[English] 日本語
Yorodumi
- PDB-8bbo: SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bbo
TitleSARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab
Components
  • IGH@ protein
  • Immunoglobulin kappa light chain
  • Spike glycoprotein
KeywordsVIRAL PROTEIN / SARS-CoV-2 / BA.2 mAb / RBD / BA.2-36
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / 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 / 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 ...immunoglobulin complex / adaptive immune response / 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 / 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 / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Surface glycoprotein / Immunoglobulin kappa light chain / IGH@ protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZhou, D. / 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: 2023
Title: Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses.
Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de ...Authors: Aiste Dijokaite-Guraliuc / Raksha Das / Daming Zhou / Helen M Ginn / Chang Liu / Helen M E Duyvesteyn / Jiandong Huo / Rungtiwa Nutalai / Piyada Supasa / Muneeswaran Selvaraj / Thushan I de Silva / Megan Plowright / Thomas A H Newman / Hailey Hornsby / Alexander J Mentzer / Donal Skelly / Thomas G Ritter / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / / Cornelius Roemer / Thomas P Peacock / Neil G Paterson / Mark A Williams / David R Hall / Elizabeth E Fry / Juthathip Mongkolsapaya / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or ...In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.
History
DepositionOct 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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
R: Spike glycoprotein
H: IGH@ protein
L: Immunoglobulin kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4464
Polymers70,2243
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-19 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.141, 99.141, 86.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

-
Components

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


Mass: 22935.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Homo sapiens (human) / References: UniProt: A0A8B6RM54
#2: Antibody IGH@ protein


Mass: 23849.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Production host: Homo sapiens (human) / References: UniProt: Q6GMX6
#3: Antibody Immunoglobulin kappa light chain / Immunoglobulin kappa light chain EU


Mass: 23439.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX7
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / 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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2% (v/v) PEG400, 0.1M imidazole pH7.0 and 24% (w/v) PEG MME 5000.

-
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: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.75→55 Å / Num. obs: 21850 / % possible obs: 100 % / Redundancy: 26.8 % / Biso Wilson estimate: 64.52 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.46 / Rpim(I) all: 0.09 / Net I/σ(I): 7.5
Reflection shellResolution: 2.75→2.8 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1103 / CC1/2: 0.39

