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- PDB-4aph: Human angiotensin-converting enzyme in complex with angiotensin-II -

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Basic information

Entry
Database: PDB / ID: 4aph
TitleHuman angiotensin-converting enzyme in complex with angiotensin-II
Components
  • ANGIOTENSIN-2
  • ANGIOTENSIN-CONVERTING ENZYME
KeywordsHYDROLASE/HORMONE / HYDROLASE-HORMONE COMPLEX / ZINC METALLOPROTEASE / METALLOPEPTIDASE
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 / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / mononuclear cell proliferation / cell proliferation in bone marrow ...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 / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of extracellular matrix assembly / mononuclear cell proliferation / cell proliferation in bone marrow / bradykinin receptor binding / regulation of angiotensin metabolic process / exopeptidase activity / substance P catabolic process / peptidyl-dipeptidase A / tripeptidyl-peptidase activity / regulation of renal output by angiotensin / positive regulation of activation of Janus kinase activity / negative regulation of calcium ion import / positive regulation of peptidyl-cysteine S-nitrosylation / response to laminar fluid shear stress / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renal system process / renin-angiotensin regulation of aldosterone production / negative regulation of gap junction assembly / metallodipeptidase activity / positive regulation of systemic arterial blood pressure / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / positive regulation of macrophage derived foam cell differentiation / cellular response to aldosterone / hormone catabolic process / bradykinin catabolic process / angiogenesis involved in coronary vascular morphogenesis / response to thyroid hormone / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of glucose import / vasoconstriction / positive regulation of CoA-transferase activity / hormone metabolic process / neutrophil mediated immunity / type 1 angiotensin receptor binding / regulation of smooth muscle cell migration / regulation of hematopoietic stem cell proliferation / low-density lipoprotein particle remodeling / positive regulation of extrinsic apoptotic signaling pathway / response to angiotensin / mitogen-activated protein kinase binding / embryo development ending in birth or egg hatching / chloride ion binding / mitogen-activated protein kinase kinase binding / positive regulation of neurogenesis / positive regulation of epidermal growth factor receptor signaling pathway / arachidonic acid secretion / eating behavior / post-transcriptional regulation of gene expression / heterocyclic compound binding / lung alveolus development / heart contraction / peptide catabolic process / positive regulation of cardiac muscle hypertrophy / response to dexamethasone / regulation of heart rate by cardiac conduction / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / positive regulation of protein tyrosine kinase activity / regulation of vasoconstriction / regulation of cardiac conduction / hematopoietic stem cell differentiation / peptidyl-dipeptidase activity / blood vessel remodeling / amyloid-beta metabolic process / angiotensin maturation / animal organ regeneration / Metabolism of Angiotensinogen to Angiotensins / positive regulation of epithelial to mesenchymal transition / nitric oxide-cGMP-mediated signaling / positive regulation of vasoconstriction / carboxypeptidase activity / sperm midpiece / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / blood vessel diameter maintenance / Peptide ligand-binding receptors / response to nutrient levels / basal plasma membrane / negative regulation of MAP kinase activity / kidney development / positive regulation of cytokine production / angiotensin-activated signaling pathway / female pregnancy / regulation of cell growth / cellular response to glucose stimulus / brush border membrane / growth factor activity / serine-type endopeptidase inhibitor activity / regulation of synaptic plasticity / hormone activity / PPARA activates gene expression / metalloendopeptidase activity
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) ...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 / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
ACETATE ION / Angiotensinogen / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMasuyer, G. / Schwager, S.L.U. / Sturrock, E.D. / Isaac, R.E. / Acharya, K.R.
CitationJournal: Sci.Rep. / Year: 2012
Title: Molecular Recognition and Regulation of Human Angiotensin-I Converting Enzyme (Ace) Activity by Natural Inhibitory Peptides.
Authors: Masuyer, G. / Schwager, S.L.U. / Sturrock, E.D. / Isaac, R.E. / Acharya, K.R.
History
DepositionApr 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Jan 25, 2017Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANGIOTENSIN-CONVERTING ENZYME
P: ANGIOTENSIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,71113
Polymers69,1172
Non-polymers1,59411
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-52 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.500, 84.660, 133.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#1: Protein ANGIOTENSIN-CONVERTING ENZYME / ACE / DIPEPTIDYL CARBOXYPEPTIDASE I / KININASE II / CD143 / ACE-T


Mass: 68068.922 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 68-656
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: CRICETULUS GRISEUS (Chinese hamster)
References: UniProt: P12821, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds, peptidyl-dipeptidase A
#2: Protein/peptide ANGIOTENSIN-2 / ANGIOTENSIN II / ANG II


Mass: 1048.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01019

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Sugars , 2 types, 2 molecules

#3: 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
#7: 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

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Non-polymers , 5 types, 294 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 4.7
Details: 50MM SODIUM ACETATE PH 4.7, 16% PEG4000, 10UM ZNSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS-2M / Detector: PIXEL / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.99→52.53 Å / Num. obs: 37104 / % possible obs: 82.9 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.7
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O8A

1o8a


Resolution: 1.99→71.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.258 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO DIFFERENT CONFIRMATIONS ARE VISIBLE FOR ANG II (CHAIN P).
RfactorNum. reflection% reflectionSelection details
Rfree0.24026 1877 5.1 %RANDOM
Rwork0.19406 ---
obs0.19638 35133 82.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.286 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.84 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.99→71.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4815 0 92 285 5192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0215187
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.9517062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9725610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24824.373263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79915839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9891527
X-RAY DIFFRACTIONr_chiral_restr0.0740.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214045
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.331.53047
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.65324918
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.01432140
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7174.52144
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
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 134 -
Rwork0.258 2436 -
obs--78.98 %
Refinement TLS params.Method: refined / Origin x: 12.1518 Å / Origin y: -5.7943 Å / Origin z: -23.9715 Å
111213212223313233
T0.0205 Å2-0.0038 Å2-0.0043 Å2-0.0066 Å20.0053 Å2--0.0145 Å2
L0.1938 °2-0.0286 °20.0057 °2-0.324 °20.1779 °2--0.3101 °2
S0.0001 Å °-0.018 Å °-0.0079 Å °0.0145 Å °0.0116 Å °-0.0374 Å °0.0014 Å °-0.0031 Å °-0.0117 Å °

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