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- PDB-4fys: Human aminopeptidase N (CD13) in complex with angiotensin IV -

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Basic information

Entry
Database: PDB / ID: 4fys
TitleHuman aminopeptidase N (CD13) in complex with angiotensin IV
Components
  • Aminopeptidase N
  • Angiotensin IV
KeywordsHYDROLASE/HORMONE / metalloprotease / HYDROLASE-HORMONE 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 / : / 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 / regulation of renal output by angiotensin / positive regulation of activation of Janus kinase activity ...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 / regulation of renal output by angiotensin / positive regulation of activation of Janus kinase activity / membrane alanyl aminopeptidase / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renal system process / renin-angiotensin regulation of aldosterone production / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of extracellular matrix assembly / positive regulation of macrophage derived foam cell differentiation / vasoconstriction / positive regulation of CoA-transferase activity / type 1 angiotensin receptor binding / low-density lipoprotein particle remodeling / positive regulation of extrinsic apoptotic signaling pathway / response to angiotensin / positive regulation of epidermal growth factor receptor signaling pathway / peptide catabolic process / positive regulation of cardiac muscle hypertrophy / metalloaminopeptidase activity / positive regulation of gap junction assembly / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of protein tyrosine kinase activity / regulation of vasoconstriction / regulation of cardiac conduction / blood vessel remodeling / Metabolism of Angiotensinogen to Angiotensins / positive regulation of epithelial to mesenchymal transition / aminopeptidase activity / nitric oxide-cGMP-mediated signaling / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / secretory granule membrane / negative regulation of MAP kinase activity / kidney development / positive regulation of cytokine production / angiotensin-activated signaling pathway / regulation of cell growth / peptide binding / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / PPARA activates gene expression / regulation of blood pressure / positive regulation of miRNA transcription / positive regulation of inflammatory response / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / virus receptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / G alpha (i) signalling events / G alpha (q) signalling events / regulation of apoptotic process / angiogenesis / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / blood microparticle / G protein-coupled receptor signaling pathway / lysosomal membrane / external side of plasma membrane / Neutrophil degranulation / positive regulation of DNA-templated transcription / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Serpin, conserved site ...Angiotensinogen, serpin domain / Angiotensinogen / Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Serpin, conserved site / Serpins signature. / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Angiotensinogen / Aminopeptidase N
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsWong, A.H. / Rini, J.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The X-ray Crystal Structure of Human Aminopeptidase N Reveals a Novel Dimer and the Basis for Peptide Processing.
Authors: Wong, A.H. / Zhou, D. / Rini, J.M.
History
DepositionJul 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase N
C: Angiotensin IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,20020
Polymers104,0272
Non-polymers3,17418
Water15,763875
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-8 kcal/mol
Surface area33960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.907, 157.907, 115.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-1955-

HOH

21A-1964-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Aminopeptidase N / AP-N / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid ...AP-N / hAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / Myeloid plasma membrane glycoprotein CD13 / gp150


Mass: 103250.734 Da / Num. of mol.: 1 / Fragment: UNP residues 66-967
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANPEP, APN, CD13, PEPN / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P15144, membrane alanyl aminopeptidase
#2: Protein/peptide Angiotensin IV / Serpin A8 / Angiotensin-1 / Angiotensin I / Ang I / Angiotensin-2 / Angiotensin II / Ang II / ...Serpin A8 / Angiotensin-1 / Angiotensin I / Ang I / Angiotensin-2 / Angiotensin II / Ang II / Angiotensin-3 / Angiotensin III / Ang III / Des-Asp[1]-angiotensin II


Mass: 775.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P01019

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Sugars , 3 types, 7 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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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 , 2 types, 886 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 875 / 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: 3.99 Å3/Da / Density % sol: 69.17 %
Crystal growTemperature: 295 K / Method: hanging drop vapor diffusion / pH: 5
Details: 2M ammonium sulfate, 0.1M sodium acetate, 10% glycerol, pH 5.0, hanging drop vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. obs: 103185 / % possible obs: 96.4 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.038.10.348199
2.03-2.078.10.318199.4
2.07-2.118.10.286199.3
2.11-2.1580.258198.7
2.15-2.27.90.237199
2.2-2.257.90.227199.1
2.25-2.317.90.212198.6
2.31-2.377.70.2198.5
2.37-2.447.70.196198.2
2.44-2.527.60.184197.8
2.52-2.617.50.173197.2
2.61-2.717.40.155196.4
2.71-2.847.20.138196.5
2.84-2.997.20.126196.1
2.99-3.177.10.124195.2
3.17-3.4270.129194.6
3.42-3.766.50.11193.5
3.76-4.316.10.085190.1
4.31-5.426.20.067190.6
5.42-357.50.054190.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.01→27.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.502 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19791 5176 5 %RANDOM
Rwork0.1685 ---
obs0.16997 97957 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.01→27.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 192 875 8411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197805
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.96610656
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1565922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59224.541381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.452151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5531542
X-RAY DIFFRACTIONr_chiral_restr0.0980.21184
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215982
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.015→2.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 365 -
Rwork0.192 6814 -
obs--90.83 %

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