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- PDB-7eq7: Co-Crystal Structure Analysis of Annexin A2 and 5alpha-EAL -

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Basic information

Entry
Database: PDB / ID: 7eq7
TitleCo-Crystal Structure Analysis of Annexin A2 and 5alpha-EAL
ComponentsAnnexin A2
KeywordsMETAL BINDING PROTEIN / CALCIUM-BINDING PROTEIN
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.111 Å
AuthorsLiu, X. / Yang, G.
CitationJournal: To be published
Title: Co-Crystal Structure Analysis of Annexin A2 and 5alpha-EAL
Authors: Liu, X. / Yang, G.
History
DepositionApr 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Annexin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7413
Polymers38,6611
Non-polymers802
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-11 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.223, 58.534, 63.122
Angle α, β, γ (deg.)90.000, 102.860, 90.000
Int Tables number4
Space group name H-MP1211

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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: 38661.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANXA2, ANX2, ANX2L4, CAL1H, LPC2D / Plasmid: pET28b-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: P07355
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.29 Å3/Da / Density % sol: 46.36 % / Mosaicity: 0.12 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 7 / Details: 100 mM Tris, 20% PEG3350, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.11→61.54 Å / Num. obs: 16783 / % possible obs: 83 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.014 / Rrim(I) all: 0.034 / Net I/σ(I): 27.1 / Num. measured all: 96130
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.11-2.233.30.326534815970.9250.2050.3892.755.6
6.68-61.5460.0240026700.9990.0090.02266.998.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5 / Resolution: 2.111→24.257 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 805 4.84 %
Rwork0.1988 15823 -
obs0.2012 16628 82.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.73 Å2 / Biso mean: 51.0913 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.111→24.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 2 167 2720
Biso mean--30 52.68 -
Num. residues----318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.111-2.24320.3428880.2707173055
2.2432-2.41620.28951170.2482237781
2.4162-2.65910.2951480.2583292799
2.6591-3.04330.31291500.24052785100
3.0433-3.83170.29431560.1984299293
3.8317-24.2570.18471460.1643301299

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