[English] 日本語
Yorodumi
- PDB-8s6m: SARS-CoV-2 BQ.1.1 RBD bound to the S2V29 and the S2H97 Fab fragments -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s6m
TitleSARS-CoV-2 BQ.1.1 RBD bound to the S2V29 and the S2H97 Fab fragments
Components
  • S2H97 Fab heavy chain
  • S2H97 Fab light chain
  • S2V29 Fab heavy chain
  • S2V29 Fab light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / Sarbecoviruses / Spike glycoprotein / fusion protein / neutralizing antibodies / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 / symbiont-mediated-mediated suppression 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 / symbiont-mediated-mediated suppression of host tetherin activity / 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 / 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 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus ...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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / 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 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
NICKEL (II) ION / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsErrico, J.M. / Park, Y.J. / Rietz, T. / Czudnochowski, N. / Nix, J.C. / Cameroni, E. / Corti, D. / Snell, G. / Marco, A.D. / Pinto, D. ...Errico, J.M. / Park, Y.J. / Rietz, T. / Czudnochowski, N. / Nix, J.C. / Cameroni, E. / Corti, D. / Snell, G. / Marco, A.D. / Pinto, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: Cell / Year: 2024
Title: A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Authors: Laura E Rosen / M Alejandra Tortorici / Anna De Marco / Dora Pinto / William B Foreman / Ashley L Taylor / Young-Jun Park / Dana Bohan / Tyson Rietz / John M Errico / Kevin Hauser / Ha V ...Authors: Laura E Rosen / M Alejandra Tortorici / Anna De Marco / Dora Pinto / William B Foreman / Ashley L Taylor / Young-Jun Park / Dana Bohan / Tyson Rietz / John M Errico / Kevin Hauser / Ha V Dang / Justin W Chartron / Martina Giurdanella / Giuseppe Cusumano / Christian Saliba / Fabrizia Zatta / Kaitlin R Sprouse / Amin Addetia / Samantha K Zepeda / Jack Brown / Jimin Lee / Exequiel Dellota / Anushka Rajesh / Julia Noack / Qiqing Tao / Yvonne DaCosta / Brian Tsu / Rima Acosta / Sambhavi Subramanian / Guilherme Dias de Melo / Lauriane Kergoat / Ivy Zhang / Zhuoming Liu / Barbara Guarino / Michael A Schmid / Gretja Schnell / Jessica L Miller / Florian A Lempp / Nadine Czudnochowski / Elisabetta Cameroni / Sean P J Whelan / Hervé Bourhy / Lisa A Purcell / Fabio Benigni / Julia di Iulio / Matteo Samuele Pizzuto / Antonio Lanzavecchia / Amalio Telenti / Gyorgy Snell / Davide Corti / David Veesler / Tyler N Starr /
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has resulted in viral escape from clinically authorized monoclonal antibodies (mAbs), creating a need for mAbs that are ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has resulted in viral escape from clinically authorized monoclonal antibodies (mAbs), creating a need for mAbs that are resilient to epitope diversification. Broadly neutralizing coronavirus mAbs that are sufficiently potent for clinical development and retain activity despite viral evolution remain elusive. We identified a human mAb, designated VIR-7229, which targets the viral receptor-binding motif (RBM) with unprecedented cross-reactivity to all sarbecovirus clades, including non-ACE2-utilizing bat sarbecoviruses, while potently neutralizing SARS-CoV-2 variants since 2019, including the recent EG.5, BA.2.86, and JN.1. VIR-7229 tolerates extraordinary epitope variability, partly attributed to its high binding affinity, receptor molecular mimicry, and interactions with RBM backbone atoms. Consequently, VIR-7229 features a high barrier for selection of escape mutants, which are rare and associated with reduced viral fitness, underscoring its potential to be resilient to future viral evolution. VIR-7229 is a strong candidate to become a next-generation medicine.
History
DepositionFeb 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: S2V29 Fab heavy chain
R: Spike protein S1
I: S2H97 Fab heavy chain
L: S2V29 Fab light chain
M: S2H97 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,41817
Polymers124,4585
Non-polymers96112
Water13,872770
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13100 Å2
ΔGint-34 kcal/mol
Surface area44780 Å2
Unit cell
Length a, b, c (Å)148.175, 48.099, 166.526
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "L" and (resid 2 through 7 or resid 9...
d_2ens_1(chain "M" and (resid 2 through 7 or resid 9...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERPROPROLD2 - 72 - 7
d_12SERSERSERSERLD9 - 179 - 17
d_13THRTHRGLYGLYLD19 - 2419 - 24
d_14SERSERGLYGLYLD26 - 3026 - 30
d_15TYRTYRASNASNLD32 - 3332 - 33
d_16VALVALLYSLYSLD35 - 4735 - 47
d_17METMETVALVALLD49 - 5349 - 53
d_18ARGARGVALVALLD56 - 6056 - 60
d_19ARGARGLEULEULD63 - 7563 - 75
d_110ILEILEALAALALD77 - 8277 - 82
d_111ASPASPTYRTYRLD84 - 9384 - 93
d_112SERSERSERSERLD9696
d_113VALVALGLYGLYLD100 - 102100 - 102
d_114GLYGLYTHRTHRLD104 - 105104 - 105
d_115VALVALTHRTHRLD109 - 213109 - 213
d_116EDOEDOEDOEDOHF301
d_21SERSERPROPROME2 - 72 - 7
d_22SERSERSERSERME9 - 179 - 17
d_23THRTHRGLYGLYME19 - 2419 - 24
d_24SERSERGLYGLYME26 - 3026 - 30
d_25TYRTYRASNASNME32 - 3332 - 33
d_26VALVALLYSLYSME35 - 4735 - 47
d_27METMETVALVALME49 - 5349 - 53
d_28ARGARGVALVALME56 - 6056 - 60
d_29ARGARGLEULEUME63 - 7563 - 75
d_210ILEILEALAALAME77 - 8277 - 82
d_211ASPASPTYRTYRME84 - 9384 - 93
d_212SERSERSERSERME9696
d_213VALVALGLYGLYME102 - 104102 - 104
d_214GLYGLYTHRTHRME106 - 107106 - 107
d_215VALVALTHRTHRME111 - 215111 - 215
d_216EDOEDOEDOEDOMP301

