[English] 日本語
Yorodumi
- PDB-8fhy: Crystal structure of the SARS-CoV-2 receptor binding domain in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fhy
TitleCrystal structure of the SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5021
Components
  • (WRAIR-5021 Fab ...) x 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / SARS-CoV-2 / viral protein / immune system / RBD / antibody / nonhuman primate / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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
MALONATE ION / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsSankhala, R.S. / Jensen, J.L. / Joyce, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-18-2-0040 United States
CitationJournal: Nat Commun / Year: 2024
Title: Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques.
Authors: Sankhala, R.S. / Lal, K.G. / Jensen, J.L. / Dussupt, V. / Mendez-Rivera, L. / Bai, H. / Wieczorek, L. / Mayer, S.V. / Zemil, M. / Wagner, D.A. / Townsley, S.M. / Hajduczki, A. / Chang, W.C. ...Authors: Sankhala, R.S. / Lal, K.G. / Jensen, J.L. / Dussupt, V. / Mendez-Rivera, L. / Bai, H. / Wieczorek, L. / Mayer, S.V. / Zemil, M. / Wagner, D.A. / Townsley, S.M. / Hajduczki, A. / Chang, W.C. / Chen, W.H. / Donofrio, G.C. / Jian, N. / King, H.A.D. / Lorang, C.G. / Martinez, E.J. / Rees, P.A. / Peterson, C.E. / Schmidt, F. / Hart, T.J. / Duso, D.K. / Kummer, L.W. / Casey, S.P. / Williams, J.K. / Kannan, S. / Slike, B.M. / Smith, L. / Swafford, I. / Thomas, P.V. / Tran, U. / Currier, J.R. / Bolton, D.L. / Davidson, E. / Doranz, B.J. / Hatziioannou, T. / Bieniasz, P.D. / Paquin-Proulx, D. / Reiley, W.W. / Rolland, M. / Sullivan, N.J. / Vasan, S. / Collins, N.D. / Modjarrad, K. / Gromowski, G.D. / Polonis, V.R. / Michael, N.L. / Krebs, S.J. / Joyce, M.G.
History
DepositionDec 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: Spike protein S1
L: WRAIR-5021 Fab Light chain
H: WRAIR-5021 Fab Heavy chain
A: Spike protein S1
B: WRAIR-5021 Fab Light chain
C: WRAIR-5021 Fab Heavy chain
D: Spike protein S1
E: WRAIR-5021 Fab Light chain
F: WRAIR-5021 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,44234
Polymers209,7429
Non-polymers2,70025
Water8,701483
1
I: Spike protein S1
L: WRAIR-5021 Fab Light chain
H: WRAIR-5021 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5969
Polymers69,9143
Non-polymers6826
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-26 kcal/mol
Surface area26710 Å2
MethodPISA
2
A: Spike protein S1
B: WRAIR-5021 Fab Light chain
C: WRAIR-5021 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,78011
Polymers69,9143
Non-polymers8668
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-18 kcal/mol
Surface area27430 Å2
MethodPISA
3
D: Spike protein S1
E: WRAIR-5021 Fab Light chain
F: WRAIR-5021 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,06614
Polymers69,9143
Non-polymers1,15211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-20 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.919, 84.127, 119.859
Angle α, β, γ (deg.)90.00, 113.68, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Antibody , 2 types, 6 molecules LBEHCF

#2: Antibody WRAIR-5021 Fab Light chain


Mass: 23356.881 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody WRAIR-5021 Fab Heavy chain


Mass: 23483.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 6 molecules IAD

#1: Protein Spike protein S1


Mass: 23073.766 Da / Num. of mol.: 3 / Fragment: receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2
#5: 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.: 3
Source method: isolated from a genetically manipulated source
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 , 3 types, 505 molecules

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


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.53→109.8 Å / Num. obs: 71266 / % possible obs: 97.8 % / Redundancy: 6.6 % / CC1/2: 0.996 / Net I/σ(I): 11.4
Reflection shellResolution: 2.53→2.58 Å / Num. unique obs: 3598 / CC1/2: 0.625

