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- PDB-9ga8: The crystal structure of human Annexin A4 from crystals grown at ... -

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Basic information

Entry
Database: PDB / ID: 9ga8
TitleThe crystal structure of human Annexin A4 from crystals grown at 4 mM Calcium
ComponentsAnnexin A4
KeywordsSIGNALING PROTEIN / Calcium/phospholipid-binding protein / complex with calcium
Function / homology
Function and homology information


phospholipase inhibitor activity / zymogen granule membrane / negative regulation of interleukin-8 production / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / negative regulation of tumor necrosis factor-mediated signaling pathway / NF-kappaB binding / transcription regulator inhibitor activity / Notch signaling pathway ...phospholipase inhibitor activity / zymogen granule membrane / negative regulation of interleukin-8 production / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / negative regulation of tumor necrosis factor-mediated signaling pathway / NF-kappaB binding / transcription regulator inhibitor activity / Notch signaling pathway / negative regulation of canonical NF-kappaB signal transduction / epithelial cell differentiation / calcium-dependent protein binding / : / nuclear membrane / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Annexin A4 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRuggiero, A. / Barra, G. / Ghilardi, O. / Scala, M.C. / Sala, M. / Di Micco, S. / Bifulco, G. / Campiglia, P. / Vitagliano, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Computational, crystallographic, and biophysical characterizations provide insights into calcium and phosphate binding by human annexin A4.
Authors: Di Micco, S. / Scala, M.C. / Sala, M. / Barra, G. / Ghilardi, O. / Campiglia, P. / Bifulco, G. / Vitagliano, L. / Ruggiero, A.
History
DepositionJul 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Annexin A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2658
Polymers36,7611
Non-polymers5047
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-69 kcal/mol
Surface area15190 Å2
Unit cell
Length a, b, c (Å)58.613, 39.620, 73.496
Angle α, β, γ (deg.)90.000, 95.141, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Annexin A4 / 35-beta calcimedin / Annexin IV / Annexin-4 / Carbohydrate-binding protein p33/p41 / Chromobindin-4 ...35-beta calcimedin / Annexin IV / Annexin-4 / Carbohydrate-binding protein p33/p41 / Chromobindin-4 / Endonexin I / Lipocortin IV / P32.5 / PP4-X / Placental anticoagulant protein II / PAP-II / Protein II


Mass: 36760.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA4, ANX4 / Production host: Escherichia coli (E. coli) / References: UniProt: P09525
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate (pH 4.6), 0.2 M ammonium sulfate, and 25 % (v/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.5→73.2 Å / Num. obs: 52824 / % possible obs: 96.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.9
Reflection shellResolution: 1.5→1.52 Å / Num. unique obs: 2410 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→58.377 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.715 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2158 2649 5.016 %
Rwork0.2021 50159 -
all0.203 --
obs-52808 96.398 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.672 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.001 Å2-0 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.5→58.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 23 171 2693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122544
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162438
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.8393414
X-RAY DIFFRACTIONr_angle_other_deg0.6821.7945606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.543524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73410487
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.09810122
X-RAY DIFFRACTIONr_chiral_restr0.0950.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023014
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02592
X-RAY DIFFRACTIONr_nbd_refined0.2410.2594
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22199
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21317
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.21390
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.221
X-RAY DIFFRACTIONr_nbd_other0.2390.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0910.26
X-RAY DIFFRACTIONr_mcbond_it2.072.0311267
X-RAY DIFFRACTIONr_mcbond_other2.0172.0331267
X-RAY DIFFRACTIONr_mcangle_it2.9083.6441582
X-RAY DIFFRACTIONr_mcangle_other2.9183.6461583
X-RAY DIFFRACTIONr_scbond_it3.6512.4661277
X-RAY DIFFRACTIONr_scbond_other3.5532.4311260
X-RAY DIFFRACTIONr_scangle_it5.4184.3361832
X-RAY DIFFRACTIONr_scangle_other5.3454.2841809
X-RAY DIFFRACTIONr_lrange_it6.43622.0113051
X-RAY DIFFRACTIONr_lrange_other6.3721.3993014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5340.4631710.4933514X-RAY DIFFRACTION91.1227
1.534-1.5760.4671800.4463623X-RAY DIFFRACTION97.1144
1.576-1.6220.4792040.4213481X-RAY DIFFRACTION97.9532
1.622-1.6720.3751830.3383499X-RAY DIFFRACTION98.3703
1.672-1.7260.2951720.2793372X-RAY DIFFRACTION98.3625
1.726-1.7870.271690.2453219X-RAY DIFFRACTION98.4311
1.787-1.8540.2231460.2043164X-RAY DIFFRACTION98.4533
1.854-1.930.2151600.1913001X-RAY DIFFRACTION98.0155
1.93-2.0160.2281520.1932830X-RAY DIFFRACTION96.8496
2.016-2.1140.2211530.1882699X-RAY DIFFRACTION95.6726
2.114-2.2280.1851510.1942572X-RAY DIFFRACTION95.9817
2.228-2.3630.1871200.1732506X-RAY DIFFRACTION97.6571
2.363-2.5260.1931350.1652329X-RAY DIFFRACTION97.2376
2.526-2.7280.1661150.162143X-RAY DIFFRACTION96.8683
2.728-2.9870.21020.1791996X-RAY DIFFRACTION96.4598
2.987-3.3390.189880.171795X-RAY DIFFRACTION95.4384
3.339-3.8530.192870.1651521X-RAY DIFFRACTION92.7336
3.853-4.7140.158620.161315X-RAY DIFFRACTION92.4782
4.714-6.6450.238750.251018X-RAY DIFFRACTION92.7844
6.645-58.3770.202240.26562X-RAY DIFFRACTION86.9436

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