[English] 日本語
Yorodumi
- PDB-8asy: SARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8asy
TitleSARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2
Components
  • Processed angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS CoV-2 / Omicron / BA.2.75 / ACE2 / complex / spike / RBD
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
TRIETHYLENE GLYCOL / Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsZhou, D. / Huo, J. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
CitationJournal: Cell Rep / Year: 2022
Title: A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75.
Authors: Huo, J. / Dijokaite-Guraliuc, A. / Liu, C. / Zhou, D. / Ginn, H.M. / Das, R. / Supasa, P. / Selvaraj, M. / Nutalai, R. / Tuekprakhon, A. / Duyvesteyn, H.M.E. / Mentzer, A.J. / Skelly, D. / ...Authors: Huo, J. / Dijokaite-Guraliuc, A. / Liu, C. / Zhou, D. / Ginn, H.M. / Das, R. / Supasa, P. / Selvaraj, M. / Nutalai, R. / Tuekprakhon, A. / Duyvesteyn, H.M.E. / Mentzer, A.J. / Skelly, D. / Ritter, T.G. / Amini, A. / Bibi, S. / Adele, S. / Johnson, S.A. / Paterson, N.G. / Williams, M.A. / Hall, D.R. / Plowright, M. / Newman, T.A.H. / Hornsby, H. / de Silva, T.I. / Temperton, N. / Klenerman, P. / Barnes, E. / Dunachie, S.J. / Pollard, A.J. / Lambe, T. / Goulder, P. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
History
DepositionAug 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Processed angiotensin-converting enzyme 2
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,91222
Polymers95,2942
Non-polymers2,61820
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint5 kcal/mol
Surface area35600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.261, 105.261, 220.753
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

-
Components

-
Protein , 2 types, 2 molecules AB

#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: 25154.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2

-
Sugars , 1 types, 6 molecules

#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / 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

-
Non-polymers , 3 types, 14 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1% (w/v) n-Octyl-b-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.85→76.2 Å / Num. obs: 29749 / % possible obs: 99.8 % / Redundancy: 26.8 % / Biso Wilson estimate: 58 Å2 / CC1/2: 0.971 / Rmerge(I) obs: 0.443 / Rpim(I) all: 0.086 / Net I/σ(I): 7.6
Reflection shellResolution: 2.85→2.9 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1411 / CC1/2: 0.279 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZF7

