[English] 日本語
Yorodumi
- PDB-7xby: The crystal structure of SARS-CoV-2 Omicron BA.1 variant RBD in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xby
TitleThe crystal structure of SARS-CoV-2 Omicron BA.1 variant RBD in complex with equine ACE2
Components
  • Angiotensin-converting enzyme
  • Spike protein S1
KeywordsVIRAL PROTEIN / complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space ...Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / Maturation of spike protein / viral translation / 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 / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / endocytosis involved in viral 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 / proteolysis / extracellular region / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
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. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / 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
BROMIDE ION / Angiotensin-converting enzyme / Spike glycoprotein
Similarity search - Component
Biological speciesEquus caballus (horse)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsXu, Z.P. / Liu, K.F. / Han, P. / Qi, J.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100752 China
CitationJournal: Nat Commun / Year: 2022
Title: Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses.
Authors: Xu, Z. / Kang, X. / Han, P. / Du, P. / Li, L. / Zheng, A. / Deng, C. / Qi, J. / Zhao, X. / Wang, Q. / Liu, K. / Gao, G.F.
History
DepositionMar 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiotensin-converting enzyme
B: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,48110
Polymers117,7152
Non-polymers7668
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-39 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.975, 113.975, 152.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Angiotensin-converting enzyme


Mass: 92299.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: ACE2 / Production host: Escherichia coli (E. coli)
References: UniProt: F6V9L3, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike protein S1


Mass: 25415.879 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 / Variant: Omicron BA.1 / 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
#4: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br / Feature type: SUBJECT OF INVESTIGATION
#5: 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
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium bromide, 0.1M Bis-Tris propane 8.5, 20 % (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 27326 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 13.1
Reflection shellResolution: 2.85→2.96 Å / Rmerge(I) obs: 1.252 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2682

-
Processing

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

6lzg


Resolution: 2.85→32.9 Å / SU ML: 0.3713 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.9189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2626 1252 4.89 %
Rwork0.2282 24364 -
obs0.2298 25616 93.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.83 Å2
Refinement stepCycle: LAST / Resolution: 2.85→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6416 0 21 0 6437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256613
X-RAY DIFFRACTIONf_angle_d0.58078985
X-RAY DIFFRACTIONf_chiral_restr0.041940
X-RAY DIFFRACTIONf_plane_restr0.00391162
X-RAY DIFFRACTIONf_dihedral_angle_d16.33622407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.960.3592940.33971410X-RAY DIFFRACTION50.49
2.96-3.10.3171440.29952636X-RAY DIFFRACTION92.79
3.1-3.260.31371460.28012867X-RAY DIFFRACTION99.47
3.26-3.460.3021460.28212869X-RAY DIFFRACTION99.93
3.46-3.730.26681360.24312868X-RAY DIFFRACTION99.87
3.73-4.10.25311540.21582858X-RAY DIFFRACTION99.7
4.1-4.70.26051340.19092909X-RAY DIFFRACTION99.35
4.7-5.910.22031600.19982901X-RAY DIFFRACTION99.48
5.91-32.90.22691380.20273046X-RAY DIFFRACTION99.07
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)
10.279093373193-0.3178529820570.7727997758471.31101755262-0.1481559442443.09304747128-0.04065215514050.0946062071549-0.03736060213930.00574330124109-0.0588640600365-0.395123822946-0.3825652606530.676151048747-0.05762040477230.431520439571-0.1628707838580.1134204078020.633446327634-0.01399083896170.3957802248940.6170681856-25.940554870710.3811345419
20.190502182953-0.370594141855-0.3957256289530.6484463847661.00429946841.13802852285-0.323593529672-0.00354011373013-0.4010096269320.1609606286010.3805668934-0.9543118620780.1168967410680.228782930727-0.1163669912390.43925598639-0.1578280382850.0235700820230.710339386823-0.1166770505721.0127589940946.5441227219-40.63382754197.12995341789
31.53546955628-0.05940699849670.1654419888481.622542219180.814127390791.337176467240.03628022802840.04477757450310.0575831205515-0.2329730557590.177807821995-0.472760230882-0.2628698353020.350361119943-0.08968223342440.341456196153-0.08091657305650.1330428017440.339851140873-0.1111123116310.50919580592538.5049065825-50.5264562848-12.7622471379
40.414905853958-0.127467240049-0.2663436558092.45361666561.437994752351.683836968080.007241228396390.051591467349-0.00699076838826-0.341594958361-0.0881689116471-0.00209133496306-0.272972356077-0.074970627640.06510566257020.2745684754-0.02040811751490.02245208190090.241762910063-0.01303574469980.25602291117923.4426110346-43.9739537282-9.4087340697
52.38603626198-1.66195551830.7048003982172.53148479064-0.6337753943671.4745287008-0.177454602733-0.2410347258111.4337136610.0578801014433-0.05838717174210.505774719066-0.361171392219-0.1774925400860.06808130257260.524041320893-0.102207383038-0.004802071476770.361917474474-0.1225966732780.76085620176821.66150415320.045717768055328.1190468702
62.61316516278-0.726454482888-0.4337100695072.172759932640.5537401629351.11859735302-0.0975849518862-0.322961453520.567900913541-0.446235509969-0.03214673409080.382779119351-0.443206970577-0.4334147210620.1238103195530.540749984190.0398628676414-0.01744222574270.387218346303-0.113445971270.52722383813412.2340664378-6.0147538172527.0896923847
71.688266797530.0140073135062-0.01111032965631.361031747830.2131638873561.31673862-0.0410277273336-0.2761299045650.009816662994270.191624510183-0.01860706254650.044316891440.05394840052940.1618518591340.0853158285790.396117167818-0.111166535393-0.003992239206950.3726445718610.02934762823780.24393984169427.8672804758-15.96836380629.0601843079
80.3257481161130.473206868254-0.7881251284653.28202346095-0.2161371999162.520619988260.1176479456490.319027817743-0.112021100937-0.0017232795614-0.110555702264-0.4473507904890.01196784657960.889998903250.1576233343640.386735317525-0.02751904321520.09781124523270.353657740824-0.01985633361420.22593801345536.63303877-19.293619136321.6053023649
92.30984139324-1.408662830260.5120168822493.553904926910.7507551116280.944697781543-0.0741304710434-0.7107838357270.5081272692360.686399846041-0.2670974375320.691825954485-0.348359066555-0.1830175953620.1567032878740.509849357307-0.05604658428480.07835885686440.395159664227-0.1516774540310.60669594088112.4934754406-2.7910783777834.14832007
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 82 )AA19 - 821 - 64
22chain 'A' and (resid 83 through 129 )AA83 - 12965 - 111
33chain 'A' and (resid 130 through 250 )AA130 - 250112 - 232
44chain 'A' and (resid 251 through 614 )AA251 - 614233 - 596
55chain 'B' and (resid 333 through 358 )BC333 - 3581 - 26
66chain 'B' and (resid 359 through 409 )BC359 - 40927 - 77
77chain 'B' and (resid 410 through 479 )BC410 - 47978 - 147
88chain 'B' and (resid 480 through 506 )BC480 - 506148 - 174
99chain 'B' and (resid 507 through 527 )BC507 - 527175 - 195

+
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