[English] 日本語
Yorodumi
- PDB-7zf3: SARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zf3
TitleSARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs
Components
  • EY6A heavy chain
  • EY6A light chain
  • Omi-3 heavy chain
  • Omi-3 light chain
  • Spike protein S1
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Omicron / RBD / antibody / Fab / Omi-3 / EY6A / VIRAL PROTEIN/IMMUNE SYSTEM
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 / symbiont-mediated suppression of host innate immune response / 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
ISOPROPYL ALCOHOL / Spike glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsZhou, D. / Huo, J. / 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 / Year: 2022
Title: Potent cross-reactive antibodies following Omicron breakthrough in vaccinees.
Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / ...Authors: Rungtiwa Nutalai / Daming Zhou / Aekkachai Tuekprakhon / Helen M Ginn / Piyada Supasa / Chang Liu / Jiandong Huo / Alexander J Mentzer / Helen M E Duyvesteyn / Aiste Dijokaite-Guraliuc / Donal Skelly / Thomas G Ritter / Ali Amini / Sagida Bibi / Sandra Adele / Sile Ann Johnson / Bede Constantinides / Hermione Webster / Nigel Temperton / Paul Klenerman / Eleanor Barnes / Susanna J Dunachie / Derrick Crook / Andrew J Pollard / Teresa Lambe / Philip Goulder / / Neil G Paterson / Mark A Williams / David R Hall / Juthathip Mongkolsapaya / Elizabeth E Fry / Wanwisa Dejnirattisai / Jingshan Ren / David I Stuart / Gavin R Screaton /
Abstract: Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA. ...Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 22, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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: EY6A heavy chain
L: EY6A light chain
A: Omi-3 heavy chain
B: Omi-3 light chain
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,38111
Polymers117,8935
Non-polymers4896
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-52 kcal/mol
Surface area45030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.517, 119.889, 134.019
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 , 1 types, 1 molecules E

#5: Protein Spike protein S1 / SARS-CoV-2 Omicron Spike protein / RBD / Spike protein receptor binding domain


Mass: 23157.164 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

-
Antibody , 4 types, 4 molecules HLAB

#1: Antibody EY6A heavy chain


Mass: 24318.260 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 EY6A light chain


Mass: 23315.855 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 Omi-3 heavy chain


Mass: 23634.482 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 Omi-3 light chain


Mass: 23466.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Non-polymers , 2 types, 6 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.0, 30% (v/v) Jeffamine ED-2001 pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.15→74 Å / Num. obs: 252075 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 77.01 Å2 / CC1/2: 0.955 / Rmerge(I) obs: 0.491 / Rpim(I) all: 0.136 / Net I/σ(I): 5
Reflection shellResolution: 3.15→3.2 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1209 / CC1/2: 0.33 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
GDA1.19_4092data collection
PHENIX1.19_4092refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QNW

