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- PDB-7nxc: Crystal structure of the receptor binding domain of SARS-CoV-2 P.... -

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Basic information

Entry
Database: PDB / ID: 7nxc
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike glycoprotein in complex with ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/HYDROLASE / SARS-CoV-2 B.1.1.7 variant / B.1.351 variant / P.1 variant / antibody / receptor-binding-domain / spike / neutralisation / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / HYDROLASE / VIRAL PROTEIN-HYDROLASE 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 / 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 / negative regulation of signaling receptor activity / carboxypeptidase activity / regulation of cytokine production / positive regulation of cardiac muscle contraction / viral life cycle / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / regulation of transmembrane transporter activity / brush border membrane / 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 / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / endopeptidase activity / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / Potential therapeutics for SARS / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / symbiont entry into host cell / membrane raft / apical plasma membrane / fusion of virus membrane with host plasma membrane / endoplasmic reticulum lumen / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / 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. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...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. / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
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: 3.14 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 China
Citation
Journal: Cell / Year: 2021
Title: Antibody evasion by the P.1 strain of SARS-CoV-2.
Authors: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M.E. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Lopez-Camacho, C. / Slon-Campos, ...Authors: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M.E. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Costa Clemens, S.A. / Naveca, F.G. / Nascimento, V. / Nascimento, F. / Fernandes da Costa, C. / Resende, P.C. / Pauvolid-Correa, A. / Siqueira, M.M. / Dold, C. / Levin, R. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S.C. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Hulswit, R.J.G. / Bowden, T.A. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
#1: Journal: Biorxiv / Year: 2021
Title: Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2
Authors: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Paesen, G.C. / Lopez-Camacho, C. / ...Authors: Dejnirattisai, W. / Zhou, D. / Supasa, P. / Liu, C. / Mentzer, A.J. / Ginn, H.M. / Zhao, Y. / Duyvesteyn, H.M. / Tuekprakhon, A. / Nutalai, R. / Wang, B. / Paesen, G.C. / Lopez-Camacho, C. / Slon-Campos, J. / Walter, T.S. / Skelly, D. / Clemens, S.A.C. / Naveca, F.G. / Nascimento, V. / Nascimento, F. / Dold, C. / Levin, R. / Dong, T. / Pollard, A.J. / Knight, J.C. / Crook, D. / Lambe, T. / Clutterbuck, E. / Bibi, S. / Flaxman, A. / Bittaye, M. / Belij-Rammerstorfer, S. / Gilbert, S. / Carroll, M.W. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Hulswit, R.J.G. / Bowden, T.A. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4187
Polymers93,3122
Non-polymers1,1065
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint11 kcal/mol
Surface area34950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.502, 103.502, 225.907
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 Processed angiotensin-converting enzyme 2


Mass: 70139.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Homo sapiens (human) / References: UniProt: Q9BYF1
#2: Protein Spike protein S1


Mass: 23171.953 Da / Num. of mol.: 1
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: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / 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
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: 3.24 Å3/Da / Density % sol: 62.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Imidazole pH 7.0 and 20% w/v Polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.14→70 Å / Num. obs: 22273 / % possible obs: 100 % / Redundancy: 25.7 % / Biso Wilson estimate: 87.49 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.5 / Rpim(I) all: 0.1 / Net I/σ(I): 5.3
Reflection shellResolution: 3.14→3.19 Å / Num. unique obs: 1047 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
GDA1.19_4092data collection
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LZG

