[English] 日本語
Yorodumi
- PDB-6zcz: Crystal structure of receptor binding domain of SARS-CoV-2 Spike ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zcz
TitleCrystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody.
Components
  • EY6A heavy chain
  • EY6A light chain
  • NanobodySingle-domain antibody
  • Spike protein S1
KeywordsVIRAL PROTEIN / EY6a / RBD / Spike glycoprotein / SARS-CoV-2 / human neutralizing antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / fusion of virus membrane with host plasma membrane / 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 / membrane / identical protein binding / plasma membrane
Similarity search - Function
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 ...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
Biological speciesSevere acute respiratory syndrome coronavirus 2
Lama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsZhou, D. / Zhao, Y. / Fry, E.E. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, China, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust101122/Z/13/Z United Kingdom
CAMS Innovation Fund for Medical Sciences (CIFMS)2018-I2M-2-002 China
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient.
Authors: Daming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / ...Authors: Daming Zhou / Helen M E Duyvesteyn / Cheng-Pin Chen / Chung-Guei Huang / Ting-Hua Chen / Shin-Ru Shih / Yi-Chun Lin / Chien-Yu Cheng / Shu-Hsing Cheng / Yhu-Chering Huang / Tzou-Yien Lin / Che Ma / Jiandong Huo / Loic Carrique / Tomas Malinauskas / Reinis R Ruza / Pranav N M Shah / Tiong Kit Tan / Pramila Rijal / Robert F Donat / Kerry Godwin / Karen R Buttigieg / Julia A Tree / Julika Radecke / Neil G Paterson / Piyada Supasa / Juthathip Mongkolsapaya / Gavin R Screaton / Miles W Carroll / Javier Gilbert-Jaramillo / Michael L Knight / William James / Raymond J Owens / James H Naismith / Alain R Townsend / Elizabeth E Fry / Yuguang Zhao / Jingshan Ren / David I Stuart / Kuan-Ying A Huang /
Abstract: The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID- ...The COVID-19 pandemic has had an unprecedented health and economic impact and there are currently no approved therapies. We have isolated an antibody, EY6A, from an individual convalescing from COVID-19 and have shown that it neutralizes SARS-CoV-2 and cross-reacts with SARS-CoV-1. EY6A Fab binds the receptor binding domain (RBD) of the viral spike glycoprotein tightly (K of 2 nM), and a 2.6-Å-resolution crystal structure of an RBD-EY6A Fab complex identifies the highly conserved epitope, away from the ACE2 receptor binding site. Residues within this footprint are key to stabilizing the pre-fusion spike. Cryo-EM analyses of the pre-fusion spike incubated with EY6A Fab reveal a complex of the intact spike trimer with three Fabs bound and two further multimeric forms comprising the destabilized spike attached to Fab. EY6A binds what is probably a major neutralizing epitope, making it a candidate therapeutic for COVID-19.
History
DepositionJun 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 12, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 21, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.5Dec 22, 2021Group: Database references / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 1.6Jan 24, 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
E: Spike protein S1
F: Nanobody
H: EY6A heavy chain
L: EY6A light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,95011
Polymers87,5274
Non-polymers4237
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-80 kcal/mol
Surface area33900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.867, 177.867, 87.715
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

-
Antibody , 3 types, 3 molecules FHL

#2: Antibody Nanobody / Single-domain antibody


Mass: 16714.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody EY6A heavy chain


Mass: 24346.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody EY6A light chain


Mass: 23315.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 2 molecules E

#1: Protein Spike protein S1


Mass: 23150.891 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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 , 2 types, 6 molecules

#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25 % (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.64→89 Å / Num. obs: 30147 / % possible obs: 99.2 % / Redundancy: 9.4 % / Biso Wilson estimate: 70.64 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.209 / Net I/σ(I): 5
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 5.3 % / Num. unique obs: 1419 / CC1/2: 0.3 / % possible all: 93

-
Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
PHENIX1.18.1_3865refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YLA

