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- PDB-1r42: Native Human Angiotensin Converting Enzyme-Related Carboxypeptida... -

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Basic information

Entry
Database: PDB / ID: 1r42
TitleNative Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2)
Components
  • (disordered segment of collectrin homology ...) x 4
  • angiotensin I converting enzyme 2
KeywordsHYDROLASE / zinc metallopeptidase domain / collectrin homology domain / native or open conformation / chloride ion binding site / zinc binding site
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / positive regulation of gap junction assembly / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / metallocarboxypeptidase activity / Metabolism of Angiotensinogen to Angiotensins / Attachment and Entry / carboxypeptidase activity / negative regulation of signaling receptor activity / positive regulation of cardiac muscle contraction / regulation of cytokine production / viral life cycle / blood vessel diameter maintenance / brush border membrane / regulation of transmembrane transporter activity / negative regulation of smooth muscle cell proliferation / cilium / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Induction of Cell-Cell Fusion / Potential therapeutics for SARS / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / cell surface / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Collectrin-like domain profile. / Collectrin domain / Renal amino acid transporter / Peptidase family M2 domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
: / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsTowler, P. / Staker, B. / Prasad, S.G. / Menon, S. / Ryan, D. / Tang, J. / Parsons, T. / Fisher, M. / Williams, D. / Dales, N.A. ...Towler, P. / Staker, B. / Prasad, S.G. / Menon, S. / Ryan, D. / Tang, J. / Parsons, T. / Fisher, M. / Williams, D. / Dales, N.A. / Patane, M.A. / Pantoliano, M.W.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis.
Authors: Towler, P. / Staker, B. / Prasad, S.G. / Menon, S. / Tang, J. / Parsons, T. / Ryan, D. / Fisher, M. / Williams, D. / Dales, N.A. / Patane, M.A. / Pantoliano, M.W.
#1: Journal: J.Am.Chem.Soc. / Year: 2002
Title: Substrate-based design of the first class of angiotensin-converting enzyme-related carboxypeptidase (ACE2) inhibitors
Authors: A Dales, N. / Gould, A.E. / Brown, J.A. / Calderwood, E.F. / Guan, B. / Minor, C.A. / Gavin, J.M. / Hales, P. / Kaushik, V.K. / Stewart, M. / Tummino, P.J. / Vickers, C.S. / Ocain, T.D. / Pantane, M.A.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Hydrolysis of biological peptides by human angiotensin-converting enzyme-related carboxypeptidase
Authors: Vickers, C. / Hales, P. / Kaushik, V. / Dick, L. / Gavin, J. / Tang, J. / Godbout, K. / Parsons, T. / Baronas, E. / Hsieh, F. / Acton, S. / Patane, M. / Nichols, A. / Tummino, P.
History
DepositionOct 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_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
Remark 999SEQUENCE The complete sequence crystallized by the authors (residues 1-740 of reference sequence GB ...SEQUENCE The complete sequence crystallized by the authors (residues 1-740 of reference sequence GB 11225609) is as follows: MSSSSWLLLSLVAVTAAQSTIEEQAKTFLDKFNHEAEDLFYQSSLASWNY NTNITEENVQNMNNAGDKWSAFLKEQSTLAQMYPLQEIQNLTVKLQLQALQ QNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNEIM ANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYW RGDYEVNGVDGYDYSRGQLIEDVEHTFEEIKPLYEHLHAYVRAKLMNAYPS YISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQAWDAQ RIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDF RILMCTKVTMDDFLTAHHEMGHIQYDMAYAAQPFLLRNGANEGFHEAVGEI MSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTLPFTYMLEK WRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSND YSFIRYYTRTLYQFQFQEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRL GKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNKNSFVGWSTDWS PYADQSIKVRISLKSALGDKAYEWNDNEMYLFRSSVAYAMRQYFLKVKNQ MILFGEEDVRVANLKPRISFNFFVTAPKNVSDIIPRTEVEKAIRMSRSRIN DAFRLNDNSLEFLGIQPTLGPPNQPPVS The electron density map for much of the collectrin homology domain (residues 616-740) is weak. Only about half of this domain was visible in the electron density map, and what can be seen is ambiguous due to topology and connectivity issues. For this reason, residues beginning at 901 are labeled as unknown (UNK). Each fragment of unknown residues has been assigned a unique chain ID. However, it should be understood that only one sequence (residues 1-740) was crystallized.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: angiotensin I converting enzyme 2
B: disordered segment of collectrin homology domain
C: disordered segment of collectrin homology domain
D: disordered segment of collectrin homology domain
E: disordered segment of collectrin homology domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,77210
Polymers76,0085
Non-polymers7645
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.638, 89.478, 112.399
Angle α, β, γ (deg.)90.00, 109.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Disordered segment of collectrin homology ... , 4 types, 4 molecules BCDE

#2: Protein/peptide disordered segment of collectrin homology domain


Mass: 528.644 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
#3: Protein/peptide disordered segment of collectrin homology domain


Mass: 1720.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
#4: Protein/peptide disordered segment of collectrin homology domain


Mass: 1549.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
#5: Protein/peptide disordered segment of collectrin homology domain


Mass: 1209.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein angiotensin I converting enzyme 2 / angiotensin converting enzyme-like protein / Angiotensin Converting Enzyme-Related Carboxypeptidase


Mass: 70999.820 Da / Num. of mol.: 1 / Fragment: Extracellular domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 11225609, UniProt: Q9BYF1*PLUS
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 3 types, 304 molecules

#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.24 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl, 200 mM MgCl2, 14% PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 16-18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
2100 mMTris-HCl1reservoirpH8.5
3200 mM1reservoirMgCl2
414 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.28 Å
DetectorDetector: AREA DETECTOR / Date: Jun 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 49286 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 52.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 21.4
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 46.7 Å / Num. obs: 47465 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.34 Å / % possible obs: 81.8 % / Num. unique obs: 5982 / Rmerge(I) obs: 0.408

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Processing

Software
NameVersionClassification
CNX2002refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→46.74 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2383730.95 / Data cutoff high rms absF: 2383730.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.287 4798 10.1 %RANDOM
Rwork0.235 ---
obs-47465 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.5529 Å2 / ksol: 0.341723 e/Å3
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.61 Å20 Å211.31 Å2
2--6.46 Å20 Å2
3---0.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5165 0 44 302 5511
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it2.041.5
X-RAY DIFFRACTIONc_mcangle_it3.092
X-RAY DIFFRACTIONc_scbond_it3.32
X-RAY DIFFRACTIONc_scangle_it4.422.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 659 9.9 %
Rwork0.379 5982 -
obs--81.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAM
Refinement
*PLUS
Lowest resolution: 46.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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