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- PDB-1hvg: STRUCTURAL AND ELECTROPHYSIOLOGICAL ANALYSIS OF ANNEXIN V MUTANTS... -

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Basic information

Entry
Database: PDB / ID: 1hvg
TitleSTRUCTURAL AND ELECTROPHYSIOLOGICAL ANALYSIS OF ANNEXIN V MUTANTS. MUTAGENESIS OF HUMAN ANNEXIN V, AN IN VITRO VOLTAGE-GATED CALCIUM CHANNEL, PROVIDES INFORMATION ABOUT THE STRUCTURAL FEATURES OF THE ION PATHWAY, THE VOLTAGE SENSOR AND THE ION SELECTIVITY FILTER
ComponentsANNEXIN VAnnexin A5
KeywordsCALCIUM/PHOSPHOLIPID BINDING / CALCIUM-PHOSPHOLIPID BINDING complex
Function / homology
Function and homology information


phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / phosphatidylserine binding / response to organic substance / phospholipid binding / sarcolemma / blood coagulation / Platelet degranulation ...phospholipase inhibitor activity / endothelial microparticle / negative regulation of coagulation / calcium-dependent phospholipid binding / phosphatidylserine binding / response to organic substance / phospholipid binding / sarcolemma / 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 / Annexin repeat, conserved site / Annexin repeat signature. / Annexin / Annexin / Annexin repeats / Annexin repeat / Annexin superfamily / Annexin repeat profile. ...Annexin A5 / 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 / Resolution: 3 Å
AuthorsBurger, A. / Huber, R.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Structural and electrophysiological analysis of annexin V mutants. Mutagenesis of human annexin V, an in vitro voltage-gated calcium channel, provides information about the structural features ...Title: Structural and electrophysiological analysis of annexin V mutants. Mutagenesis of human annexin V, an in vitro voltage-gated calcium channel, provides information about the structural features of the ion pathway, the voltage sensor and the ion selectivity filter
Authors: Burger, A. / Voges, D. / Demange, P. / Perez, C.R. / Huber, R. / Berendes, R.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal and Molecular Structure of Human Annexin V After Refinement
Authors: Huber, R. / Berendes, R. / Burger, A. / Schneider, M. / Karshikov, A. / Luecke, H. / Romish, J. / Paques, E.
History
DepositionJun 29, 1994Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANNEXIN V


Theoretical massNumber of molelcules
Total (without water)35,8491
Polymers35,8491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.900, 156.900, 36.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein ANNEXIN V / Annexin A5


Mass: 35848.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: 293 / Gene: CDNA / Organ: PLACENTA UNFUSED / Plasmid: PTRC 99A-PP4 GENE: CDNA / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P08758
Compound detailsTHE STRUCTURAL ANALYSIS SHOULD REVEAL WHETHER THE STRUCTURAL REARRANGEMENT IN DOMAIN III AS SEEN IN ...THE STRUCTURAL ANALYSIS SHOULD REVEAL WHETHER THE STRUCTURAL REARRANGEMENT IN DOMAIN III AS SEEN IN THE MUTANT E95S, WHERE A NEW CALCIUM BINDING SITE HAS BEEN FOUND, IS AN EFFECT OF CRYSTAL PACKING. THE STRUCTURE OF THE LOOP IN THE MUTANT E78Q WAS OUT IN THIS H 3 FORM WHEREAS IT WAS IN FOR THIS MUTANT IN ANOTHER CRYSTAL PACKING (PDB ENTRY 1HVE).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13 mMMOPS1drop
29 mg/mlprotein1drop
320 mM1dropCaCl2
42.1 Mammonium sulfate1reservoir
50.1 MTris-chloride1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 5103 / % possible obs: 75 % / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. measured all: 17631 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.11 Å / % possible obs: 44.1 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.199 / Rfactor obs: 0.199 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 0 0 2475
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection all: 4969
Solvent computation
*PLUS
Displacement parameters
*PLUS

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