NCS oper: (Code: givenMatrix: (-0.329829549524, 0.910417942003, -0.249703101982), (0.891325049581, 0.38747178562, 0.235383243537), (0.311050034963, -0.144930280573, -0.9392779618)Vector: 38. ...NCS oper: (Code: given
Matrix: (-0.329829549524, 0.910417942003, -0.249703101982), (0.891325049581, 0.38747178562, 0.235383243537), (0.311050034963, -0.144930280573, -0.9392779618)
Vector: 38.7500527685, -15.1524835379, 42.9681752603)

-
Components

-
Antibody , 4 types, 4 molecules HILM

#1: Antibody S2V29 Fab heavy chain


Mass: 24194.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody S2H97 Fab heavy chain


Mass: 24174.143 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 S2V29 Fab light chain


Mass: 22993.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody S2H97 Fab light chain


Mass: 22935.219 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 R

#2: Protein Spike protein S1


Mass: 30160.789 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
#7: 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

-
Non-polymers , 4 types, 781 molecules

#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M Tris pH 8.5, 20% PEG-MME 2000, and 10 mM NiCl2

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→47.35 Å / Num. obs: 138934 / % possible obs: 99.95 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.5
Reflection shellResolution: 1.67→1.73 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 13733 / CC1/2: 0.36

