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- PDB-2wxx: Crystal structure of mouse angiotensinogen in the oxidised form -

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Basic information

Entry
Database: PDB / ID: 2wxx
TitleCrystal structure of mouse angiotensinogen in the oxidised form
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 / positive regulation of norepinephrine secretion / regulation of renal output by angiotensin / operant conditioning / 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 / peristalsis / drinking behavior / smooth muscle cell differentiation / artery smooth muscle contraction / positive regulation of organ growth / positive regulation of blood pressure / G alpha (i) signalling events / 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 / intracellular sodium ion homeostasis / positive regulation of multicellular organism growth / 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 / angiotensin-mediated drinking behavior / regulation of calcium ion transport / 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 / stress-activated MAPK cascade / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of superoxide anion generation / ERK1 and ERK2 cascade / response to salt stress / extracellular matrix organization / astrocyte activation / positive regulation of endothelial cell migration / regulation of heart rate / response to cold / negative regulation of angiogenesis / cell-matrix adhesion / angiotensin-activated signaling pathway / positive regulation of cytokine production / 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 / protein import into nucleus / positive regulation of nitric oxide biosynthetic process / positive regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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: 2.95 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 / 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
C: ANGIOTENSINOGEN
D: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)198,4254
Polymers198,4254
Non-polymers00
Water00
1
A: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)49,6061
Polymers49,6061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)49,6061
Polymers49,6061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)49,6061
Polymers49,6061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ANGIOTENSINOGEN


Theoretical massNumber of molelcules
Total (without water)49,6061
Polymers49,6061
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.367, 99.416, 425.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31C
41B
12B
22C
13A
23B
33C
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A8 - 18
2111D8 - 18
3111C8 - 18
4111B8 - 18
1121B1 - 8
2121C1 - 8
1131A28 - 115
2131B28 - 115
3131C28 - 115
4131D28 - 115
1232A131 - 139
2232B131 - 139
3232C131 - 139
4232D131 - 139
1331A140 - 156
2331B140 - 156
3331C140 - 156
4331D140 - 156
1432A157 - 167
2432B157 - 167
3432C157 - 167
4432D157 - 167
1531A168 - 186
2531B168 - 186
3531C168 - 186
4531D168 - 186
1634A448 - 451
2634B448 - 451
3634C448 - 451
4634D448 - 451
1731A280 - 311
2731B280 - 311
3731C280 - 311
4731D280 - 311
1832A312 - 319
2832B312 - 319
3832C312 - 319
4832D312 - 319
1931A320 - 328
2931B320 - 328
3931C320 - 328
4931D320 - 328
11032A329 - 340
21032B329 - 340
31032C329 - 340
41032D329 - 340
11132A344 - 400
21132B344 - 400
31132C344 - 400
41132D344 - 400
11231A422 - 447
21231B422 - 447
31231C422 - 447
41231D422 - 447
11331A188 - 260
21331B188 - 260
31331C188 - 260
41331D188 - 260
11436A401 - 421
21436B401 - 421
31436C401 - 421
41436D401 - 421
11534A122 - 130
21534B122 - 130
31534C122 - 130
41534D122 - 130
11631A116 - 121
21631B116 - 121
31631C116 - 121
41631D116 - 121

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
ANGIOTENSINOGEN / SERPIN A8


Mass: 49606.137 Da / Num. of mol.: 4
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
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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 8 / Details: 18-25% PEG4000, 0.2NH4F, 0.1M TRIS-HCL, PH8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.053
DetectorType: ADSC CCD / Detector: CCD / Date: May 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.053 Å / Relative weight: 1
ReflectionResolution: 2.95→213.2 Å / Num. obs: 36592 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 9.2
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.5 / % possible all: 66

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Processing

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

Resolution: 2.95→213.2 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.864 / SU B: 48.663 / SU ML: 0.411 / Cross valid method: THROUGHOUT / ESU R Free: 0.525 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1850 5.1 %RANDOM
Rwork0.223 ---
obs0.225 34681 84.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2--2.35 Å20 Å2
3----3.79 Å2
Refinement stepCycle: LAST / Resolution: 2.95→213.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12915 0 0 0 12915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02213240
X-RAY DIFFRACTIONr_bond_other_d0.0020.028764
X-RAY DIFFRACTIONr_angle_refined_deg0.9771.97418050
X-RAY DIFFRACTIONr_angle_other_deg0.805321533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49651672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67424.638567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.712152156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.871566
X-RAY DIFFRACTIONr_chiral_restr0.0670.22127
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02114626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022532
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_it0.3021.58375
X-RAY DIFFRACTIONr_mcbond_other0.0331.53349
X-RAY DIFFRACTIONr_mcangle_it0.552213554
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.39234865
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.74.54487
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A114tight positional0.050.05
14B114tight positional0.050.05
13C114tight positional0.050.05
12D114tight positional0.140.05
21B128tight positional0.10.05
22C128tight positional0.10.05
31A3973tight positional0.30.05
32B3973tight positional0.380.05
33C3973tight positional0.310.05
34D3973tight positional0.310.05
31A758medium positional0.390.5
32B758medium positional0.460.5
33C758medium positional0.410.5
34D758medium positional0.350.5
31A76loose positional0.375
32B76loose positional0.655
33C76loose positional0.415
34D76loose positional0.465
11A114tight thermal0.020.5
14B114tight thermal0.020.5
13C114tight thermal0.020.5
12D114tight thermal0.030.5
21B128tight thermal0.020.5
22C128tight thermal0.020.5
31A3973tight thermal0.160.5
32B3973tight thermal0.180.5
33C3973tight thermal0.130.5
34D3973tight thermal0.130.5
31A758medium thermal0.172
32B758medium thermal0.152
33C758medium thermal0.122
34D758medium thermal0.122
31A76loose thermal0.310
32B76loose thermal0.1710
33C76loose thermal0.4710
34D76loose thermal0.3610
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 99 -
Rwork0.316 1853 -
obs--61.66 %
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)
12.3033-0.72590.96871.4605-1.24894.8886-0.0220.1118-0.0602-0.03620.0955-0.16530.42860.6298-0.07350.1141-0.0646-0.05070.4597-0.10870.3079-35.84426.1469-134.0841
23.07050.07210.28922.30570.81714.72340.03820.54820.1184-0.0926-0.06950.3343-0.0708-0.06270.03120.0320.0887-0.02690.43390.10260.2318-11.09993.8542-78.102
32.07510.9845-1.2792.987-1.97954.99870.0887-0.0263-0.27840.4169-0.1929-0.06750.0047-0.06350.10420.4680.0422-0.1140.39220.00250.3062-4.4336-9.7759-23.7391
41.6053-0.76581.612.8044-0.404810.0376-0.0805-0.14930.2879-0.5095-0.1004-0.1009-2.0979-0.40580.18091.2219-0.03030.12280.40160.03860.4428-2.4112-41.32828.1467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 19
2X-RAY DIFFRACTION1A31 - 403
3X-RAY DIFFRACTION1A417 - 450
4X-RAY DIFFRACTION2B1 - 18
5X-RAY DIFFRACTION2B31 - 403
6X-RAY DIFFRACTION2B417 - 450
7X-RAY DIFFRACTION3C8 - 19
8X-RAY DIFFRACTION3C31 - 403
9X-RAY DIFFRACTION3C418 - 450
10X-RAY DIFFRACTION4D8 - 19
11X-RAY DIFFRACTION4D31 - 403
12X-RAY DIFFRACTION4D417 - 450

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