[English] 日本語
Yorodumi
- PDB-8qh0: Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qh0
TitleCrystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194
Components
  • Cv2.3194 Heavy chain
  • IGK@ protein
  • Spike protein S1
KeywordsVIRAL PROTEIN / Coronavirus Neutralizing Antibody
Function / homology
Function and homology information


immunoglobulin complex / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / adaptive immune response ...immunoglobulin complex / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / adaptive immune response / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / 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 C1-set ...: / 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
Similarity search - Domain/homology
PROLINE / Spike glycoprotein / IGK@ protein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsFernandez, I. / Rey, F.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: iScience / Year: 2024
Title: Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2.
Authors: Cyril Planchais / Ignacio Fernández / Benjamin Chalopin / Timothée Bruel / Pierre Rosenbaum / Maxime Beretta / Jordan D Dimitrov / Laurine Conquet / Flora Donati / Matthieu Prot / ...Authors: Cyril Planchais / Ignacio Fernández / Benjamin Chalopin / Timothée Bruel / Pierre Rosenbaum / Maxime Beretta / Jordan D Dimitrov / Laurine Conquet / Flora Donati / Matthieu Prot / Françoise Porrot / Delphine Planas / Isabelle Staropoli / Florence Guivel-Benhassine / Eduard Baquero / Sylvie van der Werf / Ahmed Haouz / Etienne Simon-Lorière / Xavier Montagutelli / Bernard Maillère / Félix A Rey / Pablo Guardado-Calvo / Hervé Nozach / Olivier Schwartz / Hugo Mouquet /
Abstract: Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly ...Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly neutralizing antibodies cloned from the memory B cells of a single convalescent individual after infection with ancestral SARS-CoV-2. Cv2.3194, a resilient class 1 anti-RBD antibody, remains active against Omicron sub-variants up to BA.2.86. Cv2.3132, a near pan-Sarbecovirus neutralizer, targets the heptad repeat 2 membrane proximal region. When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail exhibiting a local dose-dependent synergy. Thus, remarkably robust neutralizing memory B cell antibodies elicited in response to ancestral SARS-CoV-2 infection can withstand viral evolution and immune escape. The cooperative effect of such antibody combination may confer a certain level of protection against the latest SARS-CoV-2 variants.
History
DepositionSep 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Spike protein S1
H: Cv2.3194 Heavy chain
L: IGK@ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9937
Polymers70,2693
Non-polymers7244
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-21 kcal/mol
Surface area27690 Å2
Unit cell
Length a, b, c (Å)54.388, 89.186, 174.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 2 types, 2 molecules AL

#1: Protein Spike protein S1


Mass: 23068.695 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 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P0DTC2
#3: Protein IGK@ protein


Mass: 22821.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGK@ / Production host: Homo sapiens (human) / References: UniProt: Q6PJF2

-
Antibody / Sugars , 2 types, 2 molecules H

#2: Antibody Cv2.3194 Heavy chain


Mass: 24379.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): FreeStyle293 / Production host: Homo sapiens (human)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 387 molecules

