[English] 日本語
Yorodumi
- PDB-8bh5: SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bh5
TitleSARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody
Components
  • Beta-27 heavy chain
  • Beta-27 light chain
  • Nanobody C1
  • Spike protein S1
KeywordsIMMUNE SYSTEM / Viral Protein/Immune system / SARS-CoV-2 / Omicron / BA.2.12.1 / RBD / Beta-27
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 / membrane fusion / Attachment and Entry / 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 / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / 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
PHOSPHATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHuo, J. / Zhou, 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 Discov / Year: 2022
Title: Humoral responses against SARS-CoV-2 Omicron BA.2.11, BA.2.12.1 and BA.2.13 from vaccine and BA.1 serum.
Authors: Huo, J. / Dijokaite-Guraliuc, A. / Nutalai, R. / Das, R. / Zhou, D. / Mentzer, A.J. / Fry, E.E. / Mongkolsapaya, J. / Ren, J. / Stuart, D.I. / Screaton, G.R.
History
DepositionOct 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
H: Beta-27 heavy chain
L: Beta-27 light chain
E: Spike protein S1
C: Nanobody C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,93418
Polymers84,3664
Non-polymers1,56714
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-32 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.846, 99.987, 56.486
Angle α, β, γ (deg.)90.000, 104.105, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Antibody , 3 types, 3 molecules HLC

#1: Antibody Beta-27 heavy chain


Mass: 23532.479 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 Beta-27 light chain


Mass: 23129.549 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 Nanobody C1


Mass: 14659.114 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)

-
Protein / Sugars , 2 types, 2 molecules E

#3: Protein Spike protein S1


Mass: 23044.971 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: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 171 molecules

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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.03 Å3/Da / Density % sol: 59.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium citrate tribasic dehydrate, pH 5.5, 18% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.38→55 Å / Num. obs: 38493 / % possible obs: 94.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 48.2 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.071 / Net I/σ(I): 6.3
Reflection shellResolution: 2.38→2.42 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1396 / CC1/2: 0.13