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASER2.8.3phasing
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→47.35 Å / SU ML: 0.2338 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5435
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2027 6987 5.03 %
Rwork0.1839 131943 -
obs0.1849 138930 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.76 Å2
Refinement stepCycle: LAST / Resolution: 1.67→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7807 0 59 770 8636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00578114
X-RAY DIFFRACTIONf_angle_d0.857511099
X-RAY DIFFRACTIONf_chiral_restr0.05881242
X-RAY DIFFRACTIONf_plane_restr0.00591423
X-RAY DIFFRACTIONf_dihedral_angle_d13.76612785
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 4.32039878647 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.35622330.35974349X-RAY DIFFRACTION100
1.69-1.710.35712250.34494380X-RAY DIFFRACTION100
1.71-1.730.35262260.33614320X-RAY DIFFRACTION100
1.73-1.750.34382220.31794349X-RAY DIFFRACTION99.98
1.75-1.770.30632310.31064346X-RAY DIFFRACTION100
1.77-1.80.33072110.30144378X-RAY DIFFRACTION99.98
1.8-1.820.31512460.28334309X-RAY DIFFRACTION99.98
1.82-1.850.30592440.264411X-RAY DIFFRACTION100
1.85-1.880.31262230.24834310X-RAY DIFFRACTION100
1.88-1.910.2432010.23354396X-RAY DIFFRACTION100
1.91-1.940.24152330.2254350X-RAY DIFFRACTION100
1.94-1.980.25322340.21334336X-RAY DIFFRACTION99.98
1.98-2.020.23122560.20264380X-RAY DIFFRACTION100
2.02-2.060.2212360.19334345X-RAY DIFFRACTION99.98
2.06-2.10.21942200.1994411X-RAY DIFFRACTION99.98
2.1-2.150.23222360.19394331X-RAY DIFFRACTION99.98
2.15-2.210.21422440.1854397X-RAY DIFFRACTION99.98
2.21-2.270.21832310.18594360X-RAY DIFFRACTION99.93
2.27-2.330.21292310.17884369X-RAY DIFFRACTION100
2.33-2.410.20492160.17734454X-RAY DIFFRACTION100
2.41-2.490.20742480.1754349X-RAY DIFFRACTION100
2.49-2.590.1942390.17844389X-RAY DIFFRACTION99.98
2.59-2.710.22272130.17824432X-RAY DIFFRACTION100
2.71-2.860.2122310.17934450X-RAY DIFFRACTION99.98
2.86-3.030.16922110.1834446X-RAY DIFFRACTION99.98
3.03-3.270.20352720.1774396X-RAY DIFFRACTION99.94
3.27-3.60.18982360.17084433X-RAY DIFFRACTION99.76
3.6-4.120.1732330.15734498X-RAY DIFFRACTION99.66
4.12-5.190.15862410.14194533X-RAY DIFFRACTION99.79
5.19-47.350.18282640.18434736X-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)
11.05373075473-0.0396113791114-0.7482163275650.593087855360.2239425793445.80761552377-0.0990130179440.190494421390.0290121533125-0.1542295976930.08279978399480.0670723947623-0.202281482018-0.03178883376470.0198719488490.351178558139-0.09615415099050.06163536283340.266737597844-0.0139758781770.28653139744832.28925.671-6.487
20.418243848394-0.5124066181590.7616806694731.62409189574-1.144502284071.504941974220.3393081847930.301666598042-0.4928567650810.273159717411-0.5656617871971.653452985060.198839084547-1.160344041620.0009365438907260.504861023024-0.2751380251540.2081878102411.056241244-0.3586723385711.2509843037712.39215.458-25.37
31.111617096810.539191932253-0.5669800295622.25427091697-1.564116608232.750096170950.008246091100690.00839070924768-0.116736736867-0.06098718996250.02462758864220.06896315084020.141834392348-0.0242712493806-0.03489575993920.167662363298-0.001630922748880.006805059645740.178142411913-0.006010387145080.21452487668113.5365.49141.605
43.55492964948-0.278537572997-1.981686050722.584785762560.4507457148736.62259683094-0.164970557483-0.4702124660080.07251632145830.2392213024470.05553193225190.0912408498865-0.119082868451-0.08386407671010.1118782139540.2061307326970.05325183064-0.01226611471170.3086191817150.01927366450380.2371937423620.15-5.99173.64
