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- PDB-7wnm: Structure of SARS-CoV-2 Gamma variant receptor-binding domain com... -

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Basic information

Entry
Database: PDB / ID: 7wnm
TitleStructure of SARS-CoV-2 Gamma variant receptor-binding domain complexed with high affinity human ACE2 mutant (T27F,R273Q)
Components
  • Angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / complex
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 / receptor-mediated endocytosis of virus by host cell / carboxypeptidase activity / Attachment and Entry / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / negative regulation of ERK1 and ERK2 cascade / cilium / 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 / Maturation of spike protein / viral translation / Translation of Structural Proteins / host cell surface / Virion Assembly and Release / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / 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. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal ...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. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMa, R.Y. / Han, P.C. / Wang, Q.H. / Han, P.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFC0863300 China
CitationJournal: Signal Transduct Target Ther / Year: 2022
Title: A binding-enhanced but enzymatic activity-eliminated human ACE2 efficiently neutralizes SARS-CoV-2 variants.
Authors: Zheng, A. / Wu, L. / Ma, R. / Han, P. / Huang, B. / Qiao, C. / Wang, Q. / Tan, W. / Gao, G.F. / Han, P.
History
DepositionJan 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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
B: Angiotensin-converting enzyme 2
A: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,3534
Polymers113,0672
Non-polymers2872
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, crystal structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-39 kcal/mol
Surface area33990 Å2
Unit cell
Length a, b, c (Å)103.346, 103.346, 233.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Angiotensin-converting enzyme 2 / Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related ...Angiotensin-converting enzyme homolog / ACEH / Angiotensin-converting enzyme-related carboxypeptidase / ACE-related carboxypeptidase / Metalloprotease MPROT15


Mass: 85416.414 Da / Num. of mol.: 1 / Mutation: T27F, R273Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein Spike protein S1