-
Processing

Software
NameVersionClassification
GDA1.19_4092data collection
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7zxu
Resolution: 2.38→54.78 Å / SU ML: 0.3416 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.4156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2325 1842 4.97 %
Rwork0.1857 35221 -
obs0.188 37063 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.92 Å2
Refinement stepCycle: LAST / Resolution: 2.38→54.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5705 0 101 158 5964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00185953
X-RAY DIFFRACTIONf_angle_d0.49838075
X-RAY DIFFRACTIONf_chiral_restr0.0415881
X-RAY DIFFRACTIONf_plane_restr0.00411034
X-RAY DIFFRACTIONf_dihedral_angle_d11.77532131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.3754600.34021535X-RAY DIFFRACTION51.42
2.44-2.510.3589990.32312099X-RAY DIFFRACTION70.86
2.51-2.60.36471350.30972466X-RAY DIFFRACTION82.86
2.6-2.690.32311600.2872570X-RAY DIFFRACTION88.41
2.69-2.80.29021480.24312782X-RAY DIFFRACTION93.94
2.8-2.920.28181550.22942915X-RAY DIFFRACTION99.64
2.92-3.080.24251750.21262931X-RAY DIFFRACTION100
3.08-3.270.27581370.20572992X-RAY DIFFRACTION100
3.27-3.520.22481530.18132990X-RAY DIFFRACTION99.97
3.52-3.880.21111400.17242948X-RAY DIFFRACTION100
3.88-4.440.17951780.14662960X-RAY DIFFRACTION100
4.44-5.590.21281410.13363006X-RAY DIFFRACTION100
5.59-54.780.2071610.16983027X-RAY DIFFRACTION99.91
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)
12.81747013823-0.84302157048-0.7222111569942.6453389221.461974952672.71578112217-0.0598355461695-0.0838667258035-0.1112790022610.123635261516-0.03858593544930.0197694298890.1977374751240.1292044488210.113694566740.3813949229270.02831225198580.0004502802393270.3611346335770.02307529918980.33080539375438.7990614018-38.488771899933.6745675448
21.593562862820.584218320471-0.05724818666191.538218340640.8177875155821.75687226288-0.382081284855-0.1072587228740.167247707260.1104549853190.2441177265920.268072078117-0.148863572738-0.4130347099650.0807504721050.482833477316-0.04997195712010.00716628236880.5564736752590.1159209612030.39364489535310.1068840576-22.160373241845.3147307582
35.499285416060.4412803411461.835796862752.790963965720.5721116909953.567436608190.122493232117-0.283587631771-0.6214291875640.2079909146890.1594236975460.248915235380.183737123659-0.379836456934-0.2360164401170.287007685661-0.0149827765001-0.00973653432180.3283863722080.06190958099070.3890925153245.83983293358-27.685018960642.6131874331
49.392973327490.182821101484-1.468031770614.20411278513-1.734779415932.816731595060.4058218287960.5117082794210.299159816746-0.258799070835-0.285059431858-0.210971591609-0.198196976983-0.0679034689361-0.08426930655360.482232776070.152039164798-0.002176625543590.485441243647-0.04243586826490.35932521798529.7582120889-27.828950333211.6960387613
53.27346477687-0.986919252707-0.1904706235613.431345306360.2208404825263.10478336451-0.0163473331350.320073412347-0.368090819041-0.3096176152620.07073745353030.1382413484530.233849126177-0.0346664800136-0.03358601788720.4220918812720.0334198742929-0.06374027574730.47433820986-0.05598685405090.39824933212429.1738165804-40.583075946816.0199824718
62.96507720405-1.35193621181-0.8343961972251.903573150910.9466108753870.5235625002240.01417509427970.291532187145-0.272761956332-0.0212506298949-0.1035920571440.182624505796-0.0085674486368-0.03647612906090.09711188490680.3273468324430.0178759862192-0.05453895521730.3598198495680.03564292113710.28130901582818.5976695655-26.870968581223.6036128083
73.53383186170.7604650600641.027310177651.955399365922.353726925712.89426226863-0.03566080179740.1730577876960.320208171072-0.218460467574-0.001916079608080.220925662868-0.4763658365630.210594559242-0.07431029331280.400596870352-0.04655914281550.04604381195790.4178636938420.05144873270350.46859721517211.2744683521-12.029107043330.5579637769
82.93744550541-0.747412463564-0.3931834662754.139000806481.712643995565.289739214350.0719419151077-0.05989084764940.08508383380350.02718007584540.09030084338820.167189273384-0.0797282759702-0.202598830496-0.1411865217610.291813682155-0.0263036229455-0.02841992893950.3421319235470.04678264917090.389175273345.80511478634-12.975364542533.8862975433
