[English] 日本語
Yorodumi
- PDB-2wy1: Crystal structure of rat angiotensinogen in P321 space group -

+
Open data


ID or keywords:

Loading...

-
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 / brain renin-angiotensin system / positive regulation of L-arginine import across plasma membrane / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / establishment of blood-nerve barrier / positive regulation of protein kinase C activity / smooth muscle cell proliferation ...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 / brain renin-angiotensin system / positive regulation of L-arginine import across plasma membrane / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / establishment of blood-nerve barrier / positive regulation of protein kinase C activity / smooth muscle cell proliferation / regulation of systemic arterial blood pressure by circulatory renin-angiotensin / vasopressin secretion / ovarian follicle rupture / regulation of transmission of nerve impulse / positive regulation of extracellular matrix constituent secretion / response to muscle activity involved in regulation of muscle adaptation / smooth muscle cell differentiation / type 2 angiotensin receptor binding / angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / negative regulation of neurotrophin TRK receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / positive regulation of membrane hyperpolarization / Peptide ligand-binding receptors / maintenance of blood vessel diameter homeostasis by renin-angiotensin / cell growth involved in cardiac muscle cell development / aldosterone secretion / renal system process / regulation of extracellular matrix assembly / peristalsis / positive regulation of norepinephrine secretion / regulation of renal output by angiotensin / renin-angiotensin regulation of aldosterone production / positive regulation of organ growth / positive regulation of multicellular organism growth / positive regulation of extracellular matrix assembly / operant conditioning / artery smooth muscle contraction / hormone metabolic process / positive regulation of blood pressure / vasoconstriction / drinking behavior / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of fatty acid biosynthetic process / positive regulation of cholesterol metabolic process / type 1 angiotensin receptor binding / response to angiotensin / intracellular sodium ion homeostasis / branching involved in ureteric bud morphogenesis / positive regulation of macrophage derived foam cell differentiation / 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 / negative regulation of MAP kinase activity / blood vessel development / positive regulation of cardiac muscle hypertrophy / regulation of calcium ion transport / cellular response to angiotensin / angiotensin-mediated drinking behavior / associative learning / positive regulation of gap junction assembly / sodium channel regulator activity / positive regulation of peptidyl-serine phosphorylation / regulation of cardiac conduction / positive regulation of insulin receptor signaling pathway / response to mechanical stimulus / stress-activated MAPK cascade / ERK1 and ERK2 cascade / positive regulation of epithelial to mesenchymal transition / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of epidermal growth factor receptor signaling pathway / response to cold / extracellular matrix organization / fibroblast proliferation / kidney development / response to salt stress / positive regulation of superoxide anion generation / cell-matrix adhesion / positive regulation of cardiac muscle cell apoptotic process / astrocyte activation / regulation of heart rate / positive regulation of endothelial cell migration / negative regulation of angiogenesis / positive regulation of cytokine production / angiotensin-activated signaling pathway / positive regulation of insulin secretion involved in cellular response to glucose stimulus / growth factor activity / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / positive regulation of neuron projection development / female pregnancy / cellular response to mechanical stimulus / protein import into nucleus / hormone activity / negative regulation of cell growth / vasodilation / positive regulation of miRNA transcription / regulation of blood pressure / positive regulation of fibroblast proliferation / positive regulation of reactive oxygen species metabolic process
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 (eV)
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more