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- PDB-9r19: Crystal structure of human ACE2 in complex with VHH B07 and VHH B10 -

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Basic information

Entry
Database: PDB / ID: 9r19
TitleCrystal structure of human ACE2 in complex with VHH B07 and VHH B10
Components
  • Processed angiotensin-converting enzyme 2
  • VHH B07
  • VHH B10
KeywordsHYDROLASE / HUMAN ACE2 / VHH / STRUCTURAL PROTEIN
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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / 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 / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / 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 / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / 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)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsBlachier, S. / Vaney, M.C. / Fernandez, I. / Arbabian, A. / Rey, F.A.R. / Haouz, A. / Brelot, A.
Funding support France, 1items
OrganizationGrant numberCountry
Pasteur Institute France
CitationJournal: To Be Published
Title: Crystal structure of human ACE2 in complex with VHH B07 and VHH B10
Authors: Blachier, S. / Vaney, M.C. / Fernandez, I. / Arbabian, A. / Rey, F.A.R. / Haouz, A. / Brelot, A.
History
DepositionApr 25, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Processed angiotensin-converting enzyme 2
B: Processed angiotensin-converting enzyme 2
C: Processed angiotensin-converting enzyme 2
D: VHH B10
E: VHH B10
F: VHH B10
G: VHH B07
H: VHH B07
I: VHH B07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,03526
Polymers306,0179
Non-polymers3,01817
Water1,874104
1
A: Processed angiotensin-converting enzyme 2
D: VHH B10
G: VHH B07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9629
Polymers102,0063
Non-polymers9566
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Processed angiotensin-converting enzyme 2
E: VHH B10
H: VHH B07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9629
Polymers102,0063
Non-polymers9566
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Processed angiotensin-converting enzyme 2
F: VHH B10
I: VHH B07
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1128
Polymers102,0063
Non-polymers1,1065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.920, 108.150, 146.100
Angle α, β, γ (deg.)90.00, 98.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 6 molecules DEFGHI

#2: Antibody VHH B10


Mass: 16719.365 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: AAA : linker EQKLISEEDLN : c-myc tag GAA : linker HHHHHH : His-tag GS : linker
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 cells
#3: Antibody VHH B07


Mass: 15464.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: AAA : linker EQKLISEEDLN : c-myc tag GAA : linker HHHHHH : His-tag GS : linker
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1

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Protein / Sugars , 2 types, 16 molecules ABC

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 69821.461 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: GSG linker LVPR cleaved thrombin site / Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Cell line (production host): Expi293FTM GnTI / Production host: Homo sapiens (human) / References: UniProt: Q9BYF1
#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.: 13 / 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, 108 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES pH 7.5 10% (w/v) 2-propanol 20% (w/v) PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→48.37 Å / Num. obs: 83613 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 63.78 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.135 / Rrim(I) all: 0.26 / Net I/σ(I): 9.2
Reflection shellResolution: 2.69→2.76 Å / Rmerge(I) obs: 1.48 / Num. unique obs: 6015 / CC1/2: 0.375 / Rpim(I) all: 0.905 / Rrim(I) all: 1.74

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (10-JUL-2024)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→48.3 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 1.912 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.098 / SU Rfree Blow DPI: 0.325 / SU Rfree Cruickshank DPI: 0.338
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 4180 5 %RANDOM
Rwork0.2197 ---
obs0.2214 83594 99.8 %-
Displacement parametersBiso mean: 70.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.2361 Å20 Å25.3897 Å2
2---3.1962 Å20 Å2
3---0.9601 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.69→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20123 0 186 104 20413
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00720846HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8728324HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7161SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3592HARMONIC5
X-RAY DIFFRACTIONt_it20846HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion18.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2647SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16114SEMIHARMONIC4
LS refinement shellResolution: 2.69→2.71 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3914 -4.96 %
Rwork0.3412 1589 -
all0.3436 1672 -
obs--91.41 %
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)
11.4355-0.09050.5560.5769-0.29761.1271-0.05160.09740.0747-0.0018-0.0006-0.0003-0.04750.10460.0522-0.1437-0.03230.00510.0960.0117-0.067341.5484-20.74533.8393
20.99730.11610.43170.59360.00021.733-0.0017-0.1445-0.11020.0941-0.1162-0.05520.00570.14110.1179-0.1889-0.045-0.02770.29630.1173-0.08-0.8267-30.453938.8797
31.32120.5280.47680.79560.56742.5551-0.1539-0.01670.3599-0.03160.01210.1906-0.25190.02040.1418-0.1155-0.0513-0.07490.1850.0824-0.078210.9107-13.235787.4515
44.31420.55461.64638.04683.89057.75530.0582-0.36860.23640.18920.0886-0.2012-0.25320.1398-0.1468-0.1987-0.0172-0.03230.0342-0.0818-0.143150.2455-5.391341.276
513.44181.598-0.637410.7109-2.20036.95470.02760.47122.33550.05390.06780.5443-1.1079-0.0461-0.0954-0.22560.0667-0.0654-0.20730.15020.3094-9.652.414615.349
617.5940.43271.18784.1047-0.1869.36420.26991.4619-0.9822-0.13930.0909-0.74550.10041.6305-0.3608-0.49890.0596-0.04870.4602-0.2686-0.176550.6683-20.282498.8502
79.7664-1.60551.37064.2489-3.44897.6632-0.1287-0.0209-0.2468-0.18520.230.58180.2891-0.3354-0.1013-0.26-0.0585-0.03310.00320.0734-0.0519-0.1431-8.8159-12.9156
813.3108-0.727-3.55790.6323-0.279315.5502-0.3605-1.5164-0.48510.07050.0555-0.40270.35912.59730.305-0.7074-0.1177-0.14571.30010.5102-0.370140.7214-27.737459.7885
97.47913.97295.325711.3445-2.959613.0819-0.17650.2361.1595-0.0238-0.38660.4266-1.3716-0.21230.56310.0611-0.2947-0.36830.05420.6406-0.16444.068310.389847.6619
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }

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