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

ID or keywords:

Entry

Database: PDB / ID: 2wxx

Title

Crystal structure of mouse angiotensinogen in the oxidised form

Components

ANGIOTENSINOGEN

Keywords

HORMONE / 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 / 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 / : / positive regulation of extracellular matrix constituent secretion / vasopressin secretion / Peptide ligand-binding receptors / cell growth involved in cardiac muscle cell development / Metabolism of Angiotensinogen to Angiotensins / operant conditioning / G alpha (q) signalling events / vascular associated smooth muscle cell proliferation / regulation of renal output by angiotensin / regulation of norepinephrine secretion / artery smooth muscle contraction / G alpha (i) signalling events / renin-angiotensin regulation of aldosterone production / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / drinking behavior / peristalsis / positive regulation of organ growth / smooth muscle cell differentiation / positive regulation of fatty acid biosynthetic process / positive regulation of blood pressure / positive regulation of multicellular organism growth / vasoconstriction / intracellular sodium ion homeostasis / hormone metabolic process / type 1 angiotensin receptor binding / positive regulation of vascular associated smooth muscle cell migration / organ growth / branching involved in ureteric bud morphogenesis / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / blood vessel development / negative regulation of vascular associated smooth muscle cell proliferation / associative learning / regulation of calcium ion transport / angiotensin-mediated drinking behavior / positive regulation of epithelial to mesenchymal transition / positive regulation of insulin receptor signaling pathway / stress-activated MAPK cascade / positive regulation of vascular associated smooth muscle cell proliferation / response to salt stress / ERK1 and ERK2 cascade / regulation of heart rate / response to cold / negative regulation of angiogenesis / extracellular matrix organization / cell-matrix adhesion / positive regulation of superoxide anion generation / kidney development / positive regulation of cytokine production / astrocyte activation / negative regulation of smooth muscle cell proliferation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / hormone activity / negative regulation of cell growth / regulation of blood pressure / positive regulation of neuron projection development / vasodilation / protein import into nucleus / MAPK cascade / positive regulation of nitric oxide biosynthetic process / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation / regulation of gene expression / regulation of apoptotic process / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / negative regulation of neuron apoptotic process / cell population proliferation / positive regulation of MAPK cascade / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space
Similarity search - Function

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.95 Å

Authors

Zhou, A. / Wei, Z. / Carrell, R.W. / Read, R.J.

Citation

Journal: 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

Deposition	Nov 11, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 20, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2wxx.cif.gz	645.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2wxx.ent.gz	559.1 KB	Display	PDB format
PDBx/mmJSON format	2wxx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2wxx_validation.pdf.gz	460 KB	Display	wwPDB validaton report
Full document	2wxx_full_validation.pdf.gz	489.7 KB	Display
Data in XML	2wxx_validation.xml.gz	57.1 KB	Display
Data in CIF	2wxx_validation.cif.gz	77.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wx/2wxx ftp://data.pdbj.org/pub/pdb/validation_reports/wx/2wxx	HTTPS FTP

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Related structure data

Related structure data	2wxwC 2wxyC 2wxzC 2wy0C 2wy1C 2x0bC C: citing same article (ref.)
Similar structure data	6bzq-3 2zc5-2 6c1w-2 6iwe-d 5huq-2 3szz-d 1nkq-1 6h40-1 6foq-4 6c1w-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#53 - May 2004 Serpins similarity (8) #217 - Jan 2018 Opioid Receptors similarity (2) #58 - Oct 2004 G Proteins similarity (2)

