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- PDB-8h9z: Annexin A5 protein mutant -

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Basic information

Entry
Database: PDB / ID: 8h9z
TitleAnnexin A5 protein mutant
ComponentsAnnexin A5
KeywordsLIPID BINDING PROTEIN / calcium-binding / apoptosis-detection
Function / homology
Function and homology information


phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / sarcolemma / phospholipid binding / blood coagulation / Platelet degranulation ...phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / vesicle membrane / phosphatidylserine binding / sarcolemma / phospholipid binding / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / external side of plasma membrane / focal adhesion / calcium ion binding / negative regulation of apoptotic process / signal transduction / extracellular exosome / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Annexin A5 / 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: 1.42 Å
AuthorsHua, Z.C. / Tang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81630092 China
CitationJournal: To Be Published
Title: structure dissection of the membrane aggregation mechanism induced by Annexin A5 mutation
Authors: Hua, Z.C. / Tang, W.
History
DepositionOct 26, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 2023Provider: 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 A5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3309
Polymers36,0101
Non-polymers3218
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.328, 134.651, 79.807
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Annexin A5 / Anchorin CII / Annexin V / Annexin-5 / Calphobindin I / CPB-I / Endonexin II / Lipocortin V / ...Anchorin CII / Annexin V / Annexin-5 / Calphobindin I / CPB-I / Endonexin II / Lipocortin V / Placental anticoagulant protein 4 / PP4 / Placental anticoagulant protein I / PAP-I / Thromboplastin inhibitor / Vascular anticoagulant-alpha / VAC-alpha


Mass: 36009.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Authors added a CYS in the C-terminal of the sequence for study.
Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA5, ANX5, ENX2, PP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P08758
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium chloride, 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.42→48.78 Å / Num. obs: 69662 / % possible obs: 99.5 % / Redundancy: 6.59 % / Biso Wilson estimate: 16.14 Å2 / CC1/2: 0.7564 / Net I/σ(I): 10.6
Reflection shellResolution: 1.42→1.47 Å / Num. unique obs: 2516 / Rpim(I) all: 0.4999

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AVH

1avh


Resolution: 1.42→39.9 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2652 3346 4.8 %
Rwork0.2293 66303 -
obs0.231 69649 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.15 Å2 / Biso mean: 26.7078 Å2 / Biso min: 9.62 Å2
Refinement stepCycle: final / Resolution: 1.42→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 8 335 2861
Biso mean--85.66 33.52 -
Num. residues----319
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.42-1.440.44631240.43872516264091
1.44-1.460.41331310.432827732904100
1.46-1.490.4161380.407927902928100
1.49-1.510.43161370.407427392876100
1.51-1.540.47941260.391527452871100
1.54-1.570.42751460.38972718286499
1.57-1.60.40821220.36992707282998
1.6-1.630.37221340.354427592893100
1.63-1.660.36891440.342727562900100
1.66-1.70.34521390.329127622901100
1.7-1.740.37881330.300227922925100
1.74-1.790.29051230.283927772900100
1.79-1.840.29871520.270527442896100
1.84-1.90.30821420.25922693283597
1.9-1.970.3151450.242427722917100
1.97-2.050.2641400.229327982938100
2.05-2.140.24531480.210927662914100
2.14-2.260.2161450.199527832928100
2.26-2.40.2461510.19422729288098
2.4-2.580.24341480.199928022950100
2.58-2.840.24421380.191528072945100
2.84-3.260.24931460.194628242970100
3.26-4.10.19111400.17072832297299
4.1-39.90.22031540.18552919307399

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