53.371307015431.14735197162-0.03054676821682.28202610241-0.1130507695641.834664845370.2409812217970.1103117693750.379409499133-0.1473310529540.0461160383751-0.458558537498-1.011607624720.47310033072-0.2479339365160.462795653057-0.1744113275680.08393278068030.346653477988-0.03124595335260.40870153121642.20737.25521.518
67.60279554557.51834242498-6.273424002328.23371103396-7.302162808446.702020988530.841494796283-1.925164466020.4083159071021.06929373874-1.34209465884-0.403411678341-2.219780405912.45601161390.3646897040630.940622866556-0.4418474583030.01745908347920.9997366571060.06427290665850.85238704245752.0435.75929.878
74.161882842811.37274040468-1.329463812061.47880699647-2.600396342735.299130228820.0227333419365-0.515409293066-0.1017072976120.0718137821214-0.283225764423-0.880560300335-0.4092075245341.900141115790.2867450425390.311207237016-0.0324371028575-0.01075954054310.684649622557-0.0579690878390.61273885639652.36824.92122.557
81.881699185940.702612243271-0.1760195735562.171295252980.1206519919511.430978501420.0158585189840.01283481671840.1525850244660.04987704707810.009978114505940.0913142257253-0.09394340533240.00620307909778-0.0217536973230.19930716644-0.02077225942460.01509808907540.1843432751250.01804436279870.19308041660728.15728.28431.008
90.813592257540.3551773687911.174691981731.889854468980.7268803153081.18148982602-0.0860587584708-0.059878417837-0.03498745606640.06860330222830.145951990375-0.231895698810.07148775763290.377839946345-0.08361494314430.19057131953-0.07257234480120.01777783808950.249567201493-0.009464689247590.28640375890642.04631.04128.347
102.305707673580.9316005474860.5448158917371.948437970410.3188296689572.62709470537-0.08235018600350.16742151989-0.412377196476-0.1180399707580.10365839206-0.0527730077290.414736984966-0.189546559998-0.04890577505280.325912884817-0.06888169575920.09141236400330.21410270081-0.04741436377020.30046236700726.0929.4166.718
111.803468521411.172033253620.00439963643133.675849703641.268483134770.4440705562790.2538649052960.223864129195-0.00295498120862-0.613780064278-0.167994581060.2134127195071.65876182006-0.715338738397-0.1922358417321.26535143366-0.5021734227240.008705563072310.852337695663-0.1106837392740.7580225932513.6690.067-30.967
121.462335891520.439966839516-0.4143099425242.45314794809-0.6289689881463.879784191220.0858564987263-0.1422303933620.08794111747230.451644785787-0.0523394637153-0.0268967700681-0.3690499937960.182238642814-0.03972405770580.301928532788-0.0722723964567-0.003261795471110.229687088066-0.005201671306570.21603546517623.67518.53154.871
132.898416696540.777771302865-0.6034255168727.74152321559-1.610389231393.721014233460.0434844279626-0.275197142685-0.0725038855660.3383284252120.139533174508-0.204978466778-0.375531326841-0.0550977585277-0.185691339770.2910734380240.0413333778606-0.01162073378670.3671969193220.06615369666750.23095303026914.877-3.54380.057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN M AND RESID 2:119 )M2 - 119
2X-RAY DIFFRACTION2( CHAIN M AND RESID 120:215 )M120 - 215
3X-RAY DIFFRACTION3( CHAIN H AND RESID 1:123 )H1 - 123
4X-RAY DIFFRACTION4( CHAIN H AND RESID 124:225 )H124 - 225
5X-RAY DIFFRACTION5( CHAIN R AND RESID 333:364 )R333 - 364
6X-RAY DIFFRACTION6( CHAIN R AND RESID 365:375 )R365 - 375
7X-RAY DIFFRACTION7( CHAIN R AND RESID 376:393 )R376 - 393
8X-RAY DIFFRACTION8( CHAIN R AND RESID 394:494 )R394 - 494
9X-RAY DIFFRACTION9( CHAIN R AND RESID 495:528 )R495 - 528
10X-RAY DIFFRACTION10( CHAIN I AND RESID 1:118 )I1 - 118
11X-RAY DIFFRACTION11( CHAIN I AND RESID 119:220 )I119 - 220
12X-RAY DIFFRACTION12( CHAIN L AND RESID 2:111 )L2 - 111
13X-RAY DIFFRACTION13( CHAIN L AND RESID 112:214 )L112 - 214

+
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