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- PDB-7pcb: The PDZ domain of SNX27 fused with ANXA2 -

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Basic information

Entry
Database: PDB / ID: 7pcb
TitleThe PDZ domain of SNX27 fused with ANXA2
ComponentsSorting nexin-27,Annexin A2
KeywordsPEPTIDE BINDING PROTEIN / PDZ / crystallization chaperone
Function / homology
Function and homology information


establishment of natural killer cell polarity / 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 / 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 ...establishment of natural killer cell polarity / 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 / 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 / PCSK9-AnxA2 complex / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / phosphatidylinositol-3-phosphate binding / calcium-dependent phospholipid binding / negative regulation of receptor internalization / endocytic recycling / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / virion binding / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / endosomal transport / positive regulation of receptor recycling / endosome to lysosome transport / phosphatidylserine binding / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of exocytosis / immunological synapse / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / phosphatidylinositol binding / cell-matrix adhesion / response to activity / adherens junction / intracellular protein transport / lung development / Schaffer collateral - CA1 synapse / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / early endosome membrane / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / early endosome / endosome / lysosomal membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / Neutrophil degranulation / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Ras-associating (RA) domain profile. / Annexin / Annexin ...SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Ras-associating (RA) domain profile. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Ras association (RalGDS/AF-6) domain / Annexin repeat profile. / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Annexin A2 / Sorting nexin-27
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-27,Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5077
Polymers47,2151
Non-polymers2926
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-49 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.680, 59.210, 180.960
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 Sorting nexin-27,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: 47214.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: SNX27, KIAA0488, My014, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D
Production host: Escherichia coli (E. coli) / References: UniProt: Q96L92, UniProt: P07355
#2: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium thiocyanate 0.1 M Sodium bromide 0.1 M MES 6.5 12 % 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: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→46.167 Å / Num. obs: 39829 / % possible obs: 99.6 % / Redundancy: 13.12 % / CC1/2: 0.999 / Rrim(I) all: 0.125 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 2885 / CC1/2: 0.403 / Rrim(I) all: 2.49

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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, 6SAK

5n7d

6sak


Resolution: 2→46.167 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 1989 5 %
Rwork0.1895 37788 -
obs0.1903 39777 99.58 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.6 Å2 / Biso mean: 55.2529 Å2 / Biso min: 25.44 Å2
Refinement stepCycle: final / Resolution: 2→46.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 11 254 3546
Biso mean--44.5 50.55 -
Num. residues----415
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.04990.3461380.3258262299
2.0499-2.10530.31121400.28362662100
2.1053-2.16730.29441400.2419265299
2.1673-2.23720.28491400.2247264999
2.2372-2.31720.27031380.221264999
2.3172-2.410.21831400.19482663100
2.41-2.51960.22091400.19772659100
2.5196-2.65250.2261420.19482696100
2.6525-2.81860.21541420.19542702100
2.8186-3.03620.25081420.19482682100
3.0362-3.34170.20131440.18552732100
3.3417-3.8250.18241430.17872738100
3.825-4.81830.17331460.15612759100
4.8183-46.1670.16461540.16462923100
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)
14.88640.9742-3.34046.3487-1.035610.0717-0.03671.5172-0.0611-1.4231-0.04650.5610.9048-1.45450.10650.7496-0.0165-0.17390.8263-0.06730.742-0.6171-8.335611.7976
22.3272-0.09870.03491.8156-0.91184.09580.08110.4776-0.1936-0.3434-0.05090.03210.20060.1918-0.02450.26110.01890.02740.342-0.06010.277220.83181.818421.5317
31.43740.2159-0.46911.856-1.81622.70070.0689-0.2301-0.09470.1929-0.06320.0719-0.13610.08120.03280.2718-0.02560.04130.2659-0.02640.336611.2591-3.913850.9091
42.4240.1835-0.35083.0911-1.54573.48920.16660.18710.0676-0.2331-0.06170.29550.0487-0.1289-0.14910.20540.02360.00240.2793-0.0330.28474.70266.260526.5689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 122 )A40 - 122
2X-RAY DIFFRACTION2chain 'A' and (resid 123 through 279 )A123 - 279
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 393 )A280 - 393
4X-RAY DIFFRACTION4chain 'A' and (resid 394 through 454 )A394 - 454

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