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- PDB-7e7e: The co-crystal structure of ACE2 with Fab -

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Basic information

Entry
Database: PDB / ID: 7e7e
TitleThe co-crystal structure of ACE2 with Fab
Components
  • (h11B11-Fab) x 2
  • Processed angiotensin-converting enzyme 2
KeywordsANTIVIRAL PROTEIN / ACE2 Fab
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 / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / 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 / tryptophan transport / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / regulation of vasoconstriction / regulation of cardiac conduction / peptidyl-dipeptidase activity / angiotensin maturation / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / metallocarboxypeptidase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsXiao, J.Y. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2021
Title: A broadly neutralizing humanized ACE2-targeting antibody against SARS-CoV-2 variants.
Authors: Du, Y. / Shi, R. / Zhang, Y. / Duan, X. / Li, L. / Zhang, J. / Wang, F. / Zhang, R. / Shen, H. / Wang, Y. / Wu, Z. / Peng, Q. / Pan, T. / Sun, W. / Huang, W. / Feng, Y. / Feng, H. / Xiao, J. ...Authors: Du, Y. / Shi, R. / Zhang, Y. / Duan, X. / Li, L. / Zhang, J. / Wang, F. / Zhang, R. / Shen, H. / Wang, Y. / Wu, Z. / Peng, Q. / Pan, T. / Sun, W. / Huang, W. / Feng, Y. / Feng, H. / Xiao, J. / Tan, W. / Wang, Y. / Wang, C. / Yan, J.
History
DepositionFeb 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Processed angiotensin-converting enzyme 2
H: h11B11-Fab
L: h11B11-Fab
B: Processed angiotensin-converting enzyme 2
C: h11B11-Fab
D: h11B11-Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,9338
Polymers237,8026
Non-polymers1312
Water0
1
A: Processed angiotensin-converting enzyme 2
H: h11B11-Fab
L: h11B11-Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9664
Polymers118,9013
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Processed angiotensin-converting enzyme 2
C: h11B11-Fab
D: h11B11-Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,9664
Polymers118,9013
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.779, 115.462, 224.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Processed angiotensin-converting enzyme 2


Mass: 70386.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Comamonas sp. Hi5 (bacteria) / References: UniProt: Q9BYF1
#2: Antibody h11B11-Fab


Mass: 24955.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pseudoalteromonas sp. AB293f (bacteria)
#3: Antibody h11B11-Fab


Mass: 23558.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pseudoalteromonas sp. AB293f (bacteria)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dihydrate(pH 6.5),30% (v/v) PEG 550

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 48694 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.415 / Net I/σ(I): 5.5
Reflection shellResolution: 3.8→3.87 Å / Rmerge(I) obs: 1.739 / Num. unique obs: 2472

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R4L

1r4l


Resolution: 3.8→49.84 Å / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 38.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.327 1284 4.98 %
Rwork0.2755 24504 -
obs0.2781 25788 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 284.13 Å2 / Biso mean: 118.6854 Å2 / Biso min: 36.09 Å2
Refinement stepCycle: final / Resolution: 3.8→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16055 0 2 0 16057
Biso mean--148.4 --
Num. residues----2016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8-3.950.45581340.38762561269595
3.95-4.130.43331410.350126862827100
4.13-4.350.41311410.31262682282399
4.35-4.620.33281430.284626982841100
4.62-4.980.36171410.27727132854100
4.98-5.480.32331450.261227312876100
5.48-6.270.3351410.290227462887100
6.27-7.890.28981460.26227782924100
7.89-49.840.23571520.20962909306199
Refinement TLS params.Method: refined / Origin x: -66.4715 Å / Origin y: 10.4899 Å / Origin z: -23.6932 Å
111213212223313233
T0.4002 Å20.0218 Å2-0.0312 Å2-0.4787 Å20.0085 Å2--0.4792 Å2
L0.014 °2-0.0398 °20.0042 °2-0.0652 °20.0521 °2--0.1106 °2
S0.0296 Å °-0.0201 Å °-0.0274 Å °-0.032 Å °-0.0131 Å °-0.0263 Å °0.0018 Å °0.0309 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 803
2X-RAY DIFFRACTION1allH1 - 217
3X-RAY DIFFRACTION1allL1 - 210
4X-RAY DIFFRACTION1allB19 - 803
5X-RAY DIFFRACTION1allC1 - 217
6X-RAY DIFFRACTION1allD1 - 210

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