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- PDB-7dto: Human Annexin A2 with C132-C261 intramolecular disulfide bond -

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Basic information

Entry
Database: PDB / ID: 7dto
TitleHuman Annexin A2 with C132-C261 intramolecular disulfide bond
ComponentsAnnexin A2
KeywordsCELL INVASION / disulfide bond / cell migration
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 / phosphatidylserine binding / positive regulation of receptor recycling / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / fibrinolysis / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoskeletal protein binding / lipid droplet / cell-matrix adhesion / response to activity / adherens junction / lung development / sarcolemma / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / calcium channel activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHe, L.
CitationJournal: To Be Published
Title: Human Annexin A2 with C132-C261 intramolecular disulfide bond
Authors: He, L.
History
DepositionJan 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Annexin A2


Theoretical massNumber of molelcules
Total (without water)35,4531
Polymers35,4531
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14930 Å2
Unit cell
Length a, b, c (Å)55.050, 49.292, 57.355
Angle α, β, γ (deg.)90.000, 105.360, 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: 35453.453 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
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07355

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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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 6.5 / Details: 13% PEG 550 MME, 0.1 M Bis-Tris pH 6.5, 50 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→55.31 Å / Num. obs: 29312 / % possible obs: 98.7 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.21868 / Net I/σ(I): 4.215
Reflection shellResolution: 2.8→2.873 Å / Rmerge(I) obs: 0.298 / Num. unique obs: 521

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HYU

2hyu


Resolution: 2.8→55.31 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.903 / SU B: 0.014 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.371 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 340 4.6 %RANDOM
Rwork0.2185 ---
obs0.2187 7028 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.49 Å2 / Biso mean: 41.882 Å2 / Biso min: 16.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-0 Å2-2.07 Å2
2---0.95 Å2-0 Å2
3---3.37 Å2
Refinement stepCycle: final / Resolution: 2.8→55.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 0 0 2478
Num. residues----308
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 20 -
Rwork0.298 521 -
all-541 -
obs--99.27 %

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