Deposited unit

A: ANGIOTENSINOGEN

B: ANGIOTENSINOGEN

C: ANGIOTENSINOGEN

D: ANGIOTENSINOGEN

198 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ANGIOTENSINOGEN

defined by software
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ANGIOTENSINOGEN

defined by software
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: ANGIOTENSINOGEN

defined by software
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: ANGIOTENSINOGEN

defined by software
49.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	D
3	1	C
4	1	B
1	2	B
2	2	C
1	3	A
2	3	B
3	3	C
4	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	8 - 18
2	1	1	1	D	8 - 18
3	1	1	1	C	8 - 18
4	1	1	1	B	8 - 18
1	1	2	1	B	1 - 8
2	1	2	1	C	1 - 8
1	1	3	1	A	28 - 115
2	1	3	1	B	28 - 115
3	1	3	1	C	28 - 115
4	1	3	1	D	28 - 115
1	2	3	2	A	131 - 139
2	2	3	2	B	131 - 139
3	2	3	2	C	131 - 139
4	2	3	2	D	131 - 139
1	3	3	1	A	140 - 156
2	3	3	1	B	140 - 156
3	3	3	1	C	140 - 156
4	3	3	1	D	140 - 156
1	4	3	2	A	157 - 167
2	4	3	2	B	157 - 167
3	4	3	2	C	157 - 167
4	4	3	2	D	157 - 167
1	5	3	1	A	168 - 186
2	5	3	1	B	168 - 186
3	5	3	1	C	168 - 186
4	5	3	1	D	168 - 186
1	6	3	4	A	448 - 451
2	6	3	4	B	448 - 451
3	6	3	4	C	448 - 451
4	6	3	4	D	448 - 451
1	7	3	1	A	280 - 311
2	7	3	1	B	280 - 311
3	7	3	1	C	280 - 311
4	7	3	1	D	280 - 311
1	8	3	2	A	312 - 319
2	8	3	2	B	312 - 319
3	8	3	2	C	312 - 319
4	8	3	2	D	312 - 319
1	9	3	1	A	320 - 328
2	9	3	1	B	320 - 328
3	9	3	1	C	320 - 328
4	9	3	1	D	320 - 328
1	10	3	2	A	329 - 340
2	10	3	2	B	329 - 340
3	10	3	2	C	329 - 340
4	10	3	2	D	329 - 340
1	11	3	2	A	344 - 400
2	11	3	2	B	344 - 400
3	11	3	2	C	344 - 400
4	11	3	2	D	344 - 400
1	12	3	1	A	422 - 447
2	12	3	1	B	422 - 447
3	12	3	1	C	422 - 447
4	12	3	1	D	422 - 447
1	13	3	1	A	188 - 260
2	13	3	1	B	188 - 260
3	13	3	1	C	188 - 260
4	13	3	1	D	188 - 260
1	14	3	6	A	401 - 421
2	14	3	6	B	401 - 421
3	14	3	6	C	401 - 421
4	14	3	6	D	401 - 421
1	15	3	4	A	122 - 130
2	15	3	4	B	122 - 130
3	15	3	4	C	122 - 130
4	15	3	4	D	122 - 130
1	16	3	1	A	116 - 121
2	16	3	1	B	116 - 121
3	16	3	1	C	116 - 121
4	16	3	1	D	116 - 121

NCS ensembles :

ID
1
2
3

#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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 51 % / Description: NONE
Crystal grow	pH: 8 / Details: 18-25% PEG4000, 0.2NH4F, 0.1M TRIS-HCL, PH8

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Data collection

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

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0099	refinement
MOSFLM		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 2.95→213.2 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c 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.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.271	1850	5.1 %	RANDOM
R_work	0.223	-	-	-
obs	0.225	34681	84.5 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 31.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.44 Å²	0 Å²	0 Å²
2-	-	2.35 Å²	0 Å²
3-	-	-	-3.79 Å²

Refinement step

Cycle: LAST / Resolution: 2.95→213.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12915	0	0	0	12915

