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- PDB-8wds: Crystal structure of BF.7 RBD complexed with human ACE2 -

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Entry
Database: PDB / ID: 8wds
TitleCrystal structure of BF.7 RBD complexed with human ACE2
Components
  • Angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / BF.7 / RBD / human ACE2
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 / viral translation / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / 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 / viral translation / 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 / viral life cycle / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / 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 / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / Potential therapeutics for SARS / membrane fusion / Attachment and Entry / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / apical plasma membrane / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / 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. / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S2 superfamily, coronavirus / 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, 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: 3.4 Å
AuthorsLi, W. / Xie, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: EMBO J / Year: 2024
Title: Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.
Authors: Weiwei Li / Zepeng Xu / Tianhui Niu / Yufeng Xie / Zhennan Zhao / Dedong Li / Qingwen He / Wenqiao Sun / Kaiyuan Shi / Wenjing Guo / Zhen Chang / Kefang Liu / Zheng Fan / Jianxun Qi / George F Gao /
Abstract: Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding ...Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding and immune evasion are recognized as two major drivers for evolution of the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, the underlying mechanism of interplay between two factors remains incompletely understood. Herein, we determined the structures of human ACE2 complexed with BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5 RBDs. Based on the ACE2/RBD structures of these sub-variants and a comparison with the known complex structures, we found that R346T substitution in the RBD enhanced ACE2 binding upon an interaction with the residue R493, but not Q493, via a mechanism involving long-range conformation changes. Furthermore, we found that R493Q and F486V exert a balanced impact, through which immune evasion capability was somewhat compromised to achieve an optimal receptor binding. We propose a "two-steps-forward and one-step-backward" model to describe such a compromise between receptor binding affinity and immune evasion during RBD evolution of Omicron sub-variants.
History
DepositionSep 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 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
A: Angiotensin-converting enzyme 2
B: Spike protein S1
C: Angiotensin-converting enzyme 2
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,60315
Polymers240,9134
Non-polymers2,69011
Water00
1
A: Angiotensin-converting enzyme 2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6107
Polymers120,4562
Non-polymers1,1535
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Angiotensin-converting enzyme 2
D: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,9938
Polymers120,4562
Non-polymers1,5376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.695, 137.349, 154.765
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Angiotensin-converting enzyme 2


Mass: 92556.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein Spike protein S1


Mass: 27899.781 Da / Num. of mol.: 2 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

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Sugars , 3 types, 9 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: 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-ROHGlycam 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
[][D-1-deoxy-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.: 7 / 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

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Non-polymers , 1 types, 2 molecules

#5: Chemical ChemComp-ZN / ZINC ION


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

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Details

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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M Tris pH 8.0, 20% w/v PEG 6000 (MD1-29-1-43)

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Mar 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 33045 / % possible obs: 90.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 60.77 Å2 / CC1/2: 0.991 / Net I/σ(I): 1.1
Reflection shellResolution: 3.4→3.52 Å / Num. unique obs: 3299 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 3.4→29.42 Å / SU ML: 0.4076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4821
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 1543 4.85 %
Rwork0.2318 30255 -
obs0.2336 31798 87.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.17 Å2
Refinement stepCycle: LAST / Resolution: 3.4→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12812 0 167 0 12979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004313380
X-RAY DIFFRACTIONf_angle_d0.680918199
X-RAY DIFFRACTIONf_chiral_restr0.04511936
X-RAY DIFFRACTIONf_plane_restr0.00542348
X-RAY DIFFRACTIONf_dihedral_angle_d14.64664847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.510.3711480.33767X-RAY DIFFRACTION24.98
3.51-3.640.31031120.29062160X-RAY DIFFRACTION69.29
3.64-3.780.30621420.28142747X-RAY DIFFRACTION88.86
3.78-3.960.32321550.2633003X-RAY DIFFRACTION95.73
3.96-4.160.28231330.25923092X-RAY DIFFRACTION98.38
4.16-4.420.25211530.23343059X-RAY DIFFRACTION97.72
4.42-4.760.26121540.21993071X-RAY DIFFRACTION97.46
4.76-5.240.27261660.21173052X-RAY DIFFRACTION97.46
5.24-5.990.27211530.22163097X-RAY DIFFRACTION97.07
5.99-7.530.26971700.21373028X-RAY DIFFRACTION94.81
7.53-29.420.21731570.19173179X-RAY DIFFRACTION95.04
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)
12.1037677109-0.4743227249890.6823015146210.9916727117390.2022631287321.357791424320.0386343992182-0.147414278486-0.1263421147390.1538682094980.00735522339284-0.02060535535530.249597688499-0.251258565258-0.01373879201480.388911191932-0.0285478531977-0.03628288545110.337823973122-0.0654825858770.2442684467842.19223049962-20.029496237249.4528693445
22.37659260231-0.506899276060.2720170997182.0767883405-0.298766777151.73508149117-0.0174191236068-0.5052805795170.7580345022060.17941525064-0.03091469246350.166285694851-0.428304724359-0.356776277850.06268550067670.492608622058-0.0246261511819-0.02970989013190.837617244684-0.2622144258460.651250376744-35.1208901972.611600164631.3989647865
32.5596149217-0.240902156619-0.9671764730520.8778715673290.5350887280371.3391615033-0.240504378412-0.131613569741-0.480533510137-0.0256762873834-0.101363960161-0.00830388490410.457109417383-0.07391057271620.2665583297830.441381358240.0462838129090.1171529283490.2621391659680.09388481582190.429976157768-58.1033567059-30.17839800559.21972901509
42.05786953688-0.252766258787-0.1241158020792.074976813970.05874916588482.616545117190.0825923709737-0.1934694341530.7050315750330.22186947396-0.1507181606310.299075842895-0.293495192888-0.3198406363530.1485110096710.4071584970310.009700033778160.15905979390.5114516179-0.1836354842950.708234607931-92.5020213982-4.3287441896529.6728724263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 19:614 OR RESID 901:903 ) )A19 - 614
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 19:614 OR RESID 901:903 ) )A901 - 903
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 333:527 OR RESID 601:601 ) )B333 - 527
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 333:527 OR RESID 601:601 ) )B601
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID 19:614 OR RESID 901:905 ) )C19 - 614
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID 19:614 OR RESID 901:905 ) )C901 - 905
7X-RAY DIFFRACTION4( CHAIN D AND RESID 333:527 )D333 - 527

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