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- PDB-5m3y: Crystal structure of human glycosylated angiotensinogen -

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Basic information

Entry
Database: PDB / ID: 5m3y
TitleCrystal structure of human glycosylated angiotensinogen
ComponentsAngiotensinogen
KeywordsSerine protease inhibitor / glycosylated / human angiotensiogen
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 / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of renal sodium excretion / 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 / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of renal sodium excretion / 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 / positive regulation of cholesterol metabolic process / type 1 angiotensin receptor binding / 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 epidermal growth factor receptor 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 / regulation of vasoconstriction / positive regulation of epithelial to mesenchymal transition / 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 / kidney development / regulation of cell growth / serine-type endopeptidase inhibitor activity / PPARA activates gene expression / hormone activity / positive regulation of miRNA transcription / regulation of blood pressure / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / positive regulation of inflammatory response / cell-cell signaling / regulation of cell population proliferation / : / G alpha (i) signalling events / regulation of apoptotic process / phospholipase C-activating G protein-coupled receptor signaling pathway / blood microparticle / 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: 2.3 Å
AuthorsYan, Y. / Read, R.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
British Heart FoundationPG/12/41/29679 United Kingdom
Wellcome Trust082961/Z/07/Z 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
DepositionOct 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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 1.3Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensinogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2342
Polymers50,6481
Non-polymers5871
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint5 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.350, 71.350, 125.310
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): HEK293 EBNA / Production host: Homo sapiens (human) / References: UniProt: P01019
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.15 Å3/Da / Density % sol: 60.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 2.0M Ammonium Sulfate, 0.1M Bicine, pH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→46.8 Å / Num. obs: 27827 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.6
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.702

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WXW

2wxw


Resolution: 2.3→46.8 Å / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.8
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 1402 5.05 %Random selection
Rwork0.1699 ---
obs0.1726 27786 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 39 24 3319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023371
X-RAY DIFFRACTIONf_angle_d0.4834593
X-RAY DIFFRACTIONf_dihedral_angle_d12.7952004
X-RAY DIFFRACTIONf_chiral_restr0.04549
X-RAY DIFFRACTIONf_plane_restr0.003578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.38260.28361450.2672614X-RAY DIFFRACTION95
2.3826-2.47790.26541530.24692631X-RAY DIFFRACTION94
2.4779-2.59070.25011350.24032589X-RAY DIFFRACTION95
2.5907-2.72720.23921370.23412684X-RAY DIFFRACTION95
2.7272-2.8980.25981400.22972604X-RAY DIFFRACTION95
2.898-3.12160.21781330.20322649X-RAY DIFFRACTION95
3.1216-3.43550.20651420.18762633X-RAY DIFFRACTION95
3.4355-3.9320.19531380.16412626X-RAY DIFFRACTION95
3.932-4.95150.13361450.12422659X-RAY DIFFRACTION95
4.9515-34.31540.1721300.14742684X-RAY DIFFRACTION95
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)
12.8102-0.2065-0.31742.76060.4713.9540.08370.2024-0.31880.1725-0.08520.3131-0.1992-0.37310.01280.31560.04110.06390.33790.00650.308413.010161.5337-1.5218
23.5253-0.0859-0.49723.33170.1853.27690.22430.4570.10560.0189-0.11220.349-0.566-0.3687-0.06270.34630.06350.05380.34210.01250.277814.824967.5829-5.9576
32.6450.8215-0.50376.8875-4.67993.18420.26050.11671.0121-0.20120.0256-0.7645-1.22870.6258-0.14921.0658-0.17510.35040.5367-0.0850.715325.786581.84191.8029
43.8966-0.6454-2.6073.82191.37593.9079-0.2069-0.1602-0.68620.04590.1065-0.36420.17850.54860.10950.30780.02080.00780.4740.01010.446137.99554.5145-11.5219
54.5586-0.7569-1.95033.29560.62863.5870.15820.17590.0197-0.0488-0.0086-0.0894-0.48590.2676-0.12060.3493-0.03560.0150.368-0.00140.241129.21264.636-8.7306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 86 )
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 197 )
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 242 )
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 339 )
5X-RAY DIFFRACTION5chain 'A' and (resid 340 through 450 )

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