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→99.94 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2562 3875 2.8 %
Rwork0.1953 --
obs0.197 71225 97.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→99.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14499 0 175 483 15157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315019
X-RAY DIFFRACTIONf_angle_d0.55420415
X-RAY DIFFRACTIONf_dihedral_angle_d5.572105
X-RAY DIFFRACTIONf_chiral_restr0.0452264
X-RAY DIFFRACTIONf_plane_restr0.0042616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.560.3498830.3293087X-RAY DIFFRACTION61
2.56-2.590.3671360.30174270X-RAY DIFFRACTION87
2.59-2.620.35031330.29024557X-RAY DIFFRACTION92
2.62-2.660.32421320.27694749X-RAY DIFFRACTION95
2.66-2.70.32351460.26914898X-RAY DIFFRACTION99
2.7-2.740.33231370.25554878X-RAY DIFFRACTION99
2.74-2.780.26581390.2484944X-RAY DIFFRACTION99
2.78-2.830.31311360.24114923X-RAY DIFFRACTION100
2.83-2.880.29521450.23644935X-RAY DIFFRACTION99
2.88-2.930.33861440.23774919X-RAY DIFFRACTION99
2.93-2.980.29531460.2324911X-RAY DIFFRACTION99
2.98-3.040.28251450.22574932X-RAY DIFFRACTION99
3.04-3.110.28681420.22464884X-RAY DIFFRACTION99
3.11-3.180.30131480.22114920X-RAY DIFFRACTION99
3.18-3.260.32451430.21824900X-RAY DIFFRACTION99
3.26-3.350.27391420.20284885X-RAY DIFFRACTION99
3.35-3.450.31561300.20194913X-RAY DIFFRACTION99
3.45-3.560.25191500.19384896X-RAY DIFFRACTION99
3.56-3.690.24731480.19114938X-RAY DIFFRACTION100
3.69-3.840.24671390.17534982X-RAY DIFFRACTION100
3.84-4.010.25191440.17384876X-RAY DIFFRACTION99
4.01-4.220.24161350.16054908X-RAY DIFFRACTION99
4.22-4.490.1821370.14574876X-RAY DIFFRACTION99
4.49-4.830.21371440.13944938X-RAY DIFFRACTION99
4.83-5.320.1951410.15284842X-RAY DIFFRACTION98
5.32-6.090.1931370.1854952X-RAY DIFFRACTION100
6.09-7.670.26881410.2184936X-RAY DIFFRACTION100
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)
10.77980.0560.2422.2532-0.51484.2618-0.0246-0.71970.22270.427-0.286-0.2407-0.00080.51990.40170.3914-0.08390.01050.8166-0.05990.3801-19.74-16.23724.742
22.71540.9622-0.02464.3471-2.52745.16870.0212-0.4975-0.4479-0.02750.04880.15060.11130.23220.00840.35380.03170.07030.5923-0.00910.3929-26.951-23.41722.517
32.0614-0.53910.16321.5878-1.03372.8123-0.01840.02780.1091-0.0101-0.001-0.0155-0.09830.18290.03490.3013-0.03610.03540.3891-0.01190.3854-28.653-14.3075.205
45.7435-1.77572.0183.7778-2.886.23110.56950.2726-0.7657-0.3377-0.61160.10410.84220.7360.0510.41810.00340.00740.66870.04030.437-18.652-25.09124.457
55.37712.1852-0.88711.27660.29673.334-0.42540.7982-1.3263-0.19860.335-0.16010.6302-0.4313-0.14620.44290.07930.01820.3832-0.05630.6315-48.91-29.552-14.958
63.96770.74670.54990.04720.22910.93530.1064-0.2015-0.58610.00540.00620.02950.0178-0.0101-0.17510.3933-0.0240.01240.38730.08540.4494-54.453-22.493-11.127
74.8692-2.07075.51075.3995-1.34656.44920.51820.66430.5441-0.422-0.7476-0.4421.74930.3149-0.27770.4642-0.03420.08260.5310.03990.5402-72.995-25.427-21.846
83.5160.59051.0833.7238-0.11411.77920.03030.1929-0.1113-0.1102-0.05050.16250.0637-0.3006-0.03470.3297-0.04740.12320.5371-0.02050.3638-78.977-20.192-22.344