6lzg


Resolution: 3.14→69.62 Å / SU ML: 0.4856 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2783 1094 4.93 %
Rwork0.2263 21090 -
obs0.2287 22184 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.4 Å2
Refinement stepCycle: LAST / Resolution: 3.14→69.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6405 0 70 0 6475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036656
X-RAY DIFFRACTIONf_angle_d0.59539048
X-RAY DIFFRACTIONf_chiral_restr0.0433962
X-RAY DIFFRACTIONf_plane_restr0.00411166
X-RAY DIFFRACTIONf_dihedral_angle_d13.55152404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.280.36061340.37382531X-RAY DIFFRACTION99
3.28-3.460.33971630.32932574X-RAY DIFFRACTION99.85
3.46-3.670.31841380.2872569X-RAY DIFFRACTION99.89
3.67-3.960.29871350.24442615X-RAY DIFFRACTION100
3.96-4.350.29221090.22442635X-RAY DIFFRACTION99.85
4.35-4.980.25271360.19362635X-RAY DIFFRACTION100
4.98-6.280.28641300.21342692X-RAY DIFFRACTION100
6.28-69.620.22661490.17992839X-RAY DIFFRACTION99.83
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)
10.270208886261-0.4053213211690.1476831595640.8893944828830.5376372881271.812594636190.005848556338840.0831957728821-0.0439320453624-0.06939307060780.0880175861154-0.035741517308-0.281884770196-0.200090258779-0.0426372429410.6668298638250.04243153710010.07842273500420.9345641734820.01259986453850.82715680595-37.69653338729.4008058597-12.0849312481
21.84577959819-0.779447789567-0.4526464594031.43808841970.2053379745841.283820262060.05886451303850.200658659396-0.1519149419390.0847261057126-0.2830725855830.2745188434560.326374424298-0.2803294505710.0943474643540.618509377897-0.0604953945628-0.03947187109270.750530725515-0.07789520898950.600181652937-38.190998780311.4665291489-38.9629088126
31.02856643336-0.2410377844250.240282465411.608166130720.2824304322971.01814949027-0.0559101297662-0.04915894711270.0677279222826-0.02689162586930.05464667122790.0761399223768-0.1632223194940.16021571566-0.06543467905990.733260846479-0.07990695402410.02408975325870.826806548346-0.04734347723040.667392101583-17.582786934515.286369961-35.091666176
40.6356974227270.1569284744120.4980299147951.73194346719-0.06676778861611.522624632150.0216998947126-0.110367995033-0.1869264930260.201441787413-0.1801516164210.3706049753650.3208804061950.04422711172270.106071477750.8274534375470.03157771481820.07091410516820.9399315232590.004637920160040.771589513317-21.31445558695.6651979727-10.3921720928
51.68989473377-0.6071967686620.00877133227620.855174748684-0.2712370230450.981893986902-0.009159715194270.03273990454430.1569814809-0.0426191400489-0.0497135123964-0.113603865079-0.02955063020230.06411278983690.03739832021210.66066260534-0.05960764286180.04857036449230.694225512668-0.05477614425330.60862397335-16.162706569916.4712967595-31.2565596867
61.340822361740.1068988977411.297161997610.681182535050.5231248236881.53444206098-0.324744458457-0.933444013057-0.7871727691370.616718554040.132844714030.3460170573540.161316808136-0.12674607813-0.1829565086031.058233145590.1997182852870.1764690279671.227382614450.2593042876020.912000725429-34.159007167519.637440161631.7214105627
70.636101784652-1.203379761420.03236550701242.89847589873-0.351108215290.155491715646-0.0379436472425-0.586852952752-0.2070835268410.34529439083-0.106584962047-0.5568233067670.5876933527671.44646066949-0.02050986134560.8917173663820.1536384373760.08099102242821.43376661860.01732823307910.832814808975-24.581996017420.955679633927.5424970629
80.873116814341-0.610718573714-0.1773444331490.728673748819-0.5526021751281.81764216932-0.387981069945-0.265948316689-0.2089108617850.2854168134660.288939013224-0.1791090174360.1884440492670.9919843436940.007594676341940.8445147490840.07059954400130.01349829047881.08318761197-0.01097074360090.754464604065-26.736750491126.339649703720.2526471956
90.811211308404-0.288052813376-0.519501385721.5860377042-0.4841802302060.6318259977230.251214426828-0.0384226600505-0.5420159406860.02812877356230.0436891496801-0.242098897428-0.3730075262320.00677694898641-0.05175861703850.7718271161140.0422736548517-0.07218093501510.646938639873-0.1010318789740.6666773297-35.979736957531.71138107915.0224123634
102.476148032762.10275332015-0.2753825301181.912891697740.04942253904462.086800484330.0471040416546-0.300913080020.0130580076932-0.363622459065-0.2933179974180.261514803605-1.17416135638-0.0929797552034-0.0713282660941.051401305290.04057187717440.09499550175040.920064594944-0.1196220541180.787508042688-40.591550351143.01105063025.70868135228
115.372979843660.5219697449461.832495982082.037836339811.52924655597.182396327810.0129906056998-0.2123580295710.02603527249830.3375948937050.0004277157592940.5652248749970.0577048075479-0.33774869898-0.4934603323520.6289667075880.1375782837370.03296445392250.880174449078-0.09300916437670.994393979623-33.630729555817.79095918986.72600741713
121.684348017192.744221160080.08127711349556.65823850487-2.42201749983.498336114410.721407166333-0.8258013592480.4582543915152.29380046193-0.4149444342350.0457870601061-0.306887645380.262467782785-0.1951139975031.31801600720.0625869389805-0.028034903631.20569821832-0.1056540825331.21959440248-27.957531170924.561549422834.6676957443
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 129 )AA19 - 1291 - 111
22chain 'A' and (resid 130 through 193 )AA130 - 193112 - 175
33chain 'A' and (resid 194 through 293 )AA194 - 293176 - 275
44chain 'A' and (resid 294 through 431 )AA294 - 431276 - 413
55chain 'A' and (resid 432 through 614 )AA432 - 614414 - 596
66chain 'B' and (resid 333 through 370 )BF333 - 3701 - 38
77chain 'B' and (resid 371 through 409 )BF371 - 40939 - 77
88chain 'B' and (resid 410 through 442 )BF410 - 44278 - 110
99chain 'B' and (resid 443 through 469 )BF443 - 469111 - 137
1010chain 'B' and (resid 470 through 494 )BF470 - 494138 - 162
1111chain 'B' and (resid 495 through 506 )BF495 - 506163 - 174
1212chain 'B' and (resid 507 through 527 )BF507 - 527175 - 195

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