6yla


Resolution: 2.65→35.26 Å / SU ML: 0.4913 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 33.5005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2595 1267 4.73 %
Rwork0.2146 25517 -
obs0.2167 26784 89.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.95 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5819 0 20 0 5839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00165976
X-RAY DIFFRACTIONf_angle_d0.43548122
X-RAY DIFFRACTIONf_chiral_restr0.0401890
X-RAY DIFFRACTIONf_plane_restr0.00381039
X-RAY DIFFRACTIONf_dihedral_angle_d12.95572112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.760.5185180.4111699X-RAY DIFFRACTION21.76
2.76-2.890.37551320.38192694X-RAY DIFFRACTION83.98
2.89-3.040.35851610.34263137X-RAY DIFFRACTION99.85
3.04-3.230.30911720.30283162X-RAY DIFFRACTION99.94
3.23-3.480.2961430.25373182X-RAY DIFFRACTION99.97
3.48-3.830.27031430.21983188X-RAY DIFFRACTION99.97
3.83-4.380.26521600.18483140X-RAY DIFFRACTION100
4.38-5.510.21861490.16263163X-RAY DIFFRACTION100
5.51-35.260.21871890.17973152X-RAY DIFFRACTION99.85
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)
12.70305317429-1.747357933671.254134466154.14405189722-0.3382199210232.398315636660.1000334182310.686095300994-0.700481852612-0.0315689694316-0.03652794439230.7171822117060.435138174546-0.012912491322-0.1302959384860.5361349416070.04032660679120.03169373028980.720957768973-0.1131338100341.42131828322-5.33761003079-43.18932946633.31966659921
24.76727958253-3.095793950110.296696529884.355338256490.1740234328793.065803090570.207187805120.401826020445-0.0933028545132-0.10878408448-0.2301327490260.03667211707810.01621810660960.1927585715760.02698817181450.3148069822240.02645704591580.0212736158350.5230646197140.002059260169020.845453350818-10.1234832261-25.77248692433.73160986101
33.825043999092.663111164051.666944944672.33334872279-0.2143786599725.994046734630.03098322022431.00272282972-0.195361990762-0.249773240214-0.3522736267730.285220194364-0.142550017245-0.730443464430.1883137856310.390147110509-0.00865851232009-0.09391278941110.7636738572710.03602993013770.590877957014-37.9947616386-9.23541479855-22.4844559785
45.670133311981.734745315651.511729723350.5590144453470.9327940180878.935648424610.164827407407-0.51611135823-2.393013379230.3102999652890.3897598383320.3686961295461.326490947310.0527293405663-0.5270068465390.631039144935-0.008679220463910.09075130361280.5171100507240.1727588762171.13410992371-30.9003647404-19.8020483346-15.3302737718
52.870605125390.167283368386-0.9525733303091.329529782030.5984040389223.563406007460.211611155116-0.07831008904220.0166601020861-0.223447544769-0.0833088646828-0.133441659251-0.03793150729890.1034889278820.1048921364140.460399784477-0.02349960678090.1326441412380.978570305110.424249776540.266978396623-27.5805058857-8.28907956072-18.1588527386
60.9845808340580.827157615022-1.176092039065.78521087497-3.02530904092.217591655510.03546941648980.32473978340.458201875074-0.707594226298-0.0888690823955-0.354234156607-0.2431762643720.403657660880.07967962482650.580719369989-0.0801623183406-0.01013505315560.901035125280.4430400163740.361557212955-25.2261262325-4.01252215271-18.4719442598
72.65346096544-3.002068257470.1258253990323.61934263116-0.8918996585285.74489299318-0.09869137508810.01847477124420.1642253962710.104643648795-0.0688257814930.6024992668890.110768305187-0.34015167390.3254725689560.33647509461-0.03681743759320.01710787349950.5788306284820.1098444071871.00081411028-33.0562668391-9.96061668028-10.0349943709