7qnw


Resolution: 3.15→73.28 Å / SU ML: 0.4714 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4111
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2661 1232 4.93 %
Rwork0.2076 23770 -
obs0.2104 25002 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.91 Å2
Refinement stepCycle: LAST / Resolution: 3.15→73.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8074 0 32 0 8106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00238296
X-RAY DIFFRACTIONf_angle_d0.498711278
X-RAY DIFFRACTIONf_chiral_restr0.04231256
X-RAY DIFFRACTIONf_plane_restr0.00451445
X-RAY DIFFRACTIONf_dihedral_angle_d10.86952955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.280.35641410.31212576X-RAY DIFFRACTION99.41
3.28-3.430.33671190.29062594X-RAY DIFFRACTION99.71
3.43-3.610.34731270.25082612X-RAY DIFFRACTION99.89
3.61-3.830.30011510.24562602X-RAY DIFFRACTION99.93
3.83-4.130.25551350.2092616X-RAY DIFFRACTION100
4.13-4.540.22451230.1722638X-RAY DIFFRACTION99.96
4.54-5.20.22041360.16372665X-RAY DIFFRACTION100
5.2-6.550.23651380.19312669X-RAY DIFFRACTION99.96
6.55-73.280.26161620.19052798X-RAY DIFFRACTION99.97
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)
12.546687909211.20818395658-0.7496379992313.98375332063-2.308431885485.7233060052-0.186703473858-0.1792470700460.2163704889550.0636050176283-0.18272882211-1.28028122170.3405903008350.5959192541070.1913348738050.6168362451390.0925622126236-0.03992269490370.753186305271-0.1271812972730.7542572365555.21794996573-44.42475663465.89039929677
22.45869603169-0.578532472842-1.001021613013.88459671645-0.6744762562365.373536693370.195670357194-0.134144623405-0.1520882697880.2940428251430.318885050249-0.08811782052120.3688732917730.426370605308-0.6101761612020.564028847984-0.00208791863694-0.09201456536730.732008915868-0.05582055275150.5890718682240.14431127397-40.876520357211.9982880677
31.219879936090.774603604461-0.5354552339314.73642791958-0.4911796490750.939589516970.09564887139350.1981080632240.1266967813920.6407221214850.0589910912487-0.1546709096350.1571787689650.0919061998252-0.113820796560.57486589818-0.00670041179105-0.100317526050.6557439299260.009469534372040.592416691106-8.06451181825-52.24769044754.94404973432
43.757996838040.8834503251090.9367137124283.21644644079-1.180865911210.489357886496-0.01964726109490.493047381772-0.0002787721460060.2406644291710.0691472036128-0.007860325978380.04834942324880.4953844941650.1451064572690.8605133049530.0857922249239-0.02574647203870.532730362297-0.005444769934930.547706893888-16.3644217076-69.53919816720.0990587657725
54.953979436394.360831913723.002136262199.387145592796.02774931514.884764281880.5401199641091.08912954507-0.7905132513850.879714654027-0.165809082369-1.339916970131.534024302890.901913403909-0.3751504760940.9405932242390.131941982609-0.01035668731880.8565013007240.1023711681350.799838781006-12.5922593968-78.218421899-2.03303365729
63.805164310412.210783513151.18113139438.771094815747.616400975956.8860986222-0.3638623048380.5939760534440.2944251235810.840238343618-0.673096933011.552658455671.879674964120.1784939335750.7029638342680.608352668069-0.1467065527510.1218126367720.594412839975-0.00881975528920.691742051581-23.3647879894-38.560007111-1.88528837643
75.603007388614.038035361792.204027386672.77584781970.9390110586048.69304695873-0.1948774367760.4676231363440.538348042055-0.429568274655-0.01528134992750.314286756967-0.31718208294-0.2321358639440.2354297217040.535679806765-0.000927058078703-0.04834802903180.385161057628-0.001218974625330.529468506483-15.2162185795-32.6051738691-3.12827940269
80.8392627638351.649966799071.553762126374.771367040311.924431022640.4621651420430.1477169234110.0240156759743-0.07100457099320.1770667944590.08816751838190.1503732623530.4295913063940.130683688954-0.1172123705620.60033798936-0.07529614240770.04178556856870.556431637672-0.02995010789420.571895513645-18.7863875807-41.3297769241-3.14326038968
95.10938955276-1.905269795780.3679673740544.66921192323-1.409754958725.162789750730.0928564298461-0.49634647915-0.271907415169-0.27457313354-0.1806700310970.1868240748740.6807128297880.0303708884789-0.006321923887760.718008930833-0.01327062872820.1128749268980.5020474760160.06265769109820.676344894039-27.8835603316-68.76147592364.71976204318
