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- PDB-6i3f: Crystal structure of the complex of human angiotensinogen and ren... -

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Basic information

Entry
Database: PDB / ID: 6i3f
TitleCrystal structure of the complex of human angiotensinogen and renin at 2.55 Angstrom
Components
  • Angiotensinogen
  • Renin
KeywordsHYDROLASE / angiotensinogen / renin / glycosylation / complex
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 / renin / mesonephros development ...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 / renin / mesonephros development / juxtaglomerular apparatus development / response to cGMP / regulation of renal output by angiotensin / positive regulation of extracellular matrix assembly / renin-angiotensin regulation of aldosterone production / renal system process / drinking behavior / 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 / response to immobilization stress / regulation of MAPK cascade / positive regulation of gap junction assembly / blood vessel remodeling / response to cAMP / amyloid-beta metabolic process / regulation of cardiac conduction / regulation of vasoconstriction / positive regulation of epithelial to mesenchymal transition / Metabolism of Angiotensinogen to Angiotensins / nitric oxide-cGMP-mediated signaling / cell maturation / angiotensin maturation / hormone-mediated signaling pathway / insulin-like growth factor receptor binding / 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 / male gonad development / cellular response to xenobiotic stimulus / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / apical part of cell / positive regulation of inflammatory response / cell-cell signaling / peptidase activity / regulation of cell population proliferation / : / regulation of apoptotic process / response to lipopolysaccharide / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / blood microparticle / G alpha (q) signalling events / aspartic-type endopeptidase activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / signaling receptor binding / positive regulation of DNA-templated transcription / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Angiotensinogen, serpin domain / Angiotensinogen / Renin-like domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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 / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Renin / Angiotensinogen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsYan, Y. / Read, R.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust082961/Z/07/Z United Kingdom
British Heart FoundationPG/12/41/29679 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 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _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 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 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
B: Renin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,44615
Polymers87,8712
Non-polymers2,57513
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The angiotensinogen and renin complex is a 1:1 complex as shown my gel filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-119 kcal/mol
Surface area31020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.119, 124.119, 260.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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Protein , 2 types, 2 molecules AB

#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: Protein Renin / Angiotensinogenase


Mass: 37223.000 Da / Num. of mol.: 1 / Mutation: D226A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REN / Plasmid: pCEP4 / Cell (production host): HEK293EBNA / Production host: Homo sapiens (human) / References: UniProt: P00797, renin

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 951.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 181 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 1.76M Ammonium sulfate 0.1M Tris, pH7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.55→62.06 Å / Num. obs: 39602 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.209 / Rrim(I) all: 0.225 / Net I/σ(I): 10.2
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 12.9 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4393 / CC1/2: 0.674 / Rrim(I) all: 1.35 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WXW and 2BKS

2wxw

2bks


Resolution: 2.55→62.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.995 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.245 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23392 1987 5 %RANDOM
Rwork0.20621 ---
obs0.20761 37583 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.386 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å2-0 Å2
2---0.66 Å20 Å2
3---2.15 Å2
Refinement stepCycle: 1 / Resolution: 2.55→62.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5808 0 158 170 6136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136102
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175501
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.6588327
X-RAY DIFFRACTIONr_angle_other_deg1.0691.58712768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4835753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16823.383266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70815934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0921519
X-RAY DIFFRACTIONr_chiral_restr0.0360.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021232
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_it1.2644.3133027
X-RAY DIFFRACTIONr_mcbond_other1.2634.3133026
X-RAY DIFFRACTIONr_mcangle_it2.3216.463775
X-RAY DIFFRACTIONr_mcangle_other2.3216.4613776
X-RAY DIFFRACTIONr_scbond_it1.034.63075
X-RAY DIFFRACTIONr_scbond_other1.0294.6013076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9026.8574553
X-RAY DIFFRACTIONr_long_range_B_refined4.14649.6756144
X-RAY DIFFRACTIONr_long_range_B_other4.14549.6826145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 155 -
Rwork0.302 2711 -
obs--100 %

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