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- PDB-2wy1: Crystal structure of rat angiotensinogen in P321 space group -

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Basic information

Entry
Database: PDB / ID: 2wy1
TitleCrystal structure of rat angiotensinogen in P321 space group
ComponentsANGIOTENSINOGEN
KeywordsHORMONE / RENIN / ANGIOTENSIN / HYPERTENSION / GLYCOPROTEIN / VASOCONSTRICTOR / VASOACTIVE
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 / establishment of blood-nerve barrier / positive regulation of L-arginine import across plasma membrane / aldosterone secretion / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system ...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 / establishment of blood-nerve barrier / positive regulation of L-arginine import across plasma membrane / aldosterone secretion / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / brain renin-angiotensin system / ovarian follicle rupture / regulation of transmission of nerve impulse / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / maintenance of blood vessel diameter homeostasis by renin-angiotensin / Metabolism of Angiotensinogen to Angiotensins / negative regulation of neurotrophin TRK receptor signaling pathway / positive regulation of extracellular matrix constituent secretion / Peptide ligand-binding receptors / vasopressin secretion / cell growth involved in cardiac muscle cell development / regulation of extracellular matrix assembly / operant conditioning / vascular associated smooth muscle cell proliferation / regulation of renal output by angiotensin / regulation of norepinephrine secretion / artery smooth muscle contraction / renin-angiotensin regulation of aldosterone production / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / renal system process / drinking behavior / peristalsis / positive regulation of macrophage derived foam cell differentiation / positive regulation of organ growth / positive regulation of extracellular matrix assembly / smooth muscle cell differentiation / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of fatty acid biosynthetic process / positive regulation of blood pressure / intracellular sodium ion homeostasis / positive regulation of multicellular organism growth / vasoconstriction / type 1 angiotensin receptor binding / hormone metabolic process / cellular response to angiotensin / response to angiotensin / positive regulation of vascular associated smooth muscle cell migration / positive regulation of extrinsic apoptotic signaling pathway / G alpha (q) signalling events / G alpha (i) signalling events / positive regulation of epidermal growth factor receptor signaling pathway / organ growth / branching involved in ureteric bud morphogenesis / positive regulation of cardiac muscle cell apoptotic process / blood vessel development / positive regulation of cardiac muscle hypertrophy / negative regulation of vascular associated smooth muscle cell proliferation / associative learning / regulation of calcium ion transport / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of cardiac conduction / positive regulation of epithelial to mesenchymal transition / positive regulation of insulin receptor signaling pathway / stress-activated MAPK cascade / response to mechanical stimulus / response to salt stress / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of protein metabolic process / ERK1 and ERK2 cascade / positive regulation of endothelial cell migration / regulation of heart rate / response to cold / extracellular matrix organization / negative regulation of angiogenesis / cell-matrix adhesion / positive regulation of superoxide anion generation / positive regulation of cytokine production / kidney development / angiotensin-activated signaling pathway / female pregnancy / astrocyte activation / negative regulation of smooth muscle cell proliferation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / negative regulation of cell growth / hormone activity / positive regulation of miRNA transcription / positive regulation of neuron projection development / regulation of blood pressure / cellular response to mechanical stimulus / vasodilation / protein import into nucleus / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / MAPK cascade / positive regulation of peptidyl-serine phosphorylation / response to estradiol / positive regulation of cytosolic calcium ion concentration / 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 speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANGIOTENSINOGEN
B: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)99,1772
Polymers99,1772
Non-polymers00
Water00
1
A: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)49,5881
Polymers49,5881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)49,5881
Polymers49,5881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.103, 133.103, 97.185
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A6 - 402
2112B6 - 402
1212A422 - 500
2212B422 - 500
1314A403 - 421
2314B403 - 421

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Components

#1: Protein ANGIOTENSINOGEN / SERPIN A8


Mass: 49588.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PSUMO3-RANGT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01015
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: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 8.5 / Details: 15-20% PEG4000, 0.2M MGCL2, 0.1M TRIS, PH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1.045
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 3.15→20.5 Å / Num. obs: 17386 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.9
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.1 / % possible all: 97.7

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Processing

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

Resolution: 3.15→115.47 Å / Cor.coef. Fo:Fc: 0.882 / Cor.coef. Fo:Fc free: 0.83 / SU B: 86.2 / SU ML: 0.667 / Cross valid method: THROUGHOUT / ESU R Free: 0.661 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE INITIAL PHASE INFORMATION WAS OBTAINED FROM A GD DERIVATIVE DATASET OF HUMAN ANGIOTENSINOGEN.
RfactorNum. reflection% reflectionSelection details
Rfree0.32728 883 5.1 %RANDOM
Rwork0.27499 ---
obs0.2776 16436 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.41 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å2-0.93 Å20 Å2
2---1.85 Å20 Å2
3---2.78 Å2
Refinement stepCycle: LAST / Resolution: 3.15→115.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 0 0 6444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226613
X-RAY DIFFRACTIONr_bond_other_d0.0030.024425
X-RAY DIFFRACTIONr_angle_refined_deg0.9031.9779002
X-RAY DIFFRACTIONr_angle_other_deg0.808310861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3495829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48124.457276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.267151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7991534
X-RAY DIFFRACTIONr_chiral_restr0.0640.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021271
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_it0.2921.54173
X-RAY DIFFRACTIONr_mcbond_other0.0241.51668
X-RAY DIFFRACTIONr_mcangle_it0.53226755
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3132440
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5824.52245
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2401tight positional0.010.05
2B2401tight positional0.010.05
1A3005medium positional0.040.5
2B3005medium positional0.040.5
1A2401tight thermal0.020.5
2B2401tight thermal0.020.5
1A3005medium thermal0.022
2B3005medium thermal0.022
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 55 -
Rwork0.348 1171 -
obs--93.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.93740.88640.00074.5398-0.22132.2923-0.04150.1549-0.255-0.1130.09930.07780.14910.1624-0.05780.30920.0558-0.06060.1653-0.08020.06822.8487-59.6097-35.9154
21.9199-0.5998-1.27781.5550.94964.3735-0.14990.08380.1016-0.1755-0.08220.0134-0.3867-0.01010.23210.328-0.0686-0.16840.1244-0.11710.340731.2632-14.5995-7.5091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 450
2X-RAY DIFFRACTION2B5 - 450

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