82.313494022762.892477768091.692627045837.40522624530.3317402723122.494206001660.35102403160.6806441684311.84013727186-1.102802920510.477308867031-0.329724641304-1.677756982680.891174432044-0.6774214982270.67322602335-0.0431849727970.1392910987660.661364675910.1862799352460.816268384677-37.35096297573.32304653167-20.0843606537
91.277367859470.7277033898790.0991902536871.051885813681.587109325154.04077982352-0.235838895927-0.0365637525683-0.142945768029-0.04250923200110.4788341286690.3015387933490.224299366215-0.410294309147-0.2844185404950.523699367176-0.008780012786730.03010662586990.7496501590720.1234622991360.248503236988-27.873171385-10.6833642575-20.667570386
101.69752964258-0.3030120113551.036418049521.81149332377-0.9063414134124.48306345942-0.2424626032920.8427901622430.445858231675-0.390106373362-0.0903703096397-0.1952537102960.1283768360471.190276105830.2883442439430.415921946816-0.007372697186420.01987644015650.6772823903910.1394650556660.731989684963-19.757962094-12.6324626956-12.9697932404
110.504447972033-0.106866391595-0.7074434973670.826619405859-0.01801603223991.351076731710.0221951746622-0.0928130148574-0.0445701862943-0.100803912314-0.0312589499433-0.0264614028787-0.1151859550090.0339063282313-0.281023058520.5856433706120.1656112440080.1928668794950.8354511200780.415326884903-0.259296179375-37.8976488184-2.62265980999-26.4048440819
124.652832674035.10523918448-4.781057244036.57824983421-5.642646846625.131912531790.226756981878-0.0785192556464-0.63140404538-0.416258830564-0.748928456455-0.9540909692460.5648453923060.7201445581360.7361279939640.4868670818420.140566539495-0.08474587097860.42101838007-0.1222289911561.0541399217329.9011726519-43.14527118043.50659202858
133.309771699540.656955077692-0.6433502499993.10880298288-0.5217806317623.38613466995-0.1121569294280.1186620434470.01743713066230.058053461252-0.01180077406790.1027926251770.1337726830850.1863583104420.110223311390.3357215600750.01948390609890.02822328672630.376205504825-0.02673316051760.69051631952918.8599063245-44.40213723365.99801772365
144.714416429512.15179350507-0.5818351728563.338159517921.853640005981.98145839949-0.1366076616090.2079251979230.610690193784-0.612660688155-0.08417973131950.422960473048-0.5029000866380.2610090633340.2204884461740.3569424635990.101845581159-0.07402185060640.365933021597-0.01269238621660.7569327616125.1799260203-35.79898691164.27889408458
153.5954750290.355974876117-0.3524256230122.194089611070.170337453781.06512149736-0.0483944242565-0.345089170341-0.2547351639360.3405104339220.027922927594-0.474043482851-0.0449593375490.209418151752-0.01684944064370.534561014492-0.00541135076304-0.1365425145680.3611606464680.07781996810750.69787449625632.3284333327-33.33710894412.3179204632
164.10270879948-0.5223222992460.9311205005222.803489345160.9054648071315.510037042920.05421672220820.03470460569140.01020568082110.2101015574050.381577592994-1.01075445010.7298430131780.755597261319-0.3801707436670.6182289342640.0661458361777-0.06705375365540.457702648674-0.09831492366571.139197023750.6165392265-25.798899156314.615732966
174.48728567470.928045693981-1.30352565690.43239503215-1.295217200784.5159477809-0.1045843543050.0981467996389-0.3445243955850.5728913724510.0180414639326-1.302919451760.1227592569960.8948473382510.1063746449090.5732897734460.0522022826399-0.2357819564890.560586186164-0.07813601948861.2471841117753.7414770889-22.499481669113.0695339431