98.42802443030.843415759574-0.641791186184.50440716628-0.8436890450865.54354856368-0.4017391951810.9111428891860.197907802918-0.881188610178-0.00804432076607-1.36159144048-0.2923513140491.080189710170.1399025959040.6941000725930.1318430855550.2247934615550.7521449209190.1252512548420.83350348288673.5562159723-38.12376959544.0919992937
103.309227854162.573961883390.324941955098.07950315733-0.3939915598645.524813692210.3321025906980.837048551905-0.0522257291020.02751760727430.015191086194-1.526816541760.05513087699171.05641872535-0.3058295094360.483911387290.02617975444550.09395905609490.6071922084890.07082493257240.7758866188574.1941903055-42.184037033311.675562718
112.94328144579-1.29014338271-1.085361920172.00517860568-1.260667491747.468309102060.713085374249-0.01361390982841.045195968430.07852421474-1.25929525581-1.46538467379-1.091037191750.9634434725360.5189828215050.884082684112-0.1288976311270.0579805389080.7498455762220.1623303847541.0540696651772.7291993945-25.30876263919.50997699133
121.3404489491-2.3831307466-0.8422736245156.13709119287-2.052236129937.781320306160.455911511201-0.076573245964-0.786243909180.9685501334540.299070758223-2.49833701033-0.3382162885821.11324504376-0.6125946512150.615438145954-0.0563094173469-0.2208196106540.627722975657-0.1039319110081.3102878617477.8441582853-29.364251272219.3538637005
131.792388728920.833726052307-1.044907337154.86483630420.02406354373975.813163291710.129247709567-0.03663190424690.2526447878740.213338916911-0.0313323959364-0.440521850759-0.0657536388134-0.14080653507-0.1263543542860.3494328802280.0266897007893-0.00350611562480.3318488192690.01325183270790.38354013949961.287065134-37.852174393617.9947706759
143.58404948236-0.163007481756-0.2206740129743.51527248504-0.24135223261.69265099468-0.03585698907490.0703184827467-0.0519685325019-0.11001254282-0.077367297548-0.3749645167350.03356274385450.1854676782290.1143185721880.2892767425680.05615357591380.02857819958070.3193743183340.03571268757170.27229620999258.8113954431-39.428125666812.7663641519
153.568389047970.160874442299-1.053770148972.765543535411.895828264672.83816676528-0.247589411448-0.76234013106-0.4946068151230.280027576897-0.222709238858-0.267838917950.127562399280.4570505323280.5045207042060.3902777960920.0909660037345-0.102675590250.4289692499780.05140599287040.38196178046962.8537450967-48.763967035520.3599536882
163.190472459271.6067083277-0.8859361659457.59564544334-2.025429055878.86496797078-0.426262386866-0.208823751665-1.382938145670.5382617906740.2038066626630.4298278646790.918608049006-0.2307652831330.2201972030980.60336620231-0.02097861194860.06967701248490.355160467290.03917634589610.66210681295245.8654189695-57.644834396322.1767491347
172.022633645950.541917812342-0.5196826926221.54871236671-1.077365278550.921222282227-0.2558293966690.284417622526-0.2787026767-0.7228505170730.205324891682-0.1418460634070.406555760871-0.09701950773420.1616297788220.4779352227520.05067623671090.06897535660740.428942803624-0.03129833165580.39075595320846.9949906192-44.784606682811.4521245608
180.681659687511-0.03132331234890.5443528424055.93821243104-0.2592096747138.059744984790.07075844645010.67910414480.373588055620.503926453814-0.212088800991-1.3773024275-0.3482872956981.062759721940.0183287194790.421254336972-0.050303883437-0.004900293164750.4630422649250.05676207133250.69839027131671.9082473667-36.170457877514.4196900434
197.81484591663-2.53184313560.8178973346932.0558571018-2.974954720757.75945764457-0.283669554223-1.347293164010.5071065652491.487984521660.410455733581-0.0727456326212-1.08655235983-0.513225835253-0.004207354566110.884866018569-0.0365721774522-0.06135405119560.586827102386-0.1522384192870.68135066942159.5390287229-11.960136103831.3411074409
202.011234587880.687003372661-2.493227646990.9292093286280.6385677239472.76647747107-0.428543807240.3656239312221.58730634193-0.5141133574680.0633719751015-1.50667180093-1.85115183449-0.5212515411290.2293919524450.7680456733680.02395431925760.2126426482290.5970938611390.08177963465540.9486737560956.41925645472.9037751569712.3540851635
