[English] 日本語
Yorodumi
- PDB-7bei: Crystal structure of the receptor binding domain of SARS-CoV-2 Sp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bei
TitleCrystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab
Components
  • COVOX-150 heavy chain
  • COVOX-150 light chain
  • Spike glycoproteinSpike protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / antibody / germline / V-gene / receptor-binding-domain / spike / neutralisation / protection / glycosylation / valency / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding / endocytosis involved in viral entry into host cell ...Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / suppression by virus of host tetherin activity / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / Attachment and Entry / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral entry into host cell / viral envelope / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein, betacoronavirus / Spike receptor binding domain superfamily, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...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. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein, betacoronavirus / Spike receptor binding domain superfamily, coronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / 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
NITRATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhou, D. / Zhao, Y. / 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
CitationJournal: Cell / Year: 2021
Title: The antigenic anatomy of SARS-CoV-2 receptor binding domain.
Authors: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang ...Authors: Wanwisa Dejnirattisai / Daming Zhou / Helen M Ginn / Helen M E Duyvesteyn / Piyada Supasa / James Brett Case / Yuguang Zhao / Thomas S Walter / Alexander J Mentzer / Chang Liu / Beibei Wang / Guido C Paesen / Jose Slon-Campos / César López-Camacho / Natasha M Kafai / Adam L Bailey / Rita E Chen / Baoling Ying / Craig Thompson / Jai Bolton / Alex Fyfe / Sunetra Gupta / Tiong Kit Tan / Javier Gilbert-Jaramillo / William James / Michael Knight / Miles W Carroll / Donal Skelly / Christina Dold / Yanchun Peng / Robert Levin / Tao Dong / Andrew J Pollard / Julian C Knight / Paul Klenerman / Nigel Temperton / David R Hall / Mark A Williams / Neil G Paterson / Felicity K R Bertram / C Alistair Siebert / Daniel K Clare / Andrew Howe / Julika Radecke / Yun Song / Alain R Townsend / Kuan-Ying A Huang / Elizabeth E Fry / Juthathip Mongkolsapaya / Michael S Diamond / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and ...Antibodies are crucial to immune protection against SARS-CoV-2, with some in emergency use as therapeutics. Here, we identify 377 human monoclonal antibodies (mAbs) recognizing the virus spike and focus mainly on 80 that bind the receptor binding domain (RBD). We devise a competition data-driven method to map RBD binding sites. We find that although antibody binding sites are widely dispersed, neutralizing antibody binding is focused, with nearly all highly inhibitory mAbs (IC < 0.1 μg/mL) blocking receptor interaction, except for one that binds a unique epitope in the N-terminal domain. Many of these neutralizing mAbs use public V-genes and are close to germline. We dissect the structural basis of recognition for this large panel of antibodies through X-ray crystallography and cryoelectron microscopy of 19 Fab-antigen structures. We find novel binding modes for some potently inhibitory antibodies and demonstrate that strongly neutralizing mAbs protect, prophylactically or therapeutically, in animal models.
History
DepositionDec 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 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 / _citation_author.name
Revision 1.2Apr 28, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: COVOX-150 heavy chain
L: COVOX-150 light chain
E: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,57912
Polymers72,6453
Non-polymers9349
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-61 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)81.419, 150.709, 145.504
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11L-465-

HOH

-
Components

-
Antibody , 2 types, 2 molecules HL

#1: Antibody COVOX-150 heavy chain


Mass: 24726.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody COVOX-150 light chain


Mass: 24767.592 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

#3: Protein Spike glycoprotein / Spike protein / S glycoprotein / E2 / Peplomer protein


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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 221 molecules

#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.09 M of NPS (nitrate, phosphate and sulphate), 0.1 M MES/imidazole pH 6.5, 10% (w/v) PEG 8000 and 20% (v/v) ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→52 Å / Num. obs: 33837 / % possible obs: 84.4 % / Redundancy: 22 % / Biso Wilson estimate: 44.59 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.192 / Net I/σ(I): 12.5
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 847 / CC1/2: 0.651