183.22601783941-0.05936449264951.112090339233.26337922547-0.1797835009994.55661741295-0.0730188330317-0.3640992553150.5370417330670.4385458985810.0148632304170.327178229616-0.560298922343-0.134577627511-0.01983768753850.5072461227690.003000920612150.04640249917460.388760631787-0.009349783054360.70844177369718.1914842909-33.748730548326.6258502532
193.73624368687-0.9729600929291.958989666273.65710707632-2.127049063624.42868976674-0.0995842001159-0.314636048252-0.4372406451160.5735274231420.1314866020940.0121915129073-0.418948947184-0.1147691156120.05130767810060.6517775738790.04207664587240.009593875990990.380633043171-0.08563522108050.5891460202819.5020647199-33.505206839330.2048082183
201.91450973331.121079395130.1179444348454.121483887290.9486153751932.697593950530.343844629141-0.123747389877-0.07286064208380.797549173117-0.2427585997220.06797415534080.0927399081276-0.452995703862-0.1211459099780.5281458043410.0648904888342-0.01409185596130.4626685610050.00497493997270.89681575372223.6647852385-27.583629714724.4118878587
214.99895957603-0.530446460754-2.255814718344.59316709668-0.1577697822246.97384985933-0.3088423382560.2285467840090.1320155204470.02958385767960.316592714014-1.90711361182-4.33460119021E-50.9249418348620.08585547000710.700890702846-0.01958136072830.03736374186710.554014666928-0.1055179485491.5308770906752.675126346-11.157493417511.0398168695
222.028032050161.44967351982-1.709386178526.00882532968-4.685899541926.003120415980.05262346744870.07466371095580.1100189493060.05740249259440.2229870947470.4332283913960.233307354435-0.0331158559559-0.3489542783640.6081205574460.0719815214729-0.2358938624390.523786667536-0.08936044976291.2247760829640.3505510131-13.74799015519.387515447
236.64308265062.50718570622-5.003621963296.07436320131-3.588814968078.292872690490.0950458372780.1232721285380.7734554734260.664627842643-0.00917136634836-0.401297857025-0.2461201354250.153649863848-0.1785293135540.686155299542-0.0209659658819-0.1354491423320.3787446082690.04173973753661.0800210252545.88099234-2.8762153351916.9189604511
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 333 through 393 )EA333 - 3931 - 61
22chain 'E' and (resid 394 through 527 )EA394 - 52762 - 195
33chain 'F' and (resid 2 through 17 )FC2 - 171 - 16
44chain 'F' and (resid 18 through 32 )FC18 - 3217 - 31
55chain 'F' and (resid 33 through 39 )FC33 - 3932 - 38
66chain 'F' and (resid 40 through 52 )FC40 - 5239 - 51
77chain 'F' and (resid 53 through 83 )FC53 - 8352 - 82
88chain 'F' and (resid 84 through 91 )FC84 - 9183 - 90
99chain 'F' and (resid 92 through 99 )FC92 - 9991 - 98
1010chain 'F' and (resid 100 through 120 )FC100 - 12099 - 119
1111chain 'F' and (resid 121 through 126 )FC121 - 126120 - 125
1212chain 'H' and (resid 1 through 23 )HD1 - 231 - 23
1313chain 'H' and (resid 24 through 83 )HD24 - 8324 - 83
1414chain 'H' and (resid 84 through 98 )HD84 - 9884 - 98
1515chain 'H' and (resid 99 through 143 )HD99 - 14399 - 138
1616chain 'H' and (resid 144 through 173 )HD144 - 173139 - 168
1717chain 'H' and (resid 174 through 224 )HD174 - 224169 - 219
1818chain 'L' and (resid 1 through 61 )LE1 - 611 - 61
1919chain 'L' and (resid 62 through 90 )LE62 - 9062 - 90
2020chain 'L' and (resid 91 through 114 )LE91 - 11491 - 114
2121chain 'L' and (resid 115 through 129 )LE115 - 129115 - 129
2222chain 'L' and (resid 130 through 183 )LE130 - 183130 - 183
2323chain 'L' and (resid 184 through 215 )LE184 - 215184 - 215

+
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