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- PDB-9ga7: The crystal structure of human Annexin A4 derived from crystal gr... -

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Basic information

Entry
Database: PDB / ID: 9ga7
TitleThe crystal structure of human Annexin A4 derived from crystal grown at 4 mM CaCl2 and retro-soaking
ComponentsAnnexin A4
KeywordsSIGNALING PROTEIN / Calcium/phospholipid-binding protein / complex with calcium (from retro-soaking)
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: 1.446 Å
AuthorsVitagliano, L. / Barra, G. / Ghilardi, O. / Di Micco, S. / Scala, M.C. / Sala, M. / Campiglia, P. / Bifulco, G. / 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

Downloads & links

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Assembly

Deposited unit
A: Annexin A4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1856
Polymers36,7611
Non-polymers4245
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-43 kcal/mol
Surface area15250 Å2
Unit cell
Length a, b, c (Å)58.384, 39.926, 65.904
Angle α, β, γ (deg.)90.000, 99.094, 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.: 1 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 293 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: ID30B / Wavelength: 0.99 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.4→65.1 Å / Num. obs: 51347 / % possible obs: 95.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 8.9
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.495 / Num. unique obs: 2372

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.446→65.076 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.602 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.074 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2086 2538 4.944 %
Rwork0.1863 48798 -
all0.187 --
obs-51336 95.077 %
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: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å20.001 Å2
2---0 Å2-0 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.446→65.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 21 171 2671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122524
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162427
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.8413387
X-RAY DIFFRACTIONr_angle_other_deg0.6131.7935579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.035524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80710485
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.59910120
X-RAY DIFFRACTIONr_chiral_restr0.0840.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_nbd_refined0.250.2543
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22169
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21280
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.21345
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.2113
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0130.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1440.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.230.218
X-RAY DIFFRACTIONr_nbd_other0.1760.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1980.211
X-RAY DIFFRACTIONr_mcbond_it2.0251.8521255
X-RAY DIFFRACTIONr_mcbond_other2.0051.851254
X-RAY DIFFRACTIONr_mcangle_it3.253.3271567
X-RAY DIFFRACTIONr_mcangle_other3.2513.3271568
X-RAY DIFFRACTIONr_scbond_it3.3982.3051269
X-RAY DIFFRACTIONr_scbond_other3.3632.2691254
X-RAY DIFFRACTIONr_scangle_it5.2614.0481820
X-RAY DIFFRACTIONr_scangle_other5.2193.981797
X-RAY DIFFRACTIONr_lrange_it7.79421.8372934
X-RAY DIFFRACTIONr_lrange_other7.73421.3752911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.446-1.4840.3631870.33134790.33339890.90.91591.90270.297
1.484-1.5240.2981900.29635900.29638560.9330.93498.0290.254
1.524-1.5680.311810.27834770.2837590.9340.94497.31310.238
1.568-1.6170.2961840.25133500.25336340.950.95697.24820.21
1.617-1.670.2361720.2432880.2435710.9620.9696.89160.194
1.67-1.7280.2651840.21731200.21934090.9560.96996.91990.183
1.728-1.7930.2551460.20130610.20433030.9630.97397.09360.171
1.793-1.8660.2081310.1929300.19131720.9690.97796.50060.167
1.866-1.9490.2091520.18328130.18430600.9740.9896.89540.165
1.949-2.0440.221500.16726520.1729190.970.98495.99180.153
2.044-2.1550.1881300.16825730.16928050.9790.98596.36360.161
2.155-2.2850.1751390.16123870.16226390.9810.98695.71810.156
2.285-2.4430.171060.15622410.15724760.9830.98694.790.157
2.443-2.6390.191080.15620690.15823340.9770.98693.27330.162
2.639-2.890.194840.17418840.17521260.9780.98192.56820.186
2.89-3.230.214900.17616960.17819460.9760.98191.7780.193
3.23-3.7280.193700.16914800.1717200.9780.98390.11630.192
3.728-4.5630.15700.15112200.15114550.9880.98788.65980.181
4.563-6.4370.221420.2059550.20511610.9830.98585.87420.251
6.437-65.0760.244220.225330.2216600.970.9784.09090.294

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