-
Processing

Software
NameVersionClassification
GDA1.18.1_3865data collection
PHENIX1.18.1_3865refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZCZ
Resolution: 2.3→42.75 Å / SU ML: 0.339 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8355
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 1567 4.84 %
Rwork0.1837 30799 -
obs0.186 32366 80.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 55 213 5041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484938
X-RAY DIFFRACTIONf_angle_d0.72516719
X-RAY DIFFRACTIONf_chiral_restr0.0473759
X-RAY DIFFRACTIONf_plane_restr0.0047861
X-RAY DIFFRACTIONf_dihedral_angle_d15.55971761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.3191420.2904932X-RAY DIFFRACTION26.97
2.38-2.460.3563850.30411415X-RAY DIFFRACTION41.99
2.46-2.560.3045940.2921983X-RAY DIFFRACTION57.77
2.56-2.680.32711270.26472459X-RAY DIFFRACTION71.85
2.68-2.820.27861400.24283076X-RAY DIFFRACTION89.61
2.82-2.990.28561820.22163410X-RAY DIFFRACTION99.58
2.99-3.230.25641910.21523425X-RAY DIFFRACTION99.97
3.23-3.550.2651610.1923491X-RAY DIFFRACTION100
3.55-4.060.22941870.16753461X-RAY DIFFRACTION100
4.06-5.120.17452000.13373494X-RAY DIFFRACTION100
5.12-42.750.20061580.16153653X-RAY DIFFRACTION99.95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.96886623621-0.9633224653242.19588807774.068868592-1.935466804075.343663785160.216083528331-0.317709969686-0.291966018195-0.3544019422160.6462739466881.07393803370.617375466257-1.32606732937-0.9181642290920.390143630279-0.109608368127-0.02410509481080.549082981450.1376636920470.565722605007-15.4037954505-52.86857857089.18102473841
21.945940090570.0151609142275-0.2770851792212.57402168479-0.6175080030732.543960678030.0558305215336-0.08477264477670.249802880751-0.743550033890.07845415038910.1495664286190.576005798131-0.0491049849161-0.1421711704010.451790681776-0.0818384204974-0.04423075571960.3313193435960.009299810957830.395958834544-3.04486406321-59.48403484618.05109019871
30.8673973798990.142429629113-0.3925200077255.61010395976-1.689306622932.031383183180.0549040012294-0.171257147179-0.01363448816580.03919469332070.1871971806760.8297772694160.16264439879-0.587023656744-0.2660571264920.290142859053-0.03194600258240.04354414758770.4046021327960.04203658272280.471057959886-9.13610302862-28.18207002363.63589074837
40.2682542633390.9283288745030.3314148660645.36372357063-1.258557880352.15204267872-0.0265126745437-0.123722461647-0.0547618160798-0.01963645491230.1114909786930.280829082052-0.0452562995889-0.176571206894-0.05161175033510.216504455538-0.0373324079620.06779060250860.3152031147960.003562196652430.345353697529-3.7040520435-31.62546007364.42873414372
50.873632022098-0.3008229383570.6459243610993.02244586054-0.236061483753.837075567420.03167801196170.0838792698816-0.0449392633801-0.281033348335-0.1008105759280.0075657991269-0.0567774017018-0.1885314431530.03060932823720.2423430785230.00486203691036-0.02161268849420.318369637748-0.03503121068360.2486246943054.62743988432-4.63490009329-14.6362446095
62.2858158780.3264953882171.902956170821.301736981630.8476137977041.75772047916-0.1037495383510.05578401027160.456457445661-0.1394271060440.04828036962410.138857862272-0.44265565942-0.3630691192160.1719597399870.4010840749270.0484916413175-0.05167155107160.330185685848-0.004558945721640.3454343410212.969739456272.13004623663-20.3960887587
72.13376260802-0.57202186521-0.2714885919353.85504375432-3.241805716234.42280620719-0.111426907740.368577830258-0.235941437177-0.512019621508-0.0645115676304-0.1091823813990.2952829033980.2708374991710.2590950070530.790158964925-0.01373746158880.04227209779120.391222327402-0.0475697727550.3614975551995.46419894723-37.7114536677-20.5694737816
81.47343156074-0.177266961133-0.4040363155952.79552931973-2.007063871114.08884018658-0.1624831211620.246632971121-0.308937489098-0.9731794748120.1571061767940.3121711233770.659733599131-0.007852497282970.04171891747680.727967812-0.129080739926-0.05233574456160.338650580669-0.03145134394130.397832225402-2.05214861613-42.5575461038-15.3244574693
91.28768272705-0.0974830215961-0.9083583032092.59059565092-1.715918212291.94490529717-0.1920390958390.265479186277-0.34615397312-0.7667838409610.3666598635460.7205555798150.135274863028-0.423971742847-0.05749513499880.755018174575-0.170802385277-0.09205141182630.3978745617850.0009942903845550.397239733139-3.41721742627-35.3478132218-20.0731486832