Mass: 27650.395 Da / Num. of mol.: 1 / Fragment: Receptor-binding domain / Mutation: N501Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.81 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M magnesium chloride, 0.1 M MES (pH 6.0) and 8% w/v polyethylene glycol 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 357147 / % possible obs: 99.7 % / Redundancy: 10 % / Biso Wilson estimate: 39.09 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.057 / Rrim(I) all: 0.185 / Rsym value: 0.175 / Net I/σ(I): 12.7
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.061 / Num. unique obs: 3491 / CC1/2: 0.772 / Rpim(I) all: 0.362 / Rrim(I) all: 1.122 / Rsym value: 1.061 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19rc3_4028refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 2.7→17.57 Å / SU ML: 0.2667 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.2924
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2225 1995 5.64 %
Rwork0.1938 33398 -
obs0.1954 35393 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.88 Å2
Refinement stepCycle: LAST / Resolution: 2.7→17.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 15 104 6521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00286599
X-RAY DIFFRACTIONf_angle_d0.51448971
X-RAY DIFFRACTIONf_chiral_restr0.0396938
X-RAY DIFFRACTIONf_plane_restr0.00481163
X-RAY DIFFRACTIONf_dihedral_angle_d4.3309864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.31251380.25982299X-RAY DIFFRACTION99.07
2.77-2.840.26831410.26182356X-RAY DIFFRACTION100
2.84-2.920.29691400.25082352X-RAY DIFFRACTION99.96
2.93-3.020.25141390.24142332X-RAY DIFFRACTION100
3.02-3.130.29571410.24052364X-RAY DIFFRACTION100
3.13-3.250.29951410.22662360X-RAY DIFFRACTION100
3.25-3.40.29381410.22822359X-RAY DIFFRACTION100
3.4-3.580.24521420.20632372X-RAY DIFFRACTION100
3.58-3.80.19171400.18932369X-RAY DIFFRACTION100
3.8-4.090.19521440.17232390X-RAY DIFFRACTION100
4.09-4.490.1851430.16092405X-RAY DIFFRACTION99.96
4.49-5.130.18321440.15522416X-RAY DIFFRACTION99.96
5.13-6.410.22531470.1792461X-RAY DIFFRACTION99.92
6.41-17.570.15731540.15712563X-RAY DIFFRACTION99.38
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)
12.09826731854-2.36294516098-1.348211482216.36452769891.247853496822.419000840290.1212795148820.281026223759-0.3476618396140.0350066267379-0.3021979231021.19902096070.0879587183599-0.3589204151860.1885246019860.2739812949670.0328445875819-0.04217401232120.358708002643-0.07353843131660.321985042432-50.728431383629.643712124310.6926816101
20.7381670454240.7009967120331.545730084692.214826760963.823485160136.71101195316-0.2429039603410.09060311525120.0816022505041-0.148732112479-0.02570923918360.457434527397-0.602384126237-0.2954671702910.2699153818770.3065313117280.06080270499590.08899809167940.4401157413110.04405231698960.476250758655-50.062475190937.225410462-2.33661323665
34.49092739-2.33482912699-0.3488875066273.233374734840.09594713648272.051535034420.2024628068350.638826912982-0.909926576413-0.420745079942-0.3971713638191.056690782820.359595667546-0.3038812563210.1830623050550.255474238213-0.00463302914684-0.07825464573710.464789810225-0.1462927502670.430516624225-44.108801682417.5320026568-23.5503308029
42.42301750489-1.98313265184-1.146917477593.886826805311.307515716822.498370435520.0429839793010.1301520430790.0348458878939-0.117619620040.078856577732-0.226848022181-0.007122388423070.270873908984-0.1271635057950.124390226894-0.00413249917286-0.01006467046630.399101626559-0.05629908588110.21464302617-26.528368211827.8488852092-17.8461578722
53.0040464813-1.83961946795-0.9248516799114.423706460090.5271519985212.62498328548-0.1226525887830.00253931377612-0.3938731231380.09788972529280.130364194161-0.2094845809190.6242883546950.441195973908-0.03721884839240.3261525489290.11696390529-0.05397881008990.374523913555-0.08735498636010.259228140982-27.258136799716.06714320966.32151887552
61.98071521107-0.914611287659-0.1255804418331.759302125840.06138191097942.167172967860.08592155011530.1441970352940.119204978526-0.05184106673260.0401257345454-0.257506361745-0.114743224260.482750940701-0.1161460507050.159206651741-0.01423366886560.03072033087290.376809130455-0.07219539487110.272206538221-25.601976373729.3016828404-13.9721951525
74.43362517821.473297814120.3284020858534.049188036430.1279333850875.28116006640.118998313605-0.927370252975-0.5434234794371.10982993008-0.180475602975-0.4273088975130.4846976209570.3961151987080.06452962359750.6582153924330.00216877940385-0.02189078787250.4407438915370.05568381128830.362077700236-39.943460666124.676669583246.1463038208
81.98954493781-0.8095663055950.3110056271062.12102511634-0.8457645290392.30018728896-0.124253828904-0.3003461866720.1198028668580.579769718458-0.005352483966320.0740067676203-0.268727649440.1056446923520.1219011678380.417981123044-0.04276758266150.06912291709350.260776111493-0.0464759640520.220650865738-46.401189512633.326568688234.3614284999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 19 through 82 )BA19 - 821 - 64
22chain 'B' and (resid 83 through 129 )BA83 - 12965 - 111
33chain 'B' and (resid 130 through 193 )BA130 - 193112 - 175
44chain 'B' and (resid 194 through 293 )BA194 - 293176 - 275
55chain 'B' and (resid 294 through 431 )BA294 - 431276 - 413
66chain 'B' and (resid 432 through 614 )BA432 - 614414 - 596
77chain 'A' and (resid 334 through 409 )AB334 - 4091 - 76
88chain 'A' and (resid 410 through 527 )AB410 - 52777 - 194

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