#5: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

-
Details

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: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350, 0.2 M lithium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9198 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 1.87→43.2 Å / Num. obs: 70747 / % possible obs: 99.5 % / Redundancy: 13.2 % / Biso Wilson estimate: 37.05 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.2
Reflection shellResolution: 1.87→1.94 Å / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 6950 / CC1/2: 0.613 / Rpim(I) all: 0.681 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→43.2 Å / SU ML: 0.2985 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2091 3401 4.81 %
Rwork0.1849 67346 -
obs0.1861 70747 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.12 Å2
Refinement stepCycle: LAST / Resolution: 1.87→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 47 384 5154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00634880
X-RAY DIFFRACTIONf_angle_d0.81396633
X-RAY DIFFRACTIONf_chiral_restr0.0545742
X-RAY DIFFRACTIONf_plane_restr0.0061851
X-RAY DIFFRACTIONf_dihedral_angle_d11.96121740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.90.57291360.48122659X-RAY DIFFRACTION96.61
1.9-1.920.44211400.42052759X-RAY DIFFRACTION99.21
1.92-1.950.34581320.34862750X-RAY DIFFRACTION98.94
1.95-1.990.38211360.30762768X-RAY DIFFRACTION99.15
1.99-2.020.30781590.26892770X-RAY DIFFRACTION99.32
2.02-2.060.26341450.23612758X-RAY DIFFRACTION99.45
2.06-2.10.26491420.23032788X-RAY DIFFRACTION99.09
2.1-2.140.24751530.21752724X-RAY DIFFRACTION99.28
2.14-2.190.27451330.23312799X-RAY DIFFRACTION99.36
2.19-2.240.27661330.24072782X-RAY DIFFRACTION99.35
2.24-2.290.29211400.20652779X-RAY DIFFRACTION99.83
2.29-2.360.26741380.1912799X-RAY DIFFRACTION99.73
2.36-2.420.2451590.19242800X-RAY DIFFRACTION99.87
2.42-2.50.24171420.18672785X-RAY DIFFRACTION99.69
2.5-2.590.21381240.18272822X-RAY DIFFRACTION99.97
2.59-2.70.21911240.19182840X-RAY DIFFRACTION99.9
2.7-2.820.23841480.18952815X-RAY DIFFRACTION99.93
2.82-2.970.22571330.18552813X-RAY DIFFRACTION99.86
2.97-3.150.18281360.17862849X-RAY DIFFRACTION99.97
3.15-3.40.19451450.17182854X-RAY DIFFRACTION99.93
3.4-3.740.17741500.16762841X-RAY DIFFRACTION99.87
3.74-4.280.15861550.14922849X-RAY DIFFRACTION99.6
4.28-5.390.15041360.14252917X-RAY DIFFRACTION99.8
5.39-43.20.19821620.1823026X-RAY DIFFRACTION99.1
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)
11.999650335850.2753782045220.6446766368150.997966687422-0.1801036712922.404823234050.2443184218570.005117186832380.2347696382670.119745556731-0.05834698204070.0354193483281-0.01695590706180.048860594014-0.1331746683070.33564376498-0.0305522631436-0.01512329505730.298963442583-0.0007601514300980.30277474839720.327-4.48172.518
22.63733993668-0.5066258809872.433688560750.106910161264-0.49677469312.30066865263-0.150162103938-0.05667301746210.4673177908420.1001501931180.03868071606540.0289235075714-0.08505733265370.007924455272650.1490583964810.4708040505580.00970614577662-0.02923127238210.365473050151-0.02595211998260.47752843337119.9961.46281.415
34.52489426043-5.354357597992.004876139378.21282256616-0.9064803332425.34939669605-0.827369859458-1.58302786028-0.03309100641051.568820174880.677245779837-0.1163689461-0.119090918642-0.6358208605280.185382877340.58123384327-0.03559061857360.0005055485958690.511565125178-0.007132810543420.36455408507518.934-2.91285.474
42.388129257-0.3185978632570.3829940924032.446035779110.391718394123.01574511019-0.1573664933220.914553218146-0.253652375287-0.161807285959-0.157327907065-0.1676599061480.2054119888391.040374286250.1716524091250.3365011286370.05696772703570.03111198940150.5964354436280.08909268152280.31790064722922.314-3.5542.126
55.898384840921.048181869591.521744882424.039144892161.526170702594.62085943952-0.05939237328931.15271234232-0.148041209695-0.648216070913-0.1018884458610.2097308404860.009973228047590.5214306338160.2294616788390.3679498645190.02996813698140.004488811045560.604269832210.05741978252040.32939708894412.833-0.6535.535
63.48655216902-0.352009206421-1.140034594872.41774783766-2.332336474132.888339517630.03456301637160.5586229404650.307345885832-0.0696742918958-0.225686697844-0.192012975536-0.1455066631390.5112096786680.1796806228320.301962265022-0.0408298934044-0.003820330253820.5421156312460.1068893741480.38228826086317.1856.91338.444
72.47103069123-0.9059110250311.574021109521.26357379271-1.00207455011.53033568966-0.003536527087620.6310791228110.245836090064-0.00483135522615-0.142855564655-0.126609706008-0.1540622102880.5031505524770.1458432820040.311671394607-0.03653768687710.01803278721580.5058012941360.05237523600410.33139677238122.0210.06347.124
82.361871014471.00081804249-0.6392315203752.8637404983-1.262030380221.718103777560.00759099421359-0.0147300780984-0.0801640295920.09751504578370.0780666014060.02003192024420.003488782304420.105393519404-0.08874416586860.265957196894-0.00693350851916-0.02999495983550.3187675933290.02079804166310.30625179827620.982-16.69870.501