100.213343911561-0.36089653465-0.01640261550322.54604015714-2.057955834912.99410481504-0.32322533641-0.1441055031160.141102404443-0.05816274729490.331770233422-0.04141139377240.162611457095-0.3715820466330.2105131378790.539885959866-0.0529961373811-0.02467011214310.3791928751880.0207897053660.4194163688664.35429888402-40.4937149083-4.0425671842
110.2709568823530.745030994606-0.5878519467672.34561880068-2.203882418312.121725522710.0268842021475-0.141634830995-0.433467685228-0.548706459369-0.145375912558-0.2505073564010.287123452247-0.3384896474630.05118434062720.733078072527-0.0323485843397-0.07023384437160.412841366815-0.04311212048420.3033872656524.7253896818-24.6356971564-30.8910503578
124.18736645360.8644344490940.4216542113533.81563182918-1.381237541132.969879803250.152953951246-0.06017772539160.103211744419-0.171813071292-0.00579920752594-0.02149559684110.27950718425-0.122227227215-0.1427004681280.2629832364220.03140189392690.02608340373430.2959591089080.002120670399970.21340900455913.5914478162-7.03809072199-21.5594991919
136.511240597441.216063045780.6605973674342.30276279486-1.701848548432.77939738105-0.06450387993120.57499145392-0.5623615727480.359891121489-0.229184720229-0.7657793014620.8431605866230.6565166289270.1395160238030.4073911151020.03701807367650.0470245492890.436313920280.008821984327830.40017147946325.748852268-12.3927110956-20.848918154
144.667934515151.819991964881.696207688162.188284325340.8232984278063.732197076660.301944228689-0.0673506144493-0.170133997118-0.208178290812-0.2480121672420.07536704153220.689225691188-0.0962788234915-0.009325226383720.4552212368540.0114076057834-0.02087663544120.2889611142140.01227180914430.2797408484586.62733365115-16.9199592918-22.3737396034
153.892635311921.407720388130.5760303458783.522201804330.9449704639193.448073595590.256481730144-0.1338271169160.02462713304240.0140932028158-0.241765255806-0.6158891452380.1240908662630.488409385442-0.07717578550560.3296954194740.05095172978940.04890080724290.3430009802490.08954905351240.35128844215422.9279948039-5.67526779538-17.8438055569
164.291769239041.767378345211.104064795594.780448177551.399070997213.94315464378-0.1084907957280.578278092455-0.259455893335-0.7467285180340.278090645143-0.9446065566140.08370671877670.760158722063-0.08957545283280.4028980176060.03418046810280.1214487771960.4961693192250.008201645837450.39487509243521.3329767639-9.70028125368-29.4227662811
174.1003322711-3.732149918491.120997176747.6446436095-3.910024784817.705289365230.0704571040482-0.0597183178119-0.66014274126-1.15931240590.0328185932691-0.2107989154411.50433021254-0.0926413201278-0.2954418925040.530722349008-0.07161419289660.01081500955890.3550972431790.02792736455970.5419415275610.825159359023-72.08776281214.8282370281
180.9823169257861.49725965607-1.515360909023.41238273042-4.587959048786.578322534650.245503497354-0.799995389864-0.0829714321141-0.00481242197498-0.792400900148-1.169023307650.4446076923112.071059361650.6759660771980.5355990633540.07726435785660.02597116862080.8934583558610.1912179267750.6998794164512.2653357884-66.257580391822.1872032726
193.69092629094-0.953555792664-0.2052702288574.12785621728-1.845421921943.190109063190.00310024818241-0.0328627447749-0.0673072086967-0.4537499864630.0489296901219-0.1321651083450.468882272171-0.0468276474893-0.04792479322160.29655543594-0.04258260843220.01437216935480.2503593808470.01461987197340.2949610464210.0681100016599-57.78301240849.04818435613
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 460 through 479 )EF460 - 479127 - 146
22chain 'E' and (resid 480 through 527 )EF480 - 527147 - 194
33chain 'H' and (resid 1 through 39 )HA1 - 391 - 39
44chain 'H' and (resid 40 through 113 )HA40 - 11340 - 113
55chain 'H' and (resid 114 through 179 )HA114 - 179114 - 175
66chain 'H' and (resid 180 through 220 )HA180 - 220176 - 216
77chain 'L' and (resid 1 through 18 )LD1 - 181 - 18
88chain 'L' and (resid 19 through 75 )LD19 - 7519 - 75
99chain 'L' and (resid 76 through 90 )LD76 - 9076 - 90
1010chain 'L' and (resid 91 through 104 )LD91 - 10491 - 104
1111chain 'L' and (resid 105 through 115 )LD105 - 115105 - 115
1212chain 'L' and (resid 116 through 146 )LD116 - 146116 - 146
1313chain 'L' and (resid 147 through 157 )LD147 - 157147 - 157
1414chain 'L' and (resid 158 through 176 )LD158 - 176158 - 178
1515chain 'L' and (resid 177 through 199 )LD177 - 199179 - 201
1616chain 'L' and (resid 200 through 215 )LD200 - 215202 - 217
1717chain 'E' and (resid 334 through 364 )EF334 - 3641 - 31
1818chain 'E' and (resid 365 through 393 )EF365 - 39332 - 60
1919chain 'E' and (resid 394 through 459 )EF394 - 45961 - 126

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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