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- PDB-2wxw: Crystal structure of human angiotensinogen -

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Basic information

Entry
Database: PDB / ID: 2wxw
TitleCrystal structure of human angiotensinogen
ComponentsANGIOTENSINOGEN
KeywordsHORMONE / GLYCOPROTEIN / HYPERTENSION / VASOCONSTRICTOR / RENIN / SERPINS / VASOACTIVE / ANGIOTENSIN
Function / homology
Function and homology information


regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / : / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / positive regulation of activation of Janus kinase activity / regulation of renal output by angiotensin ...regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / : / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / positive regulation of activation of Janus kinase activity / regulation of renal output by angiotensin / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renal system process / renin-angiotensin regulation of aldosterone production / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / positive regulation of macrophage derived foam cell differentiation / vasoconstriction / positive regulation of CoA-transferase activity / type 1 angiotensin receptor binding / low-density lipoprotein particle remodeling / positive regulation of extrinsic apoptotic signaling pathway / response to angiotensin / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of gap junction assembly / positive regulation of protein tyrosine kinase activity / regulation of vasoconstriction / regulation of cardiac conduction / blood vessel remodeling / Metabolism of Angiotensinogen to Angiotensins / positive regulation of epithelial to mesenchymal transition / nitric oxide-cGMP-mediated signaling / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / negative regulation of MAP kinase activity / kidney development / positive regulation of cytokine production / angiotensin-activated signaling pathway / regulation of cell growth / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / PPARA activates gene expression / regulation of blood pressure / positive regulation of miRNA transcription / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / G alpha (i) signalling events / G alpha (q) signalling events / regulation of apoptotic process / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood microparticle / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / cytosol
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, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family ...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, conserved site / Serpins signature. / 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)49,8961
Polymers49,8961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.285, 133.285, 123.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ANGIOTENSINOGEN / SERPIN A8


Mass: 49895.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSUMO3-HANGT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01019

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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: 5.7 Å3/Da / Density % sol: 78 % / Description: NONE
Crystal growpH: 8 / Details: 2-2.5N NACL, 0.2M CACL2, 0.1M TRIS-HCL, PH8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→31.5 Å / Num. obs: 17197 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 4.5 / % possible all: 89.9

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Processing

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

Resolution: 3.3→94.07 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.921 / SU B: 105.656 / SU ML: 0.711 / Cross valid method: THROUGHOUT / ESU R: 1.203 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.318 852 5 %RANDOM
Rwork0.309 ---
obs0.31 16076 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.73 Å2
Baniso -1Baniso -2Baniso -3
1-6.96 Å20 Å20 Å2
2--6.96 Å20 Å2
3----13.93 Å2
Refinement stepCycle: LAST / Resolution: 3.3→94.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 0 0 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223458
X-RAY DIFFRACTIONr_bond_other_d0.0010.022255
X-RAY DIFFRACTIONr_angle_refined_deg0.7591.9614710
X-RAY DIFFRACTIONr_angle_other_deg0.76435545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9355436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94524.759145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41515567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0761513
X-RAY DIFFRACTIONr_chiral_restr0.0450.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213828
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02667
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_it0.141.52185
X-RAY DIFFRACTIONr_mcbond_other0.011.5878
X-RAY DIFFRACTIONr_mcangle_it0.25523521
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.15531273
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.2834.51189
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: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.58 51 -
Rwork0.552 1088 -
obs--91.93 %
Refinement TLS params.Method: refined / Origin x: 13.447 Å / Origin y: -45.3082 Å / Origin z: -7.3984 Å
111213212223313233
T0.1991 Å2-0.1678 Å2-0.0325 Å2-0.2084 Å20.009 Å2--0.269 Å2
L5.0427 °2-0.2169 °2-1.7864 °2-3.5244 °2-0.4759 °2--10.4516 °2
S0.197 Å °-0.3476 Å °0.4566 Å °0.142 Å °0.0823 Å °-0.3116 Å °-0.7297 Å °0.0433 Å °-0.2792 Å °

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