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- PDB-9ga6: The crystal structure of human Annexin A4 derived from crystals g... -

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Basic information

Entry
Database: PDB / ID: 9ga6
TitleThe crystal structure of human Annexin A4 derived from crystals grown in 40 mM of CaCl2
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: 1.27 Å
AuthorsVitagliano, L. / Barra, G. / Ghilardi, O. / Di Micco, S. / Bifulco, G. / Campiglia, P. / Sala, M. / Scala, M.C. / Ruggiero, A.
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)37,73313
Polymers36,7611
Non-polymers97312
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration coupled with LS (SEC-LS)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-90 kcal/mol
Surface area15580 Å2
Unit cell
Length a, b, c (Å)58.742, 39.906, 73.456
Angle α, β, γ (deg.)90.000, 93.910, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
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: ID30B / Wavelength: 0.991874 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991874 Å / Relative weight: 1
ReflectionResolution: 1.27→58.6 Å / Num. obs: 86437 / % possible obs: 95.8 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.059 / Rrim(I) all: 0.089 / Net I/σ(I): 7.8
Reflection shellResolution: 1.27→1.29 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 4117 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→58.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.825 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1891 4312 4.99 %
Rwork0.1739 82107 -
all0.175 --
obs-86419 95.599 %
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: 11.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å20 Å2-0 Å2
2--0.002 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.27→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 51 285 2835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122592
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162477
X-RAY DIFFRACTIONr_angle_refined_deg1.8961.8353482
X-RAY DIFFRACTIONr_angle_other_deg0.6661.7915706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.84524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38110494
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.85110122
X-RAY DIFFRACTIONr_chiral_restr0.0930.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
X-RAY DIFFRACTIONr_nbd_refined0.2550.2557
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.22152
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21315
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2168
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3130.227
X-RAY DIFFRACTIONr_nbd_other0.3010.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.10.21
X-RAY DIFFRACTIONr_mcbond_it1.2851.0781280
X-RAY DIFFRACTIONr_mcbond_other1.2521.0791280
X-RAY DIFFRACTIONr_mcangle_it1.8681.9381602
X-RAY DIFFRACTIONr_mcangle_other1.8771.941603
X-RAY DIFFRACTIONr_scbond_it2.921.3981312
X-RAY DIFFRACTIONr_scbond_other2.7741.3711289
X-RAY DIFFRACTIONr_scangle_it4.0182.4241876
X-RAY DIFFRACTIONr_scangle_other3.9742.3741841
X-RAY DIFFRACTIONr_lrange_it5.39114.4143086
X-RAY DIFFRACTIONr_lrange_other5.35512.6463018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.3010.3243250.2995859X-RAY DIFFRACTION93.4139
1.301-1.3360.3123190.2945867X-RAY DIFFRACTION95.0376
1.336-1.3750.2692880.2685644X-RAY DIFFRACTION94.3684
1.375-1.4170.2442820.2445696X-RAY DIFFRACTION97.5841
1.417-1.4640.2252330.2165568X-RAY DIFFRACTION98.3054
1.464-1.5150.1862670.1815383X-RAY DIFFRACTION98.1584
1.515-1.5720.2013240.1715131X-RAY DIFFRACTION98.0762
1.572-1.6360.1832890.1644668X-RAY DIFFRACTION93.0717
1.636-1.7090.1612530.1544741X-RAY DIFFRACTION97.5391
1.709-1.7920.1672480.1564546X-RAY DIFFRACTION97.6574
1.792-1.8890.1731800.1534342X-RAY DIFFRACTION97.2892
1.889-2.0040.1781930.1554099X-RAY DIFFRACTION96.9286
2.004-2.1420.1822250.1533793X-RAY DIFFRACTION96.7261
2.142-2.3130.1651650.1443468X-RAY DIFFRACTION93.2974
2.313-2.5340.1611960.143214X-RAY DIFFRACTION95.092
2.534-2.8320.1891440.1542904X-RAY DIFFRACTION93.7558
2.832-3.2690.1861500.172511X-RAY DIFFRACTION92.8148
3.269-4.0010.134960.1572102X-RAY DIFFRACTION90.1189
4.001-5.6450.17910.1681647X-RAY DIFFRACTION91.1379
5.645-58.60.286440.245924X-RAY DIFFRACTION87.4435

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