92.97525930030.918390140382-1.795275184743.84402492995-2.057699673793.11508036291-0.0734884441071-0.0326291177081-0.2469106308410.1693909171110.00921035040416-0.2017932698780.1733616530320.1083232804710.03183512643780.320829019593-0.0505084283601-0.06701834774570.30547356973-0.01758464387940.24273910045424.267-17.470.143
105.650937743351.66007441761.788600137182.201781063481.520561927364.251566626380.05737600570290.29528316668-0.428446717817-0.0614772643284-0.1468911384460.2470569473090.52406290957-0.2757580519970.05163967386870.397656366022-0.013164080464-0.02644473390280.28365341287-0.02967892729540.363723741403-19.257-2.07410.773
111.460030236920.6593617699511.02547812742.479857023921.336537228373.230932065640.05383797200450.06717458456360.002679191638870.093883389692-0.09024331577940.01334960012640.120376650063-0.01478772014430.02573476483410.3151237831840.0105672756383-0.01912347539050.2678650549070.03540637814760.292928078161-8.896.64122.805
128.68535693967-4.634983552012.000029590384.233903758282.000033189011.99998590265-0.6784009406597.061491816875.80056992491-0.1331231390880.249418187564-7.66710825743-2.290743957335.826813332090.4038017555080.939963593023-0.375925489999-0.05516570488590.6924322403460.05701198793061.54005738365-29.399-8.2932.829
132.60364103707-0.9505960075920.698321571384.38748787486-1.357475330475.418387120530.110257500368-0.7034671653170.1580154414510.759171095743-0.306451410957-0.131963118978-0.6702535286760.2344471905380.1871711831870.2775735401820.0352047952227-0.04655843062180.336283768287-0.05730491162260.225872532483-1.9878.64158.276
140.501019433781-0.07502724504160.8697038843121.84299269362-1.794351669153.65239600307-0.0281628522184-0.1121447142920.1657575614040.205473098275-0.01187065531340.191377028799-0.496932257876-0.1081144567950.05794757188280.34093845829-0.0196691875692-0.004599154698710.3047003723570.008417060666890.349890360785-2.7311.44848.045
154.74661959545-0.2129035898280.4672742491650.8021092293381.023791150311.424921029420.00335406391731-0.563898182742-0.674146200666-0.06478953972640.2118048630560.1241929992090.358632009183-0.0778982810142-0.2093994542140.331895530788-0.003459885205510.02849640606820.3190500619080.05336668822520.3161893664971.658-0.1448.382
161.16302152806-0.3534314615291.425153849051.12530899344-2.284245634685.128068261730.093792242407-0.036895404599-0.152437382312-0.1580803688280.02401081781620.0982508142320.371962741541-0.24590921567-0.06998822049340.323301088412-0.03202998209680.02842246558850.2640310511480.01658288531890.327810642623-8.5572.7941.902
172.101366591460.7718733126220.1408474000615.8532951834-1.709632881973.80752974169-0.0287661092023-0.1184597530870.120175152273-0.03686640092750.05808569129980.284040598061-0.308733746979-0.307964722796-0.03416470114040.3147189766390.01295721182690.008809260750140.3372983756810.002520010922850.331089488692-9.5499.43350.302
181.63761018783-0.605752308034-0.2576430221140.66389334517-1.039318108633.20307460897-0.0223017625127-0.02590931886080.0949876251678-0.0948076806629-0.0655538627578-0.024704625811-0.006291012087780.1225311622570.1200843232980.309223485515-0.0308668544853-0.02378511992230.2477209504010.01352864503260.294433707561.2675.39849.61
193.381686934971.253935617710.7799621485191.28670786532-0.1281035530524.027424569240.0908341874577-0.652275569123-0.389165050290.03538468067550.150864735086-0.01640819921680.125165767048-0.313239146157-0.2306351995490.299800941963-0.0278357622810.02185848757940.2013194235240.001617083858940.25752310188912.434-7.16676.872
202.853951585830.2154493193430.9770261386951.13619675451-0.264979762352.03464199704-0.1394410571250.1085843553030.09553600728230.1473615724970.1747851634090.058230461743-0.015033565398-0.11318807076-0.1026180872610.364375946924-0.0270349115034-0.02150159078960.3419340641820.01543556104190.31060897832716.625-2.02975.61
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 162:192 )H162 - 192
2X-RAY DIFFRACTION2( CHAIN H AND RESID 193:207 )H193 - 207
3X-RAY DIFFRACTION3( CHAIN H AND RESID 208:219 )H208 - 219
4X-RAY DIFFRACTION4( CHAIN L AND RESID 2:18 )L2 - 18
5X-RAY DIFFRACTION5( CHAIN L AND RESID 19:39 )L19 - 39
6X-RAY DIFFRACTION6( CHAIN L AND RESID 40:76 )L40 - 76
7X-RAY DIFFRACTION7( CHAIN L AND RESID 77:114 )L77 - 114
8X-RAY DIFFRACTION8( CHAIN L AND RESID 115:164 )L115 - 164
9X-RAY DIFFRACTION9( CHAIN L AND RESID 165:214 )L165 - 214
10X-RAY DIFFRACTION10( CHAIN A AND RESID 333:393 )A333 - 393
11X-RAY DIFFRACTION11( CHAIN A AND RESID 394:526 )A394 - 526
12X-RAY DIFFRACTION12( CHAIN A AND RESID 601:601 )A601
13X-RAY DIFFRACTION13( CHAIN H AND RESID 1:17 )H1 - 17
14X-RAY DIFFRACTION14( CHAIN H AND RESID 18:39 )H18 - 39
15X-RAY DIFFRACTION15( CHAIN H AND RESID 40:51 )H40 - 51
16X-RAY DIFFRACTION16( CHAIN H AND RESID 52:63 )H52 - 63
17X-RAY DIFFRACTION17( CHAIN H AND RESID 64:82 )H64 - 82
18X-RAY DIFFRACTION18( CHAIN H AND RESID 83:113 )H83 - 113
19X-RAY DIFFRACTION19( CHAIN H AND RESID 114:138 )H114 - 138
20X-RAY DIFFRACTION20( CHAIN H AND RESID 139:161 )H139 - 161

+
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