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- PDB-8tor: ACE2-peptide 2 complex -

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Basic information

Entry
Database: PDB / ID: 8tor
TitleACE2-peptide 2 complex
Components
  • Angiotensin-converting enzyme 2
  • Peptide 2
KeywordsPROTEIN BINDING / peptidase / enzyme / SARS-CoV-2 / receptor / angiotensin
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 / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction ...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 / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of signaling receptor activity / carboxypeptidase activity / Attachment and Entry / positive regulation of cardiac muscle contraction / viral life cycle / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / regulation of transmembrane transporter activity / cilium / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / virus receptor activity / regulation of cell population proliferation / regulation of inflammatory response / endopeptidase activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / 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 / identical protein binding / membrane / plasma membrane
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChristie, M. / Payne, R.J.
Funding support Australia, 4items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP220102497 Australia
Australian Research Council (ARC)CE200100012 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1141142 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1153493 Australia
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Discovery of High Affinity Cyclic Peptide Ligands for Human ACE2 with SARS-CoV-2 Entry Inhibitory Activity.
Authors: Bedding, M.J. / Franck, C. / Johansen-Leete, J. / Aggarwal, A. / Maxwell, J.W.C. / Patel, K. / Hawkins, P.M.E. / Low, J.K.K. / Siddiquee, R. / Sani, H.M. / Ford, D.J. / Turville, S. / ...Authors: Bedding, M.J. / Franck, C. / Johansen-Leete, J. / Aggarwal, A. / Maxwell, J.W.C. / Patel, K. / Hawkins, P.M.E. / Low, J.K.K. / Siddiquee, R. / Sani, H.M. / Ford, D.J. / Turville, S. / Mackay, J.P. / Passioura, T. / Christie, M. / Payne, R.J.
History
DepositionAug 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme 2
E: Peptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,91410
Polymers74,3202
Non-polymers1,5938
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-35 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.199, 180.199, 70.068
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AE

#1: Protein Angiotensin-converting enzyme 2


Mass: 72592.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2 / Production host: Homo sapiens (human) / References: UniProt: Q9BYF1
#2: Protein/peptide Peptide 2


Mass: 1728.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic cyclic peptide / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 3 molecules

#3: 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
#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
#6: 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: obtained synthetically / 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 , 4 types, 77 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG5KMME, magnesium formate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→45.12 Å / Num. obs: 43006 / % possible obs: 99.7 % / Redundancy: 10.5 % / Biso Wilson estimate: 42.67 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3651 / CC1/2: 0.859 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.12 Å / SU ML: 0.2841 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.3067
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2063 2230 5.19 %
Rwork0.18 40762 -
obs0.1813 42992 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4941 0 104 72 5117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00475181
X-RAY DIFFRACTIONf_angle_d0.64727030
X-RAY DIFFRACTIONf_chiral_restr0.0409747
X-RAY DIFFRACTIONf_plane_restr0.0055896
X-RAY DIFFRACTIONf_dihedral_angle_d22.9853701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.34021440.2982453X-RAY DIFFRACTION96.61
2.25-2.30.28061470.26512540X-RAY DIFFRACTION100
2.3-2.360.26451800.23832506X-RAY DIFFRACTION99.96
2.36-2.420.25661530.22432563X-RAY DIFFRACTION99.93
2.42-2.490.25671090.22242572X-RAY DIFFRACTION99.96
2.49-2.570.26931640.20852511X-RAY DIFFRACTION100
2.57-2.660.23781500.21552556X-RAY DIFFRACTION99.93
2.66-2.770.27061290.21432555X-RAY DIFFRACTION99.96
2.77-2.90.28041520.22862542X-RAY DIFFRACTION100
2.9-3.050.21951250.19782590X-RAY DIFFRACTION100
3.05-3.240.22921280.19612545X-RAY DIFFRACTION100
3.24-3.490.22341210.18652568X-RAY DIFFRACTION99.93
3.49-3.840.19611260.16832574X-RAY DIFFRACTION100
3.84-4.40.17271140.14222603X-RAY DIFFRACTION100
4.4-5.540.16891440.14792540X-RAY DIFFRACTION100
5.54-45.120.14991440.15432544X-RAY DIFFRACTION99.85
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)
12.701992095630.6161346029190.3280764540541.439344682260.1512452503210.597086874378-0.05478363005490.4415502333390.296260683983-0.240576020910.0705505758212-0.0726643079525-0.1202677942860.137246020327-0.02087803899260.2929799485160.008872991619530.02770752241190.3497940056390.02277066079140.292805976955-33.28614.38-23.788
20.9975807875010.2527291934050.2847710637061.808814643620.19548413150.744411266493-0.07409054865960.282430242921-0.39382566834-0.147587108604-0.169926202117-0.0462099434210.255071953024-0.06238341247530.2116462805770.517650354787-0.0174999552294-0.01212189921040.623961572607-0.0848002630070.83848105992-17.43412.523-25.853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 18:614 OR RESID 801:804 ) )A18 - 614
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 18:614 OR RESID 801:804 ) )A801 - 804
3X-RAY DIFFRACTION2( CHAIN E AND RESID 0:13 )E0 - 13

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