7zf7


Resolution: 2.85→76.18 Å / SU ML: 0.4938 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2647 1439 4.87 %
Rwork0.2173 28089 -
obs0.2195 29528 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.5 Å2
Refinement stepCycle: LAST / Resolution: 2.85→76.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 167 0 6631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00166802
X-RAY DIFFRACTIONf_angle_d0.43359219
X-RAY DIFFRACTIONf_chiral_restr0.0386974
X-RAY DIFFRACTIONf_plane_restr0.00331178
X-RAY DIFFRACTIONf_dihedral_angle_d11.55012463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.950.38211380.36432540X-RAY DIFFRACTION92.28
2.95-3.070.37821600.34322749X-RAY DIFFRACTION99.52
3.07-3.210.37041300.32592794X-RAY DIFFRACTION99.66
3.21-3.380.36031640.26782761X-RAY DIFFRACTION99.63
3.38-3.590.30631270.23942797X-RAY DIFFRACTION99.73
3.59-3.870.26481320.22672816X-RAY DIFFRACTION99.76
3.87-4.260.21511420.192829X-RAY DIFFRACTION99.9
4.26-4.870.21641540.17432840X-RAY DIFFRACTION100
4.87-6.140.24491430.19792896X-RAY DIFFRACTION99.87
6.14-76.180.23941490.18733067X-RAY DIFFRACTION99.84
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)
10.159473784575-0.38304072210.2386743779420.8101112267670.6509016636681.2341767955-0.1178120163020.00135579922680.08136781587770.04632460161940.00357031924460.276616798941-0.25040986252-0.15970747429-0.04731766638110.701620478461-0.008282095498570.1024130352070.930822589758-0.05054939046740.78773979125-38.353548029229.7495917875-11.3509502094
21.41922252183-1.44074005793-0.6430729389161.60773151093-0.07500736208261.779594774450.07880006051490.185988704962-0.0696376129959-0.0151974862851-0.2023428468470.03902533014470.180675846426-0.5123993319320.05715661544510.608718142097-0.0165040415706-0.08492313885970.695882966404-0.07266289687310.664507638271-38.046337588210.9271960321-37.8029456594
31.014721920920.03071943524010.089967417371.73631924052-0.2198649541121.42518171215-0.03465647601810.1163537044410.0511888357567-0.2017049603960.06822439073520.119025001127-0.04360079262160.184265951357-0.02829023259890.540933354193-0.05236211982420.02874423393720.677202602923-0.0633887430850.604769027512-17.713843113615.6473018453-33.9064226702
40.282563510742-0.0734438947114-0.04362021143790.6382572791310.2224093219050.5922808903370.032848835662-0.00126879875182-0.1920160213790.24004493619-0.1565578411950.216972268690.2773636781230.0865879197060.03124612463460.742369582118-0.02242970875410.04893057814140.870551919203-0.0408984185710.678569097811-21.09659371466.6274408585-8.90163281853
50.89220854787-0.3268092286040.06727936245740.933339024985-0.3114800389690.6204404178740.0582320651774-0.1518239914130.1482885618490.0209088528555-0.00962451470681-0.0784238149478-0.0960941945750.0802037724097-0.01505654019840.575178021593-0.04568028191970.02793465224460.70935958148-0.06671543341710.606327393687-16.312352860417.0053957825-30.1160674187
61.133163325680.2788642215950.1061965709281.057463779050.4783916646850.618235255454-0.240097221338-0.171108256535-0.6182454841510.05691554352120.4016643686580.128243996230.7259157665850.0866370325673-0.02728049080830.8747277792530.1481832598720.08689336552050.959541341614-0.04751251828130.781222928092-37.362241586623.012544186431.9431894441
70.0974643720322-0.1358944516340.04018181867140.149464749629-0.02917622675940.006969980148440.009454423176890.4321854054450.0804039284628-0.0871820449473-0.3509630035640.08186710032851.282557658570.5704363170580.03089881759961.244069776970.203476803768-0.04639702026691.23764226587-0.1693315562351.11184679696-25.692972676515.729590324329.2319362444
81.14871024095-0.5366818585880.6332195039911.26512037006-0.8298125212720.6076529099640.0991599609022-1.3840386293-0.6632994869830.551336481930.846183511751.54382066967-0.0699184360126-0.726531667227-0.01558892915921.00897673520.172904263892-0.07404159512131.00264820151-0.1483778392511.01952428759-21.179191255522.047741237139.850807635
90.734341885698-0.411142822608-0.4530454400180.48979818040.1607048872340.621739492058-0.3448591109250.0933772877751-0.219119765984-0.0510068618657-0.115301132232-0.2866426942140.3913557799580.836876946964-0.03680662696490.871882948301-0.1151468216890.02986443478420.973603485383-0.0887294892110.7796488786-28.454559244729.600185490720.1743350411
101.18129992431-0.706169740279-0.6360865169192.22042198530.4556333483911.48856694062-0.0504271216317-0.0564856893715-0.08495631197790.1849963709290.150192808447-0.129661789579-0.1425181602990.296393616901-0.07174996743810.749021067353-0.1047344424020.03850363889020.799347020411-0.08184697714870.789188797377-35.238163296331.296388559915.0806227879
110.0209984134841-0.5301818063550.4782805110295.24665252189-5.231723723755.290091926640.132247837617-0.209164951843-0.4686137139010.5733988910450.6216248340620.2210463660430.0358198247988-0.273753135839-0.03105280367481.475795928880.0765248646482-0.0583605399831.42309426357-0.07955574006540.942852505126-27.167078644225.605381081348.8857115749
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 334 through 364 )BC334 - 3641 - 31
77chain 'B' and (resid 365 through 380 )BC365 - 38032 - 47
88chain 'B' and (resid 381 through 393 )BC381 - 39348 - 60
99chain 'B' and (resid 394 through 421 )BC394 - 42161 - 88
1010chain 'B' and (resid 422 through 516 )BC422 - 51689 - 183
1111chain 'B' and (resid 517 through 533 )BC517 - 533184 - 200

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more