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- PDB-8tot: ACE2-peptide2 complex crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 8tot
TitleACE2-peptide2 complex crystal form 2
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 / 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 / maternal process involved in female pregnancy / angiotensin maturation / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / carboxypeptidase activity / negative regulation of signaling receptor activity / Attachment and Entry / 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 / negative regulation of ERK1 and ERK2 cascade / cilium / metallopeptidase activity / endocytic vesicle membrane / 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 / 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 / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / membrane / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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

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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: Angiotensin-converting enzyme 2
C: Cyclic peptide 2
D: Cyclic peptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,45419
Polymers148,6414
Non-polymers3,81315
Water181
1
A: Angiotensin-converting enzyme 2
C: Cyclic peptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1379
Polymers74,3202
Non-polymers1,8167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-42 kcal/mol
Surface area26140 Å2
MethodPISA
2
B: Angiotensin-converting enzyme 2
D: Cyclic peptide 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,31710
Polymers74,3202
Non-polymers1,9978
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-35 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.661, 89.308, 118.508
Angle α, β, γ (deg.)90.000, 116.930, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Angiotensin-converting enzyme 2


Mass: 72592.398 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 11 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.: 4
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
#4: 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
#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.: 6 / 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 , 3 types, 5 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.54 Å3/Da / Density % sol: 65.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000, ammonium acetate, sodium citrate, glycerol

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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: Aug 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→49.88 Å / Num. obs: 51159 / % possible obs: 99.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 65.1 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.7
Reflection shellResolution: 2.8→2.88 Å / Num. unique obs: 4019 / CC1/2: 0.777

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.24 Å / SU ML: 0.4145 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5009
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2417 2340 4.58 %
Rwork0.21 48755 -
obs0.2115 51095 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9962 0 247 1 10210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008410483
X-RAY DIFFRACTIONf_angle_d0.964314237
X-RAY DIFFRACTIONf_chiral_restr0.05251524
X-RAY DIFFRACTIONf_plane_restr0.00791816
X-RAY DIFFRACTIONf_dihedral_angle_d5.70441426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.43951010.45062543X-RAY DIFFRACTION88.58
2.86-2.920.43561300.39112870X-RAY DIFFRACTION99.9
2.92-2.990.44681070.36022903X-RAY DIFFRACTION99.87
2.99-3.060.32791030.30742901X-RAY DIFFRACTION99.93
3.06-3.140.28761520.27182843X-RAY DIFFRACTION100
3.14-3.240.29421300.25982875X-RAY DIFFRACTION100
3.24-3.340.31091490.25922892X-RAY DIFFRACTION99.9
3.34-3.460.30261650.24632840X-RAY DIFFRACTION100
3.46-3.60.28671380.24132887X-RAY DIFFRACTION99.9
3.6-3.760.28651100.20782929X-RAY DIFFRACTION99.9
3.76-3.960.2391440.17722857X-RAY DIFFRACTION99.97
3.96-4.210.20431550.17582866X-RAY DIFFRACTION99.97
4.21-4.530.20751370.17042889X-RAY DIFFRACTION99.87
4.53-4.990.19921530.15522894X-RAY DIFFRACTION99.97
4.99-5.710.20061710.17922875X-RAY DIFFRACTION99.93
5.71-7.190.2311750.1972886X-RAY DIFFRACTION99.97
7.19-49.240.17531200.1723005X-RAY DIFFRACTION99.59
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)
11.495980617730.3979343599090.6917883322121.984827737940.6397574530931.400573087240.0651507587908-0.0477524974759-0.00605922008220.0253555827908-0.1329329274980.153070573995-0.0172744700889-0.03608366215230.054962119490.452860819666-0.01487388462110.01507305510560.4664201484810.02672712480360.48973444238322.0850.14512.015
22.06363678033-0.8211324704070.5863099762111.86742407921-0.1101028498510.9988696787360.06868696532860.02234525694290.0119084724621-0.183209370067-0.1162735645790.0486156515213-0.00818987330266-0.007722159706170.04528335020.492533263528-0.0124869585017-0.008781737284530.446352206180.02044033121930.43285501530947.613-0.466-38.325
31.916058279070.02979740897470.6245602261614.38764505530.3462280605180.8640667089770.0569566860076-0.2319181728890.2545402658750.0243841617706-0.1026089332770.10310603467-0.189168537318-0.258471032310.006927568196380.5905472911130.0496384871278-0.06822106210890.586272900076-0.0642877013920.7206496856519.61-3.7483.684
41.29389365431-0.2033698696040.2344123762043.68099687094-1.124163964091.790451013590.01448205786370.289606418959-0.179654180903-0.2060664256470.00162709082201-0.1927845250570.3673149553230.146943318242-0.02261277387690.6932799345450.0225766374576-0.06588547114220.643923049674-0.08612499609760.70525480306534.3753.416-45.96
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 19:614 OR RESID 701:701 ) )A19 - 614
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 19:614 OR RESID 701:701 ) )A701
3X-RAY DIFFRACTION2( CHAIN B AND RESID 19:614 )B19 - 614
4X-RAY DIFFRACTION3( CHAIN C AND RESID 0:13 )C0 - 13
5X-RAY DIFFRACTION4( CHAIN D AND RESID 0:13 )D0 - 13

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