380.27032608
3.0114-3.17010.33391370.26742608
3.1701-3.36870.29881380.25582613
3.3687-3.62870.28141360.22552582
3.6287-3.99370.23051390.19662638
3.9937-4.57110.2111370.16692611
4.5711-5.75730.20751380.18672614
5.7573-45.4670.19411410.16352652
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)
18.13030.5901-2.80714.3774-1.42433.8134-0.013-0.37370.25590.60550.0069-1.0121-0.38310.31070.03260.93160.1067-0.24610.6811-0.17890.748732.614-0.636-47.8701
21.15260.1743-0.22422.0841-1.06491.7809-0.09920.2059-0.0872-0.23930.12590.22480.1015-0.2126-0.04010.465-0.004-0.04710.3595-0.02740.252638.891710.9302-11.3289
31.01920.14791.12511.68610.3185.79510.08470.112-0.0448-0.0079-0.10970.18670.5714-0.12480.06740.9579-0.0759-0.05030.440.03340.428310.936355.0036-59.2321
40.67980.25160.26921.72510.59541.57740.07370.04010.02930.0279-0.0273-0.14710.01770.0606-0.06710.60560.0042-0.08470.3315-0.01850.287312.710733.7013-36.8821
56.97022.9921-1.7054.5096-4.20744.1632-0.1421-0.17031.66760.42150.4715-0.2624-1.7319-0.4892-0.33381.23370.2221-0.0720.7337-0.03121.603441.4348-4.9473-51.6438
65.16662.8761-4.744.591-5.44656.9852-0.7014-0.221-0.687-0.4808-0.11630.32340.91420.09660.75091.86990.051-0.21070.45720.01660.62968.171242.4147-67.0463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 50 through 138 )A50 - 138
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 462 )A139 - 462
3X-RAY DIFFRACTION3chain 'C' and (resid 49 through 170 )C49 - 170
4X-RAY DIFFRACTION4chain 'C' and (resid 171 through 462 )C171 - 462
5X-RAY DIFFRACTION5chain 'B' and (resid 786 through 790 )B786 - 790
6X-RAY DIFFRACTION6chain 'D' and (resid 785 through 790 )D785 - 790

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