-
Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PS6

7ps6


Resolution: 2.75→49.57 Å / SU ML: 0.4107 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.6982
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 1102 5.06 %
Rwork0.2242 20668 -
obs0.2256 21770 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.7 Å2
Refinement stepCycle: LAST / Resolution: 2.75→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 14 0 4752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184868
X-RAY DIFFRACTIONf_angle_d0.46746622
X-RAY DIFFRACTIONf_chiral_restr0.0425736
X-RAY DIFFRACTIONf_plane_restr0.004850
X-RAY DIFFRACTIONf_dihedral_angle_d10.34971739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.870.31161130.33792538X-RAY DIFFRACTION98.08
2.87-3.030.35571530.30152542X-RAY DIFFRACTION100
3.03-3.210.34381200.29722612X-RAY DIFFRACTION99.96
3.22-3.460.33141170.27472599X-RAY DIFFRACTION99.96
3.46-3.810.29221660.24862554X-RAY DIFFRACTION100
3.81-4.360.23011280.20562600X-RAY DIFFRACTION100
4.36-5.50.19661610.17692581X-RAY DIFFRACTION100
5.5-49.570.21631440.18322642X-RAY DIFFRACTION99.86
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)
13.39998855016-0.03778093574732.09826530840.1331086499290.1462619576731.924354954220.643779088774-0.008366661714580.930991121137-0.889967706008-0.355549476935-0.171442574439-1.607180365261.10024791202-0.1799430810111.25521358064-0.3341009394860.3094327993540.929836758925-0.2305577817230.765018806655-33.36509842713.273462984821.30879266791
25.08577836764-2.22839059616-2.036590646145.803304541615.340890780564.881164905350.56779292425-0.5009493639371.67844384927-0.109086120441-0.4392173861390.145010636865-2.414431270510.267321936216-1.530577984831.65960712548-0.6456637257210.9679253659761.09607940533-0.137943102520.281661311033-29.285135361611.0522676453-5.63561616447
37.31064673625-1.12424841323-4.2318503963.62951165616-1.443092737756.380142579540.810543676923-0.5590345524231.321484852120.4835577813670.548062767004-0.743727888349-1.28634264226-0.0860368662211-0.4148693021971.34344848206-0.7393078253030.1115584196431.26984412343-0.6098305910870.667113067575-26.432510224713.280164667610.2621690989
4-0.01195104338920.0338669919928-0.014839300550.00402458241832-0.008596765664570.021013061782-0.212751405590.3275048319991.55532044826-0.447567097053-0.320461969995-0.726085798888-1.23222470379-0.207239691590.02974155779011.96971109605-0.3818185031370.3604789004661.223128493690.05524655553521.65802358658-20.110417999118.76337911970.252222464716
52.17730972308-0.775205389851-1.548704519292.400177623650.8308401892652.910097370580.210564305156-0.6471311878040.27124784577-0.146345171560.0542496415773-0.682360165821-0.6563352991491.43549704301-0.2709520173230.594659897632-0.2275018670060.04872322778061.2486942793-0.2393449363150.647989415452-24.0538008279-4.534754705736.26883007698
60.1445001372330.54064753192-0.03957583230043.96009559182-0.08642031641220.0544359612597-0.247947073030.0277182932682-0.535376344216-0.781353691669-0.406017053107-1.47406133290.2911305818580.1087567366440.01764294355180.7957215244810.1362712389950.06066876652351.386649602980.07533606821691.07203526245-20.5785316853-26.7726487977-0.0589722745294
72.193250419172.672173313671.261361870363.409496917462.55495459246.612134913010.512603051547-1.0289527805-0.7885521891551.73207017801-0.578459376147-1.907125421841.974708184210.7833700250150.7503110206730.8757025833660.190896716756-0.08862536019641.208627965260.2640545543081.05861066146-25.5723844752-25.68866937483.74281385817
81.8356162731-0.644309318163-0.0220413844152.254933535062.075651075392.489226177990.266252275641-0.794446112919-0.0340852790763-0.146470892319-0.0738951350957-0.587908032088-0.3437895671471.62157011968-0.04044995780180.553878022031-0.151897617371-0.05325285875721.16059813025-0.3202921880570.744466511422-30.2591130218-2.2960262235313.1795691615
93.530478661840.227277003929-0.6609974739062.45142744192-0.08811152761964.179093335750.3546490641070.52319228044-0.440524324398-0.426326540054-0.1925199707270.3678937663750.6383841140110.211989284024-0.09313122808540.6349062348570.131365166550.03558113587280.5670131692420.07457821597310.604785621935-54.5663180919-31.9950554186-0.0206584039304
102.71096802951.344799597250.1090439239144.451300731630.4480415510293.33289422034-0.18465764572-0.191531870629-0.138199048932-0.06666281058850.203844593048-0.02446255859590.008456004115190.351330704177-0.04490521150690.3587019397580.07269722604820.03548267147350.4107976467050.03815023455730.370487335638-47.7626577623-24.8377847434.27879040546
114.287318106011.2262863480.8168002995063.276574938581.100153847552.5079467624-0.3514227681850.03692390222690.00744556572414-0.4580129089880.2292077310950.302100493972-0.04302745220430.08302737631340.05450194025170.3992765923680.06133810922190.07098916418610.4045675253870.03159485222250.352364150171-56.7538131677-25.22744987950.237160716745
