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- PDB-8tou: ACE2-peptide 2 complex crystal form 3 -

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Basic information

Entry
Database: PDB / ID: 8tou
TitleACE2-peptide 2 complex crystal form 3
Components
  • Angiotensin-converting enzyme 2
  • Cyclic peptide 2
KeywordsPROTEIN BINDING / peptidase / enzyme / SARS-CoV-2 / 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 / maternal process involved in female pregnancy ...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 / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / endocytic vesicle membrane / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / viral translation / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / receptor-mediated virion attachment to host cell / cilium / apical plasma membrane / membrane raft / endoplasmic reticulum lumen / symbiont entry into host cell / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / 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: 3.1 Å
AuthorsFranck, C. / Payne, R.J. / Christie, M.
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 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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
B: Cyclic peptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5098
Polymers74,3202
Non-polymers1,1896
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-42 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.802, 196.263, 52.507
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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 Cyclic peptide 2


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

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Sugars , 2 types, 4 molecules

#3: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: 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.: 3 / 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 , 2 types, 2 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: DL-Glutamic acid monohydrate, DL-Alanine, Glycine; DL-Lysine, HEPES, MOPS, MPD; PEG1000, PEG 3350

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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 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→49.07 Å / Num. obs: 17451 / % possible obs: 99.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 71.16 Å2 / CC1/2: 0.993 / Net I/σ(I): 5.8
Reflection shellResolution: 3.1→3.32 Å / Num. unique obs: 3003 / CC1/2: 0.588

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→45.33 Å / SU ML: 0.4507 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 832 4.78 %
Rwork0.2109 16565 -
obs0.2124 17397 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.79 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5236 0 76 0 5312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425463
X-RAY DIFFRACTIONf_angle_d0.80147418
X-RAY DIFFRACTIONf_chiral_restr0.0466780
X-RAY DIFFRACTIONf_plane_restr0.0053954
X-RAY DIFFRACTIONf_dihedral_angle_d6.4962721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.30.34721270.31782629X-RAY DIFFRACTION96.4
3.3-3.550.29021280.25742723X-RAY DIFFRACTION99.76
3.55-3.910.23711240.2122754X-RAY DIFFRACTION99.86
3.91-4.470.23331590.18212731X-RAY DIFFRACTION99.48
4.47-5.630.21361440.1832784X-RAY DIFFRACTION99.93
5.63-45.330.23671500.20472944X-RAY DIFFRACTION99.74
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)
11.267415135090.8200670826960.1089508490781.574252572280.2404621848170.5868109577440.006248747405370.03702356356890.03907074421110.03980781749-0.0251847500304-0.0435859241598-0.0312332939413-0.02028179644510.01563210528640.446544495954-0.0198625581182-0.02857077322580.46059831480.09245563488910.441490158817-23.60823.9030.594
21.44424633879-0.0800094519380.4637560151510.625098607547-0.2808363691160.393025035030.006036615175510.1487114476040.153075518773-0.1771344955150.1176299106870.1623994388450.0124732492894-0.0707294968435-0.1472468524050.570890374144-0.09061989501910.0275746740690.6208823966490.0638821866770.722107711197-18.2439.0841.736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:623 )A18 - 623
2X-RAY DIFFRACTION2( CHAIN B AND ( RESID 1:13 OR RESID 14:14 ) )B1 - 13
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 1:13 OR RESID 14:14 ) )B14

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