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	13240
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	8764
X-RAY DIFFRACTION	r_angle_refined_deg	0.977	1.974	18050
X-RAY DIFFRACTION	r_angle_other_deg	0.805	3	21533
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.496	5	1672
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.674	24.638	567
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.712	15	2156
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.87	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.067	0.2	2127
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	14626
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2532
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.302	1.5	8375
X-RAY DIFFRACTION	r_mcbond_other	0.033	1.5	3349
X-RAY DIFFRACTION	r_mcangle_it	0.552	2	13554
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.392	3	4865
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.7	4.5	4487
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	114	tight positional	0.05	0.05
1	4	B	114	tight positional	0.05	0.05
1	3	C	114	tight positional	0.05	0.05
1	2	D	114	tight positional	0.14	0.05
2	1	B	128	tight positional	0.1	0.05
2	2	C	128	tight positional	0.1	0.05
3	1	A	3973	tight positional	0.3	0.05
3	2	B	3973	tight positional	0.38	0.05
3	3	C	3973	tight positional	0.31	0.05
3	4	D	3973	tight positional	0.31	0.05
3	1	A	758	medium positional	0.39	0.5
3	2	B	758	medium positional	0.46	0.5
3	3	C	758	medium positional	0.41	0.5
3	4	D	758	medium positional	0.35	0.5
3	1	A	76	loose positional	0.37	5
3	2	B	76	loose positional	0.65	5
3	3	C	76	loose positional	0.41	5
3	4	D	76	loose positional	0.46	5
1	1	A	114	tight thermal	0.02	0.5
1	4	B	114	tight thermal	0.02	0.5
1	3	C	114	tight thermal	0.02	0.5
1	2	D	114	tight thermal	0.03	0.5
2	1	B	128	tight thermal	0.02	0.5
2	2	C	128	tight thermal	0.02	0.5
3	1	A	3973	tight thermal	0.16	0.5
3	2	B	3973	tight thermal	0.18	0.5
3	3	C	3973	tight thermal	0.13	0.5
3	4	D	3973	tight thermal	0.13	0.5
3	1	A	758	medium thermal	0.17	2
3	2	B	758	medium thermal	0.15	2
3	3	C	758	medium thermal	0.12	2
3	4	D	758	medium thermal	0.12	2
3	1	A	76	loose thermal	0.3	10
3	2	B	76	loose thermal	0.17	10
3	3	C	76	loose thermal	0.47	10
3	4	D	76	loose thermal	0.36	10

LS refinement shell

Resolution: 2.95→3.03 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.357	99	-
R_work	0.316	1853	-
obs	-	-	61.66 %

Refinement TLS params.

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

ID	L11 (°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)
1	2.3033	-0.7259	0.9687	1.4605	-1.2489	4.8886	-0.022	0.1118	-0.0602	-0.0362	0.0955	-0.1653	0.4286	0.6298	-0.0735	0.1141	-0.0646	-0.0507	0.4597	-0.1087	0.3079	-35.8442	6.1469	-134.0841
2	3.0705	0.0721	0.2892	2.3057	0.8171	4.7234	0.0382	0.5482	0.1184	-0.0926	-0.0695	0.3343	-0.0708	-0.0627	0.0312	0.032	0.0887	-0.0269	0.4339	0.1026	0.2318	-11.0999	3.8542	-78.102
3	2.0751	0.9845	-1.279	2.987	-1.9795	4.9987	0.0887	-0.0263	-0.2784	0.4169	-0.1929	-0.0675	0.0047	-0.0635	0.1042	0.468	0.0422	-0.114	0.3922	0.0025	0.3062	-4.4336	-9.7759	-23.7391
4	1.6053	-0.7658	1.61	2.8044	-0.4048	10.0376	-0.0805	-0.1493	0.2879	-0.5095	-0.1004	-0.1009	-2.0979	-0.4058	0.1809	1.2219	-0.0303	0.1228	0.4016	0.0386	0.4428	-2.4112	-41.328	28.1467

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 19
2	X-RAY DIFFRACTION	1	A	31 - 403
3	X-RAY DIFFRACTION	1	A	417 - 450
4	X-RAY DIFFRACTION	2	B	1 - 18
5	X-RAY DIFFRACTION	2	B	31 - 403
6	X-RAY DIFFRACTION	2	B	417 - 450
7	X-RAY DIFFRACTION	3	C	8 - 19
8	X-RAY DIFFRACTION	3	C	31 - 403
9	X-RAY DIFFRACTION	3	C	418 - 450
10	X-RAY DIFFRACTION	4	D	8 - 19
11	X-RAY DIFFRACTION	4	D	31 - 403
12	X-RAY DIFFRACTION	4	D	417 - 450

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