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- PDB-1w7b: Annexin A2: Does it induce membrane aggregation by a new multimer... -

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Basic information

Entry
Database: PDB / ID: 1w7b
TitleAnnexin A2: Does it induce membrane aggregation by a new multimeric state of the protein.
ComponentsANNEXIN A2
KeywordsCALCIUM-BINDING PROTEIN / ANNEXINS / CALCIUM-BINDING PROTEINS / MEMBRANE-BINDING PROTEINS
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 / Dissolution of Fibrin Clot / S100 protein binding / virion binding / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / positive regulation of receptor recycling / phosphatidylserine binding / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate 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 / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A2 / Annexin / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsRosengarth, A. / Luecke, H.
CitationJournal: Annexins / Year: 2004
Title: Annexin A2: Does It Induce Membrane Aggregation by a New Multimeric State of the Protein
Authors: Rosengarth, A. / Luecke, H.
History
DepositionSep 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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)38,7191
Polymers38,7191
Non-polymers00
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.352, 62.834, 119.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ANNEXIN A2 / ANNEXIN II / LIPOCORTIN II / CALPACTIN I HEAVY CHAIN / CHROMOBINDIN 8 / P36 / PROTEIN I / PLACENTAL ...ANNEXIN II / LIPOCORTIN II / CALPACTIN I HEAVY CHAIN / CHROMOBINDIN 8 / P36 / PROTEIN I / PLACENTAL ANTICOAGULANT PROTEIN IV / PAP-IV


Mass: 38719.098 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSE420/ANXA2 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P07355
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION ALA 65 GLU IN CHAIN A CALCIUM-REGULATED MEMBRANE-BINDING PROTEIN WHOSE AFFINITY ...ENGINEERED MUTATION ALA 65 GLU IN CHAIN A CALCIUM-REGULATED MEMBRANE-BINDING PROTEIN WHOSE AFFINITY FOR CALCIUM IS GREATLY ENHANCED BY ANIONIC PHOSPHOLIPIDS. IT BINDS TWO CALCIUM IONS WITH HIGH AFFINITY.
Sequence detailsOUR SEQUENCE STARTS AT RESIDUE PRO21 BECAUSE NO ELECTRON DENSITY FOR THE FIRST 20 AMINO ACIDS WAS VISIBLE.

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 6.5 / Details: 2.5 M NACL 0.1 M ACETATE PH 4.5 0.2 M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→99 Å / Num. obs: 59682 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 1 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 39
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 1 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 3 / % possible all: 88.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→30.38 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 76710.56 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIUM LIKELYHOOD
Details: NO ELECTRON DENSITY FOR THE FIRST 20 AMINO ACIDS WAS VISIBLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4968 10.1 %RANDOM
Rwork0.216 ---
obs0.216 49336 87 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2515 Å2 / ksol: 0.356357 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.19 Å20 Å20 Å2
2--8.74 Å20 Å2
3----4.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.52→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2562 0 0 351 2913
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 1.52→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.329 490 10.3 %
Rwork0.319 4289 -
obs--68.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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