120.8384421855031.11006409525-0.6956389154384.1074166994-0.02935006976630.916172427396-0.137753875382-0.3639445518951.16123142056-0.3350315518960.00540550178763-1.123882193530.0173630179937-0.321633709359-0.01288987276360.3841946349720.0659008119013-0.07652845990880.5969250751040.02408100557540.654252740315-92.4246616549-27.3787719768-8.74340664941
134.366339034681.119115280360.09690024968581.39220966638-0.372906184331.328149746760.01114895412310.109505926109-0.7809189967650.103959459522-0.116921895937-0.255738026577-0.06095590038320.4178774788150.1510402546030.3108275101040.0464009426430.03793421202540.4137293057940.08463913977040.532075507834-80.2935230215-29.3705524686-9.604002812
146.76907440578-0.63530655397-1.799586197920.4044626069080.1837352472191.4232741459-0.6553064426110.91985257045-1.566223084510.19058267544-0.0317160241315-0.1422755367480.525782593719-0.007347990601830.1794327553860.6153463570720.01768245891690.04131122173540.579976735281-0.07533749800840.773413035458-86.7371033318-36.1965563994-12.4982191996
153.40458260831-1.192480579460.6672662301941.08915156604-0.1280971912171.948029350250.0843722404749-0.1372363712270.2205719507690.2322750195410.4694241825780.596046186903-0.8457167548150.0241908321287-0.3514770691110.666466739975-0.01134461858110.1018665579070.3868054059260.002837279531350.599708360843-64.8247677519-2.504724342962.45122943776
163.8289252247-0.4805588900390.6717246698983.22412865929-0.4757851896173.003982864980.192710446091-0.1100361143950.400977501775-0.02072766570050.07495071487350.0228248107682-0.4153132526970.342344302891-0.1975669132280.392024981826-0.08525181096790.1170670711140.32870959652-0.03135093837930.367542310607-54.0773959048-5.01546141871-0.178647009006
173.61863281854-1.325682276711.814555310682.062942263370.5245392656873.33607226011-0.155558824456-0.1641818648480.2114686343570.0601284524340.2428008184330.121324363711-0.3016907220670.118296885203-0.2405606177520.51644050036-0.02875277892530.141664917640.418040654694-0.01249500802270.434227689785-57.1861132858-4.564466660011.53709240885
181.410744645120.02702383000010.4953420860140.06887669052260.1094059440320.29293767340.3621239752880.5732974934740.560412327358-0.393240696828-0.03421126321280.504215564273-0.715354671421-0.257951106785-0.3929437829370.6859127726460.0737434045119-0.01417608263140.5795757584840.1699584310050.713113305253-78.5144416171-5.10794450329-6.41888233431
192.802578971870.384859510966-0.6339699555123.70823430985-0.9055815279732.21989159229-0.409748739264-0.0714939467077-0.633198526388-0.1842766795780.458419823564-0.507385909125-0.124682271392-0.566386472963-0.1379404802680.4814410800950.02777605790460.02541213782680.5479973860640.1634075805780.609030376229-88.3103033106-24.5336414122-2.36882795362
203.22218377081.42119551621-2.35998530391.47974417957-2.155448094453.02610198439-0.137927689535-0.985594933448-0.2287610480261.189561814420.02239392416140.31319221431-1.20538819334-1.23354661549-0.2814484269580.6475250593130.1590480536560.1130024587890.9049188712420.1451208249270.6630071151-93.441801941-19.85581977529.08353810909
213.570531645210.04205607079181.253130044923.07093167023-1.759624653292.764993138880.4349323759990.006866236348290.0477669516190.363337438016-0.1088952156880.481652381977-0.849809124426-0.1285139645020.1685214488620.6661691398470.157804446694-0.01326246899890.5281680182950.06303448242820.518099920926-79.3647774703-16.2998799498-3.33634046977
222.711446470320.166196312894-0.217705573152.87624331093-1.522023368622.86672067450.0979462929994-0.419520632652-0.08696494617830.6823108949060.2815553264220.901232507184-0.311227793601-0.519822074436-0.2888159583310.4593502722730.1284619771520.08047848613630.7331991161870.1654406221840.721941288382-94.3981042091-23.09185897763.89969248522
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'R' and (resid 335 through 353 )RA335 - 3531 - 19
22chain 'R' and (resid 354 through 364 )RA354 - 36420 - 30
33chain 'R' and (resid 365 through 380 )RA365 - 38031 - 46
44chain 'R' and (resid 381 through 394 )RA381 - 39447 - 60
55chain 'R' and (resid 395 through 469 )RA395 - 46961 - 135
66chain 'R' and (resid 470 through 479 )RA470 - 479136 - 145
77chain 'R' and (resid 480 through 494 )RA480 - 494146 - 160
88chain 'R' and (resid 495 through 515 )RA495 - 515161 - 181
99chain 'H' and (resid 1 through 16 )HC1 - 161 - 16
1010chain 'H' and (resid 17 through 100 )HC17 - 10017 - 100
1111chain 'H' and (resid 101 through 125 )HC101 - 125101 - 125
1212chain 'H' and (resid 126 through 140 )HC126 - 140126 - 140
1313chain 'H' and (resid 141 through 209 )HC141 - 209141 - 209
1414chain 'H' and (resid 210 through 222 )HC210 - 222210 - 222
1515chain 'L' and (resid 1 through 18 )LD1 - 181 - 18
1616chain 'L' and (resid 19 through 61 )LD19 - 6119 - 61
1717chain 'L' and (resid 62 through 101 )LD62 - 10162 - 101
1818chain 'L' and (resid 102 through 112 )LD102 - 112102 - 112
1919chain 'L' and (resid 113 through 142 )LD113 - 142113 - 142
2020chain 'L' and (resid 143 through 154 )LD143 - 154143 - 154
2121chain 'L' and (resid 155 through 173 )LD155 - 173155 - 173
2222chain 'L' and (resid 174 through 211 )LD174 - 211174 - 211

+
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