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

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Basic information

Entry
Database: PDB / ID: 7zvx
TitleCrystal structure of human Annexin A2 in complex with full phosphorothioate 5-10 2'-methoxyethyl DNA gapmer antisense oligonucleotide solved at 2.4 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


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 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 / calcium-dependent phospholipid binding / negative regulation of receptor internalization / collagen fibril organization / S100 protein binding / Dissolution of Fibrin Clot / virion binding / osteoclast development / positive regulation of low-density lipoprotein receptor activity / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / cytoskeletal protein binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / response to activity / adherens junction / lung development / 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 / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / 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 / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A2 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile.
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: 2.4 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 17, 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

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Assembly

Deposited unit
A: Annexin A2
B: 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)91,74528
Polymers90,4974
Non-polymers1,24824
Water4,342241
1
A: Annexin A2
C: 2'-methoxyethyl DNA gapmer antisense oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,88314
Polymers45,2482
Non-polymers63512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Annexin A2
D: 2'-methoxyethyl DNA gapmer antisense oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,86114
Polymers45,2482
Non-polymers61312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.230, 60.360, 128.430
Angle α, β, γ (deg.)90.000, 97.170, 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

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


Mass: 10098.352 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),(K39)(N7X)(N7X)(K2F)(K39)(GS)(OKN)(PST)(GS)(GS)(PST)(PST)(AS)(PST)(GS),(K39)(N7X)(N7X)(K2F)(K39)(GS)(OKN)(PST)(GS)(GS) ...Details: (K39)(N7X)(N7X)(K2F)(K39)(GS)(OKN)(PST)(GS)(GS)(PST)(PST)(AS)(PST)(GS),(K39)(N7X)(N7X)(K2F)(K39)(GS)(OKN)(PST)(GS)(GS)(PST)(PST)(AS)(PST)(GS),(K39)(N7X)(N7X)(K2F)(K39)(GS)(OKN)(PST)(GS)(GS)(PST)(PST)(AS)(PST)(GS),(K39)(N7X)(N7X)(K2F)(K39)(GS)(OKN)(PST)(GS)(GS)(PST)(PST)(AS)(PST)(GS)
Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 12% w/v PEG 8000, 24% v/v ethylene glycol, 0.02 M sodium formate/ammonium acetate/trisodium citrate/sodium potassium L-tartrate/sodium oxamate, 0.1 M MES/imidazole pH 6.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→44.47 Å / Num. obs: 29215 / % possible obs: 96.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.59 Å2 / CC1/2: 1 / Net I/σ(I): 8.96
Reflection shellResolution: 2.4→2.54 Å / Num. unique obs: 4021 / CC1/2: 0.54

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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: 2.4→35.85 Å / SU ML: 0.3537 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2416 1456 5 %
Rwork0.1852 27676 -
obs0.1881 29132 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→35.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 150 63 241 5277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815255
X-RAY DIFFRACTIONf_angle_d0.94487070
X-RAY DIFFRACTIONf_chiral_restr0.0466788
X-RAY DIFFRACTIONf_plane_restr0.0076993
X-RAY DIFFRACTIONf_dihedral_angle_d6.4016915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.38581030.32961967X-RAY DIFFRACTION69.79
2.48-2.580.32761500.25892851X-RAY DIFFRACTION99.93
2.58-2.70.32621500.25532859X-RAY DIFFRACTION99.83
2.7-2.840.31191510.24222862X-RAY DIFFRACTION99.5
2.84-3.020.27751500.19232849X-RAY DIFFRACTION99.67
3.02-3.250.28421500.17762847X-RAY DIFFRACTION99.6
3.25-3.580.22431470.16882799X-RAY DIFFRACTION96.91
3.58-4.10.2131500.14962847X-RAY DIFFRACTION99.5
4.1-5.160.2051520.15062892X-RAY DIFFRACTION99.67
5.16-35.850.18341530.18442903X-RAY DIFFRACTION97.76

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