101.5247646121.131058809762.394789124036.51994063431-2.000173176666.412874789580.062266331649-0.254117867381-0.1430799027931.04156733762-0.259422224007-0.133101718675-0.725969711722-0.1790261924330.2734577803380.5925302918360.09014384889540.09712603815560.598462730953-0.0156712254880.54702865861-26.7527449408-61.43601231672.80817920815
112.08357527765-2.731666767940.3469204536685.38674704878-1.529312134574.20197967996-0.78618388449-0.719739864412-0.05777327514570.6993570792521.234222684370.1945287746840.613904630174-1.40128601875-0.7348635188011.06981260744-0.0912975548087-0.006389664497130.6851626202910.1243936618590.77401681861-30.3591486447-70.87760260110.8493338774
121.584543004720.3560715344391.409802837263.12057470493-2.302819360717.067036184630.275229313125-0.747147287705-0.1204829459891.152120505650.9483438057310.90264847513-0.511005251064-1.85114849481-1.052276225130.646625190455-0.1997236527070.002657123625010.9162556008150.1773193808981.13129782457-37.7104234852-69.31886560022.46843303266
135.553501382012.000231356793.755277110482.75292458086-0.7465956201454.622433611240.5911498287410.345254032590.537254880558-0.528144298133-0.8850114876220.5880055826670.150031771456-1.373201004220.1861548292440.361175273119-0.08547599359740.01783806424350.7534276809850.05771673134830.518969002983-51.1736808957-28.745920189125.669894963
144.221487904383.008123586140.1739509779023.876969264550.4498040265026.05471184314-0.1250911474380.4514239226510.0245949635383-0.1586109235580.2377826517110.2703469558930.279782184855-0.0342235546344-0.1254904433980.6131273088140.04761792225850.03850340359310.5437669730090.004032556808780.458359578892-39.5409240068-26.367420067526.5921747407
155.145857117372.26224286689-2.522212231921.08911588103-0.4317316304914.60690398895-0.3420720515360.8497300835030.0409903648980.4731581125950.5144503268660.5994109425010.742397831155-0.908589577479-0.06200506337360.7093503140390.03152590398140.01823836080980.8126970081870.1114085366260.340903018612-44.9147741406-29.091785580921.5203423362
168.739683027378.019432028752.425943347537.190986312192.195835044438.02475886462-0.02910881472870.3543629899090.101750502205-0.321506384438-0.1147031809290.867537342283-0.2369883833150.5604784208290.205580994310.4908336442240.06545247429940.09540416456170.56605359120.07175024342280.740184097404-41.0924318776-25.075169971935.8390623789
176.72349731960.2256672752-2.489354309965.054953223682.285382750771.995306072-0.5009293317831.1835885615-0.649177126775-1.805703064980.7263862153720.458614943249-0.141083992668-0.7002621275970.1150066816651.0936978537-0.05934513614450.08891447727890.8095290273550.1015474395450.433223360627-57.7347105325-40.222481267123.4858828206
186.54261360601-0.398744341943-3.723283454222.352460623-2.552042985545.33598183936-1.69115492151-0.893886827587-0.187444061488-0.550655229638-1.096002977730.318029951242.26015041197-1.516811756791.100643496340.638021032593-0.1637560298950.1315411409580.877493437994-0.1406116225030.871140178225-76.6804309339-41.867669681243.3934019249
196.60777568790.0301515663937-2.240781445240.743412594322-2.334346014047.401425038280.687697364538-0.569861665670.114910022413-0.242587191309-0.0955510497608-0.549605197781-1.998044155690.145602443988-0.9570361879440.9350246849930.02852246403320.1454317550140.723844505437-0.1135307332130.715615607186-66.6857171233-39.18849487335.4736629673
202.963563718810.7818650556560.2882014547814.57539891531-1.093093832950.3755567790981.5860763398-0.2940472459470.7080285071250.765261658055-0.6496455991790.291299316485-1.91802400876-0.3316558476430.5833700538761.510560024880.09227878073580.67701081180.441594611054-0.0525557003461.45399761078-66.6209005257-31.147913731445.7928915467
215.052943985160.5959648377761.965416050249.66693845648-0.6726544002940.840017467834-0.4140411916610.452994490558-0.636858339617-0.8850901962511.786765843641.663410315560.1585527945481.02605776591.635989960340.6402552985170.05275375420730.1963641097920.6852425761630.02140709930790.590899285401-62.1709769348-48.209563436333.2173115055
