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- PDB-7p72: The PDZ domain of SNX27 complexed with the PDZ-binding motif of MERS-E -

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Basic information

Entry
Database: PDB / ID: 7p72
TitleThe PDZ domain of SNX27 complexed with the PDZ-binding motif of MERS-E
Components
  • Envelope small membrane protein
  • Sorting nexin-27,Annexin A2
KeywordsPEPTIDE BINDING PROTEIN / PDZ / complex
Function / homology
Function and homology information


establishment of natural killer cell polarity / disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / 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 / positive regulation of low-density lipoprotein particle clearance ...establishment of natural killer cell polarity / disruption of cellular anatomical structure in another organism / viral budding from Golgi membrane / 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 / 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 / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / cornified envelope / vesicle budding from membrane / negative regulation of receptor internalization / plasma membrane protein complex / regulation of synapse maturation / osteoclast development / calcium-dependent phospholipid binding / endocytic recycling / phosphatidylinositol-3-phosphate binding / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / endosomal transport / endosome to lysosome transport / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / host cell Golgi membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / immunological synapse / 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 / phosphatidylinositol binding / response to activity / adherens junction / intracellular protein transport / lung development / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / Schaffer collateral - CA1 synapse / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / early endosome membrane / midbody / host cell Golgi apparatus / basolateral plasma membrane / protease binding / angiogenesis / collagen-containing extracellular matrix / vesicle / early endosome / endosome / lysosomal membrane / intracellular membrane-bounded organelle / glutamatergic synapse / calcium ion binding / Neutrophil degranulation / apoptotic process / 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 / cytosol / cytoplasm
Similarity search - Function
Envelope small membrane protein, MERS-CoV-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Annexin A2 ...Envelope small membrane protein, MERS-CoV-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / SNX27, atypical FERM-like domain / SNX27, PX domain / SNX27, RA domain / SNX17/27/31 / Annexin A2 / Ras association (RalGDS/AF-6) domain / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Ras-associating (RA) domain profile. / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / 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
Envelope small membrane protein / Annexin A2 / Sorting nexin-27
Similarity search - Component
Biological speciesHomo sapiens (human)
Middle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGogl, G. / Cousido-Siah, A. / Trave, G.
CitationJournal: Nat Commun / Year: 2022
Title: Quantitative fragmentomics allow affinity mapping of interactomes.
Authors: Gogl, G. / Zambo, B. / Kostmann, C. / Cousido-Siah, A. / Morlet, B. / Durbesson, F. / Negroni, L. / Eberling, P. / Jane, P. / Nomine, Y. / Zeke, A. / Ostergaard, S. / Monsellier, E. / Vincentelli, R. / Trave, G.
History
DepositionJul 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 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
B: Envelope small membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8039
Polymers49,4182
Non-polymers3857
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-56 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.170, 83.950, 106.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 47821.320 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: Protein/peptide Envelope small membrane protein / E protein / sM protein


Mass: 1596.711 Da / Num. of mol.: 1 / Mutation: N-terminal biotin label / Source method: obtained synthetically
Source: (synth.) Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)
References: UniProt: K9N5R3
#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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% polyethylene glycol 8000, 100 mM imidazole buffered at pH 8.0

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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: 2.15→45 Å / Num. obs: 30598 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.998 / Rrim(I) all: 0.252 / Net I/σ(I): 8.97
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.34 / Num. unique obs: 2226 / CC1/2: 0.719 / Rrim(I) all: 2.26 / % possible all: 100

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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: 2.15→44.994 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1529 5.01 %
Rwork0.1991 28980 -
obs0.2011 30509 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.13 Å2 / Biso mean: 47.2219 Å2 / Biso min: 17.12 Å2
Refinement stepCycle: final / Resolution: 2.15→44.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 17 254 3507
Biso mean--50.51 48.07 -
Num. residues----409
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1501-2.21950.3361370.30612601
2.2195-2.29880.33541350.30012567
2.2988-2.39080.28771360.24572592
2.3908-2.49960.22691370.23962600
2.4996-2.63140.3121370.2342596
2.6314-2.79620.271400.22592654
2.7962-3.01210.241370.20472594
3.0121-3.31510.23591390.18562643
3.3151-3.79460.24121400.17642646
3.7946-4.780.17851410.15332681
4.78-44.9940.2331500.18852806
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)
14.9271-1.7071-5.27881.97511.78976.27540.00640.37150.06260.02570.09490.04310.1604-0.6455-0.10090.7122-0.03770.01140.5890.04130.4972-27.3129-17.500942.4352
20.8423-0.21020.61421.2417-0.08662.2396-0.0629-0.01950.01580.21340.02550.0059-0.1454-0.00860.04150.226-0.02460.01790.211-0.00710.2285-7.4482-13.773316.8391
36.59230.5189-5.117.89221.25854.31220.04040.61240.06290.27420.1399-0.4707-0.4125-0.8119-0.23260.63710.11160.12390.68960.17890.8335-32.0158-5.057145.3495
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 155 )A38 - 155
2X-RAY DIFFRACTION2chain 'A' and (resid 156 through 460 )A156 - 460
3X-RAY DIFFRACTION3chain 'B' and (resid 77 through 82 )B77 - 82

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