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- PDB-6i3i: Crystal structure of reactive center loop (RCL) cleaved angiotens... -

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Basic information

Entry
Database: PDB / ID: 6i3i
TitleCrystal structure of reactive center loop (RCL) cleaved angiotensinogen
ComponentsAngiotensinogen
KeywordsHORMONE / angiotensinogen / reactive center loop
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 / negative regulation of neurotrophin TRK receptor signaling pathway / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / maintenance of blood vessel diameter homeostasis by renin-angiotensin / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / positive regulation of extracellular matrix assembly ...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 / negative regulation of neurotrophin TRK receptor signaling pathway / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / maintenance of blood vessel diameter homeostasis by renin-angiotensin / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / positive regulation of extracellular matrix assembly / renin-angiotensin regulation of aldosterone production / renal system process / vasoconstriction / positive regulation of branching involved in ureteric bud morphogenesis / type 1 angiotensin receptor binding / positive regulation of cholesterol metabolic process / response to angiotensin / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of cardiac muscle hypertrophy / negative regulation of MAP kinase activity / positive regulation of gap junction assembly / blood vessel remodeling / regulation of cardiac conduction / positive regulation of epithelial to mesenchymal transition / regulation of vasoconstriction / positive regulation of epidermal growth factor receptor signaling pathway / Metabolism of Angiotensinogen to Angiotensins / nitric oxide-cGMP-mediated signaling / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / positive regulation of cytokine production / angiotensin-activated signaling pathway / growth factor activity / regulation of cell growth / kidney development / serine-type endopeptidase inhibitor activity / PPARA activates gene expression / hormone activity / positive regulation of miRNA transcription / : / regulation of blood pressure / positive regulation of fibroblast proliferation / positive regulation of reactive oxygen species metabolic process / positive regulation of inflammatory response / cell-cell signaling / regulation of cell population proliferation / regulation of apoptotic process / blood microparticle / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsYan, Y. / Read, R.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust082961/Z/07/Z United Kingdom
British Heart FoundationPG/12/41/29679 United Kingdom
Wellcome Trust100140 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structural basis for the specificity of renin-mediated angiotensinogen cleavage.
Authors: Yan, Y. / Zhou, A. / Carrell, R.W. / Read, R.J.
History
DepositionNov 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 27, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Angiotensinogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8692
Polymers50,6481
Non-polymers2211
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, It ran as a monomer in size exclusion column.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint2 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.140, 80.140, 117.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Angiotensinogen / Serpin A8


Mass: 50647.656 Da / Num. of mol.: 1 / Mutation: N137Q,N271Q,N295Q,C232S,C308S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGT, SERPINA8 / Plasmid: pCEP4 / Cell (production host): HEK293EBNA / Production host: Homo sapiens (human) / References: UniProt: P01019
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 3.55 Å3/Da / Density % sol: 65.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5M ammonium sulfate, 0.1M Tris pH8.5 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.97→66.14 Å / Num. obs: 15316 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.214 / Rrim(I) all: 0.254 / Net I/σ(I): 6.5
Reflection shellResolution: 2.97→3.05 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.282 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1106 / CC1/2: 0.53 / Rrim(I) all: 1.505 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wxw

2wxw


Resolution: 2.97→66.14 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.186 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R: 1.089 / ESU R Free: 0.343 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23743 726 4.7 %RANDOM
Rwork0.21797 ---
obs0.21889 14563 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.732 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å2-0 Å2
2--0.29 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.97→66.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 14 2 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0143408
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173131
X-RAY DIFFRACTIONr_angle_refined_deg0.7541.6444640
X-RAY DIFFRACTIONr_angle_other_deg0.6691.6337303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6295425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62823.718156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14415562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4941512
X-RAY DIFFRACTIONr_chiral_restr0.0320.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
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_it1.6747.0441709
X-RAY DIFFRACTIONr_mcbond_other1.6747.0431708
X-RAY DIFFRACTIONr_mcangle_it3.05510.5582131
X-RAY DIFFRACTIONr_mcangle_other3.05410.5592132
X-RAY DIFFRACTIONr_scbond_it1.2937.2231699
X-RAY DIFFRACTIONr_scbond_other1.2937.2251700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.39610.7412510
X-RAY DIFFRACTIONr_long_range_B_refined5.23381.6123505
X-RAY DIFFRACTIONr_long_range_B_other5.23381.613506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.97→3.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 52 -
Rwork0.336 1053 -
obs--100 %

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