225.642720849420.6485714993991.919192236083.652041667644.026044388148.22029289971-0.0187932065588-0.4396053963470.7711343070711.36521337392-0.4714968987180.561995920445-0.0337970019217-1.379292522480.05191504386330.983868771304-0.008263885347720.2856631512840.513317481038-0.1540131532910.786345091461-73.2250488092-35.811880644445.969379256
233.182799676230.617019785925-2.299871829071.60963653072.049001252125.371262073340.3385276559750.89029748011.280714494880.4235137057680.2426050168910.166809169232-2.47000017838-1.39137057537-0.5418321843471.587198936060.2614467766750.2519751552410.8914746893210.1203688515660.850321941-71.7183653796-33.143526963333.8076993088
245.00313625018-0.06818592326820.3045433451853.67778279721-0.7098753809362.44161212374-0.34741014246-0.845437243479-0.6072387234740.6397133047830.122643672174-0.4705749006571.493608526790.6195008498210.08566301699411.06245727563-0.0139157243953-0.01895516880870.609383954952-0.0392301453960.507024311914-36.5829950767-40.542343037550.5716620254
255.764300203320.5515343363270.02900932690174.76433973528-0.7191038342943.719090229380.0950511150686-0.73549203335-0.1915689458250.320529061867-0.0585503203359-0.3149894196230.2211138444910.261766110851-0.0981930289890.789322039495-0.04652359011070.06354534749950.6919918464650.01394347485460.491840894974-34.4892007955-30.391489007648.1763626194
261.84889188930.8637156781792.624773130412.68877251165-2.070312657857.32477433230.09129938170690.1039934838170.561649093419-0.06382371489320.1818600526670.3315353657960.0163600598468-0.251539422013-0.4990922573340.849053048297-0.02435447226130.01894396260040.6338745937430.01584991279710.520949813924-38.1421160992-33.355890181144.9315871404
273.602682622541.084333251120.1275951605510.2739897777160.05512228338980.3053701828750.491916689976-0.184906012791-0.2800232969750.0719610452107-0.2975220786640.06573657248010.5484133409590.0728217951183-0.06892586442950.856210050645-0.09233352273860.2325551414870.57725651088-0.02794951236130.656819377424-58.5644451694-44.669178712354.3738424605
286.483916418372.11558343772.057306098170.9057447370240.5941937504734.51460330055-0.516913106671-0.1046488006141.203155472650.258998085055-0.2561484570560.885490379414-0.196904939245-0.9040321893630.1385478158280.842907216261-0.01976270438780.1215675608580.7668314386750.04027131433690.770481397992-74.2588981918-47.644407266840.1357419517
296.322489300221.642503671523.077881740473.027775456830.8891667197652.169484849730.1177600922050.302649918953-0.4032071919620.2777130932150.0939501097786-0.205221780915-0.02768645400560.452025670455-0.1136284927130.73416354483-0.002366645950290.1442945662420.5352012521620.004798726176830.52819908743-62.9366168264-51.78341992148.1165813239
307.371728717391.176887483220.2896093389141.52299437555-0.481490894835.036482644190.5363733557850.706934987975-1.94356177505-0.634830207171-0.236076778866-0.5710032611440.411630872830.0190453730744-0.05111619305180.874916533872-0.07843031241990.1239802156930.63836877777-0.1444587733180.591470587832-72.7242244654-54.055650157239.0169421757
314.456157263220.5107999666022.178940763010.8557517685460.8785064368444.365522552520.02831881703870.203092273090.4124618257440.223350026905-0.2789682675570.3690553208070.03695836394640.28917584662-0.1470484052480.758788370724-0.1687644657840.01764187604990.5880999315080.06607527834780.689333483656-73.4516638791-56.005528926351.3392741476
325.262490432660.184841729473-0.901602865762.857467443080.9145039660866.463002183140.113264442797-0.295350623642-0.7402182704520.509748312886-0.03579791502510.003835177953150.6560613583680.3920938783-0.339846227940.778945972254-0.1510528915080.05711534148980.618464684209-0.1459031755990.610492993447-2.11657554522-13.176142940629.4680024311
336.18330278784-0.57385302031-6.777103167326.327409640350.6664265686787.49715898051-0.145732411453-0.630817107965-0.08536760797940.138850933770.1333891169670.1942272131110.01985519474410.6077530003830.07311486379260.453522514664-0.0232875853208-0.1688618949340.634655173522-0.09910264781740.613375703454-0.437136037923-19.823614909821.295042012
343.48736934472-0.926299526513-3.141137310252.4886772232-1.422832238844.817825669720.155962879761-0.384045981023-0.08982247015290.212549486888-0.0736162578088-0.5324198524250.3863801173320.431580365282-0.08906371035920.591365333494-0.0384349184059-0.009393451418690.631017460153-0.111353203470.588089171059-6.93031888206-19.303752462219.7104493825
