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- PDB-7zvn: Crystal structure of human Annexin A2 in complex with full phosph... -

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Basic information

Entry
Database: PDB / ID: 7zvn
TitleCrystal structure of human Annexin A2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 1.87 A resolution
Components
  • 2'-methoxyethyl DNA gapmer antisense oligonucleotide
  • Annexin A2
KeywordsLIPID BINDING PROTEIN / nucleic acid binding / ASO / antisense oligonucleotide / phosphorothioate
Function / homology
Function and homology information


AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / positive regulation of vesicle fusion / myelin sheath adaxonal region / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair ...AnxA2-p11 complex / membrane raft assembly / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / positive regulation of vacuole organization / phospholipase A2 inhibitor activity / positive regulation of low-density lipoprotein particle clearance / positive regulation of vesicle fusion / myelin sheath adaxonal region / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / cadherin binding involved in cell-cell adhesion / cornified envelope / Schmidt-Lanterman incisure / vesicle budding from membrane / plasma membrane protein complex / calcium-dependent phospholipid binding / osteoclast development / negative regulation of receptor internalization / Dissolution of Fibrin Clot / S100 protein binding / collagen fibril organization / vesicle membrane / epithelial cell apoptotic process / phosphatidylserine binding / positive regulation of receptor recycling / basement membrane / positive regulation of exocytosis / Smooth Muscle Contraction / regulation of neurogenesis / cytoskeletal protein binding / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / lipid droplet / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lung development / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / response to activity / adherens junction / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / RNA polymerase II transcription regulator complex / nuclear matrix / calcium-dependent protein binding / azurophil granule lumen / late endosome membrane / melanosome / : / protease binding / midbody / angiogenesis / basolateral plasma membrane / vesicle / early endosome / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Annexin A2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHyjek-Skladanowska, M. / Anderson, B. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Skowronek, K. / Seth, P. / Nowotny, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structures of annexin A2-PS DNA complexes show dominance of hydrophobic interactions in phosphorothioate binding.
Authors: Hyjek-Skladanowska, M. / Anderson, B.A. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Poznanski, J.T. / Skowronek, K. / Seth, P. / Nowotny, M.
History
DepositionMay 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Feb 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: Annexin A2
C: 2'-methoxyethyl DNA gapmer antisense oligonucleotide
D: 2'-methoxyethyl DNA gapmer antisense oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,78119
Polymers45,7393
Non-polymers1,04216
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.621, 57.502, 70.478
Angle α, β, γ (deg.)90.000, 90.241, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / DNA chain , 2 types, 3 molecules ACD

#1: Protein 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: 35150.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: first residue derived from the expression construct
Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Plasmid: pET28_HisSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07355
#2: DNA chain 2'-methoxyethyl DNA gapmer antisense oligonucleotide


Mass: 5294.467 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: (K39)(N7X)(N7X)(K2F)(K39)(GS)(OKN)(PST)(GS)(GS)(PST)(PST)(AS)(PST)(GS)
Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 368 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 4% w/v PEG 4000, 14% v/v glycerol, 0.03 M MgCl2/CaCl2, 0.1 M bicine/Trizma base pH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.87→43.75 Å / Num. obs: 36723 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.29 Å2 / CC1/2: 1 / Net I/σ(I): 12.14
Reflection shellResolution: 1.87→1.99 Å / Num. unique obs: 35540 / CC1/2: 0.72

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSv3data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LPU

5lpu


Resolution: 1.87→43.75 Å / SU ML: 0.2346 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 2010 5.47 %
Rwork0.1671 34708 -
obs0.1688 36718 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.78 Å2
Refinement stepCycle: LAST / Resolution: 1.87→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 569 56 352 3411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093497
X-RAY DIFFRACTIONf_angle_d1.02554772
X-RAY DIFFRACTIONf_chiral_restr0.0547510
X-RAY DIFFRACTIONf_plane_restr0.0079956
X-RAY DIFFRACTIONf_dihedral_angle_d8.75291095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.38721370.33692428X-RAY DIFFRACTION97.79
1.92-1.970.29791530.25232460X-RAY DIFFRACTION100
1.97-2.030.28581330.20242460X-RAY DIFFRACTION99.96
2.03-2.10.2311460.18572456X-RAY DIFFRACTION99.96
2.1-2.170.2171540.17592472X-RAY DIFFRACTION100
2.17-2.260.22551330.17732459X-RAY DIFFRACTION99.92
2.26-2.360.20661500.16282506X-RAY DIFFRACTION99.96
2.36-2.480.20761460.16042457X-RAY DIFFRACTION100
2.48-2.640.20081420.16372478X-RAY DIFFRACTION100
2.64-2.840.21091450.16332483X-RAY DIFFRACTION100
2.84-3.130.20671440.16232493X-RAY DIFFRACTION100
3.13-3.580.18231350.15082500X-RAY DIFFRACTION99.81
3.58-4.510.15621380.1352512X-RAY DIFFRACTION100
4.51-43.750.17441540.17612544X-RAY DIFFRACTION99.26

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