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- PDB-2wy0: Crystal structure of mouse angiotensinogen in the oxidised form w... -

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Basic information

Entry
Database: PDB / ID: 2wy0
TitleCrystal structure of mouse angiotensinogen in the oxidised form with space group P6122
ComponentsANGIOTENSINOGEN
KeywordsHORMONE / GLYCOPROTEIN / HYPERTENSION / VASOCONSTRICTOR / RENIN / SERPINS / VASOACTIVE / ANGIOTENSIN
Function / homology
Function and homology information


renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure / negative regulation of tissue remodeling / uterine smooth muscle contraction / positive regulation of L-lysine import across plasma membrane / positive regulation of L-arginine import across plasma membrane / establishment of blood-nerve barrier / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / aldosterone secretion ...renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure / negative regulation of tissue remodeling / uterine smooth muscle contraction / positive regulation of L-lysine import across plasma membrane / positive regulation of L-arginine import across plasma membrane / establishment of blood-nerve barrier / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / aldosterone secretion / positive regulation of angiotensin-activated signaling pathway / ovarian follicle rupture / regulation of transmission of nerve impulse / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / positive regulation of extracellular matrix constituent secretion / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / positive regulation of membrane hyperpolarization / negative regulation of neurotrophin TRK receptor signaling pathway / maintenance of blood vessel diameter homeostasis by renin-angiotensin / vasopressin secretion / Metabolism of Angiotensinogen to Angiotensins / regulation of extracellular matrix assembly / cell growth involved in cardiac muscle cell development / Peptide ligand-binding receptors / G alpha (q) signalling events / operant conditioning / positive regulation of norepinephrine secretion / peristalsis / regulation of renal output by angiotensin / positive regulation of extracellular matrix assembly / renin-angiotensin regulation of aldosterone production / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / renal system process / renal sodium ion absorption / drinking behavior / smooth muscle cell differentiation / artery smooth muscle contraction / positive regulation of organ growth / G alpha (i) signalling events / positive regulation of blood pressure / vasoconstriction / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of fatty acid biosynthetic process / type 1 angiotensin receptor binding / positive regulation of cholesterol metabolic process / response to angiotensin / positive regulation of multicellular organism growth / intracellular sodium ion homeostasis / positive regulation of macrophage derived foam cell differentiation / positive regulation of vascular associated smooth muscle cell migration / hormone metabolic process / positive regulation of extrinsic apoptotic signaling pathway / branching involved in ureteric bud morphogenesis / positive regulation of cardiac muscle hypertrophy / blood vessel development / regulation of calcium ion transport / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / associative learning / sodium channel regulator activity / regulation of cardiac conduction / positive regulation of insulin receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of cardiac muscle cell apoptotic process / positive regulation of epidermal growth factor receptor signaling pathway / stress-activated MAPK cascade / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of superoxide anion generation / response to salt stress / ERK1 and ERK2 cascade / extracellular matrix organization / positive regulation of endothelial cell migration / astrocyte activation / regulation of heart rate / response to cold / negative regulation of angiogenesis / positive regulation of cytokine production / cell-matrix adhesion / angiotensin-activated signaling pathway / growth factor activity / kidney development / serine-type endopeptidase inhibitor activity / positive regulation of neuron projection development / hormone activity / negative regulation of cell growth / regulation of long-term neuronal synaptic plasticity / positive regulation of miRNA transcription / regulation of blood pressure / vasodilation / positive regulation of fibroblast proliferation / positive regulation of reactive oxygen species metabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein import into nucleus / positive regulation of nitric oxide biosynthetic process / positive regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / regulation of gene expression / regulation of inflammatory response
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Angiotensinogen, serpin domain / Angiotensinogen / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.38 Å
AuthorsZhou, A. / Wei, Z. / Carrell, R.W. / Read, R.J.
CitationJournal: Nature / Year: 2010
Title: A Redox Switch in Angiotensinogen Modulates Angiotensin Release.
Authors: Zhou, A. / Carrell, R.W. / Murphy, M.P. / Wei, Z. / Yan, Y. / Stanley, P.L. / Stein, P.E. / Pipkin, F.B. / Read, R.J.
History
DepositionNov 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ANGIOTENSINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8848
Polymers49,6061
Non-polymers2787
Water1,820101
1
C: ANGIOTENSINOGEN
hetero molecules

C: ANGIOTENSINOGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,76916
Polymers99,2122
Non-polymers55614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area2860 Å2
ΔGint-72 kcal/mol
Surface area37600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.650, 64.650, 461.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein ANGIOTENSINOGEN / SERPIN A8


Mass: 49606.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PSUMO3-MANGT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11859
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 4.25 / Details: 1.6-2 NA2HPO4, PH4.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.38→76.9 Å / Num. obs: 23004 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.9
Reflection shellResolution: 2.38→2.5 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / % possible all: 64.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0099refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.38→76.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 16.249 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1179 5.1 %RANDOM
Rwork0.206 ---
obs0.208 21825 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.42 Å20 Å2
2--0.84 Å20 Å2
3----1.25 Å2
Refinement stepCycle: LAST / Resolution: 2.38→76.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 16 101 3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223389
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9764612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62624.626147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.42215556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5131517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6891.52123
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2923443
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73531266
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7884.51167
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 48 -
Rwork0.32 800 -
obs--48.35 %
Refinement TLS params.Method: refined / Origin x: 13.1431 Å / Origin y: -24.0178 Å / Origin z: -15.0182 Å
111213212223313233
T0.037 Å20.0534 Å20.0396 Å2-0.1894 Å20.0895 Å2--0.0865 Å2
L1.1955 °2-0.1037 °20.2573 °2-1.7825 °2-1.4973 °2--1.8557 °2
S0.0157 Å °0.0853 Å °-0.0748 Å °-0.0637 Å °-0.0072 Å °-0.1513 Å °0.0151 Å °-0.099 Å °-0.0085 Å °

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