359.41566104416-2.06279515759-2.149968726974.846359176290.1067121302356.449357706650.0694116617403-0.1644166175760.550882579311-0.706446035108-0.227195449124-0.405345274225-0.125349133012-0.5915522107260.02667533188630.547128135905-0.0343085787999-0.08353754526430.4589795613640.03227407035150.459432883822-15.741863535-19.830263333722.2138494506
362.34819259172-1.84210364183.919807506316.81025219984-1.122569503967.05640165898-0.310732715447-2.213531783911.295650273451.197005352490.250886240658-1.267732430690.04875413465430.354334967935-0.2032604408440.7193837129580.166412014214-0.09109059511071.27388942664-0.05863404351750.609791977379-10.2529156846-21.909490896543.4802351783
376.431469492180.7595778899631.56972701471-0.04353146811150.1942296415023.560522125980.148801636681-0.6086912912370.9410875474240.06208044075770.07138846503640.29988563141-0.706995242143-0.307847993699-0.2903113472920.7425154551220.05176047028030.1225961029750.478827117746-0.04944994301410.769707240103-28.6060656715-9.5380210661333.703364842
381.46193787921.728524204722.257596557113.278868856871.78405901298.038075303340.665415384351-0.135053936792-0.2858954417480.201747371083-0.0979963752221-0.1471837772391.56429263869-1.44364275991-0.6048619438860.871976807229-0.191175735097-0.2643141949740.8864638116190.3243435775720.715836228121-15.3285671317-27.581210513841.1082734895
396.521368295322.76175041313-4.430264614747.74357417061-3.976754990868.227158631490.304902998442-0.1858211510110.503923766372-0.4368342292840.2167591878440.624794488349-0.3318205468520.331025245635-0.08389530324150.4838637478810.0438470458271-0.02403251980680.531281448065-0.0274809748180.465186948979-3.72051831257-13.937603830717.5525005905
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 33 )HA1 - 331 - 33
22chain 'H' and (resid 34 through 99 )HA34 - 9934 - 99
33chain 'H' and (resid 100 through 142 )HA100 - 142100 - 137
44chain 'H' and (resid 143 through 196 )HA143 - 196138 - 191
55chain 'H' and (resid 197 through 222 )HA197 - 222192 - 217
66chain 'L' and (resid 1 through 18 )LB1 - 181 - 18
77chain 'L' and (resid 19 through 75 )LB19 - 7519 - 75
88chain 'L' and (resid 76 through 114 )LB76 - 11476 - 114
99chain 'L' and (resid 115 through 151 )LB115 - 151115 - 151
1010chain 'L' and (resid 152 through 173 )LB152 - 173152 - 173
1111chain 'L' and (resid 174 through 198 )LB174 - 198174 - 198
1212chain 'L' and (resid 199 through 214 )LB199 - 214199 - 214
1313chain 'A' and (resid 1 through 17 )AD1 - 171 - 17
1414chain 'A' and (resid 18 through 72 )AD18 - 7218 - 72
1515chain 'A' and (resid 73 through 90 )AD73 - 9073 - 90
1616chain 'A' and (resid 91 through 111 )AD91 - 11191 - 111
1717chain 'A' and (resid 112 through 124 )AD112 - 124112 - 124
1818chain 'A' and (resid 125 through 140 )AD125 - 140125 - 135
1919chain 'A' and (resid 141 through 159 )AD141 - 159136 - 154
2020chain 'A' and (resid 160 through 170 )AD160 - 170155 - 165
2121chain 'A' and (resid 171 through 180 )AD171 - 180166 - 175
2222chain 'A' and (resid 181 through 198 )AD181 - 198176 - 193
2323chain 'A' and (resid 199 through 218 )AD199 - 218194 - 213
2424chain 'B' and (resid 1 through 18 )BG1 - 181 - 18
2525chain 'B' and (resid 19 through 76 )BG19 - 7619 - 76
2626chain 'B' and (resid 77 through 103 )BG77 - 10377 - 103
2727chain 'B' and (resid 104 through 120 )BG104 - 120104 - 120
2828chain 'B' and (resid 121 through 141 )BG121 - 141121 - 141
2929chain 'B' and (resid 142 through 174 )BG142 - 174142 - 174
3030chain 'B' and (resid 175 through 190 )BG175 - 190175 - 190
3131chain 'B' and (resid 191 through 214 )BG191 - 214191 - 214
3232chain 'E' and (resid 333 through 353 )EI333 - 3531 - 21
3333chain 'E' and (resid 354 through 380 )EI354 - 38022 - 48
3434chain 'E' and (resid 381 through 409 )EI381 - 40949 - 77
3535chain 'E' and (resid 410 through 437 )EI410 - 43778 - 105
3636chain 'E' and (resid 438 through 451 )EI438 - 451106 - 119
3737chain 'E' and (resid 452 through 494 )EI452 - 494120 - 162
3838chain 'E' and (resid 495 through 506 )EI495 - 506163 - 174
3939chain 'E' and (resid 507 through 527 )EI507 - 527175 - 195

+
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