212.97735586523-2.658244581130.2731580798054.76602476193-0.9265326944513.180088719560.135738538523-0.3638140461450.6801039468071.16579836079-0.209547592922-1.146795822280.1265620812260.657148165026-0.06951018005680.823639404890.0297014875241-0.2002088754490.514848834658-0.1868878197550.89768834957466.7286870603-13.760706418528.1823869682
228.60095562037-4.16110719483-0.7803821123667.72140003643-2.010192461584.382376687830.2654946229040.433950394072-0.1874119092420.465825007617-0.00460342438981-0.0343679045257-0.196999617487-0.0163450097816-0.2304184012810.523005454549-0.01932387240340.05423837326760.381672313635-0.07868371924450.59294348325657.9528691285-15.496152839116.0808838604
236.28889221056-1.590003497550.8368868120585.98544202885-0.7811051194996.679515556950.0822516288609-0.2455528355960.4522749588450.286466886814-0.0411795635144-1.66161765015-0.2256758547041.06746745313-0.3796181769630.390384469099-0.0564224874214-0.1082043903710.50656698857-0.1498842035870.89179915784472.9094386726-16.268877716418.1079433917
247.34217085473-1.957867323310.9148497290797.24239221610.164758291455.087168904240.2045616432520.774810163721.04693049544-0.3405903675750.128850939116-1.70254175909-0.6609317141510.845682019965-0.3373768997780.554031529117-0.02900540294870.1927471288730.4695020663010.0599032640670.85639411915567.5046720984-9.2130389511313.2049311323
253.9559664252-2.59640448945-1.309367045536.13852899594-0.8064209800742.818802512210.3425105204-0.02870359564640.7792675678010.110751943278-0.182874761812-1.07598594019-0.1942508366090.519943182076-0.03515395841150.613465122743-0.0806115212530.0299434068010.468432644156-0.0458755329530.75879267269661.5423676683-7.5594398036718.2121442736
266.03296085893-1.77035684551-0.5625672172135.739558628070.3026753098973.73520363418-0.272673574999-0.4991924961410.3374428010951.118925291310.225768077337-0.1607247138590.526347543591-0.09589677959090.07241496563050.56420100060.04377433306940.01981115712010.310006325454-0.01487423822690.44129964204260.3298356434-21.869591373322.1980558602
274.091745724420.0775229783559-4.03309322682.980950820483.3219085897.848997457730.5861714390021.18394865370.001905049773080.3108050024850.159817692479-0.490607771337-1.25373145638-0.592943159006-0.663685053380.6414732374710.07363300512230.05312841556170.4296648990940.0938490887070.5830011409551.7136340388-2.1133890739613.7734366586
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 113 )HA1 - 1131 - 113
22chain 'H' and (resid 114 through 138 )HA114 - 138114 - 136
33chain 'H' and (resid 139 through 220 )HA139 - 220137 - 218
44chain 'L' and (resid 1 through 30 )LF1 - 301 - 30
55chain 'L' and (resid 31 through 62 )LF31 - 6231 - 62
66chain 'L' and (resid 63 through 137 )LF63 - 13763 - 137
77chain 'L' and (resid 138 through 163 )LF138 - 163138 - 163
88chain 'L' and (resid 164 through 213 )LF164 - 213164 - 213
99chain 'E' and (resid 333 through 349 )EJ333 - 3491 - 17
1010chain 'E' and (resid 350 through 364 )EJ350 - 36418 - 32
1111chain 'E' and (resid 365 through 375 )EJ365 - 37533 - 43
1212chain 'E' and (resid 376 through 393 )EJ376 - 39344 - 61
1313chain 'E' and (resid 394 through 421 )EJ394 - 42162 - 89
1414chain 'E' and (resid 422 through 459 )EJ422 - 45990 - 127
1515chain 'E' and (resid 460 through 469 )EJ460 - 469128 - 137
1616chain 'E' and (resid 470 through 479 )EJ470 - 479138 - 147
1717chain 'E' and (resid 480 through 506 )EJ480 - 506148 - 174
1818chain 'E' and (resid 507 through 525 )EJ507 - 525175 - 187
1919chain 'C' and (resid 1 through 8 )CQ1 - 81 - 8
2020chain 'C' and (resid 9 through 17 )CQ9 - 179 - 17
2121chain 'C' and (resid 18 through 32 )CQ18 - 3218 - 32
2222chain 'C' and (resid 33 through 52 )CQ33 - 5233 - 52
2323chain 'C' and (resid 53 through 60 )CQ53 - 6053 - 60
2424chain 'C' and (resid 61 through 73 )CQ61 - 7361 - 73
2525chain 'C' and (resid 74 through 99 )CQ74 - 9974 - 99
2626chain 'C' and (resid 100 through 117 )CQ100 - 117100 - 117
2727chain 'C' and (resid 118 through 124 )CQ118 - 124118 - 124

+
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://pdbjlvh1.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