92.7836-0.43252.1050.6715-0.39221.7536-0.08160.0140.4096-0.02540.04180.0519-0.2618-0.23180.05160.4070.01840.06380.45520.04650.3931-46.197-3.064-9.852
106.475-1.65252.07251.0148-1.10141.9879-0.22120.47450.7495-0.22880.0842-0.2873-0.31590.24030.33680.3866-0.04670.03150.45250.14270.4762-42.2040.824-15.557
112.7178-0.91530.96720.86790.42192.1305-0.08760.0863-0.0130.45230.17620.1928-0.29040.1312-0.04160.3459-0.02960.01540.52310.09920.3484-52.019-5.749-10.897
122.7614-1.50881.46081.5747-1.63967.90991.2368-0.4219-0.42610.2559-0.4602-0.23450.61190.4312-0.84950.5045-0.0032-0.02130.4876-0.08030.5084-87.035-16.127-11.356
136.07940.92030.47653.21282.05034.12840.252-0.68010.35650.2898-0.34220.4091-0.58620.0629-0.0770.50470.01740.05390.38790.01980.3663-75.649-7.854-9.048
143.49910.659-0.20433.1613-0.18441.78650.1274-0.47360.07010.3709-0.15410.17860.0021-0.1441-0.01990.3167-0.0290.03780.35960.00640.307-78.977-9.363-7.757
153.1574-1.9974-1.73291.86481.0194.694-0.04870.20840.3217-0.3905-0.2802-0.1648-0.4849-0.3811-0.11930.4716-0.06250.09740.52270.05110.48718.854-20.806-75.083
162.7205-1.9566-1.80033.26073.11383.90610.22310.2573-0.1937-0.5589-0.16830.0529-0.0962-0.13450.01510.39780.0701-0.01290.4472-0.00060.27641.826-24.484-72.793
170.1633-0.25320.09273.33213.67924.96330.0466-0.2436-0.4153-0.11130.4194-0.50770.24250.5626-0.37140.4270.0170.02190.6323-0.06740.453913-33.418-68.018
183.5937-0.3544-0.10423.78892.01831.0623-0.017-0.4404-0.21370.31490.134-0.3096-0.05510.0667-0.10490.3491-0.0749-0.01270.4408-0.00970.38390.526-25.503-57.581
194.3071-1.5036-1.05792.48691.32364.77940.16330.04870.27310.0223-0.1211-0.1321-0.3165-0.1119-0.04510.3784-0.02780.00870.36410.03440.29261.192-19.483-57.995
201.490.0251-2.07232.86242.62115.27690.2810.18770.0931-0.2238-0.0440.0147-0.1483-0.3011-0.17760.33430.0206-0.07340.4270.00640.3479-15.465-16.209-53.223
212.23140.0384-1.31922.3207-0.25543.2369-0.038-0.18260.05930.03350.2431-0.3077-0.26570.529-0.04040.3522-0.03330.05270.3801-0.00240.41157.042-18.612-57.185
224.00242.42412.83932.50871.39342.51430.6088-0.3754-1.61840.4485-0.02930.29850.1724-0.2311-0.65750.47460.03790.09950.62150.06490.60694.991-37.977-79.801
238.9639-5.17055.11043.3697-3.43293.50290.0193-0.741-0.33350.45120.17380.17560.1631-0.5922-0.21240.7535-0.07080.05420.53820.02110.3048-15.579-27.268-24.797
244.9622-3.52443.10883.6265-1.58723.23350.3538-0.6875-0.73160.06530.34120.73130.6435-0.5381-0.1950.6703-0.009-0.05560.32440.01620.4938-9.487-35.575-28.137
252.3021-1.16621.32252.5655-0.27073.68880.09080.2623-0.0933-0.07850.04110.15130.45050.0704-0.1240.4603-0.029-0.00370.3214-0.01810.2489-8.389-27.692-34.527
261.00510.13270.26911.02960.06321.87130.1163-0.0232-0.10370.17050.0404-0.16960.27420.159-0.14270.28660.0230.09580.26120.01010.3164-3.458-21.75-9.059
275.20640.8704-1.18673.27230.07388.1163-0.00830.4571-0.4635-0.0058-0.8054-0.05130.6534-0.89970.13340.35060.06830.00270.4452-0.01530.3919-7.132-27.488-2.691
281.78360.1379-0.45182.0340.51554.7115-0.04540.0106-0.0382-0.1971-0.1030.232-0.2605-0.10690.00250.32950.02-0.02470.32690.02010.2961-3.921-20.069-0.58
292.53930.5546-1.42825.83232.81366.3013-0.173-0.26380.03570.5743-0.15190.63970.73110.0371-0.02010.43360.0761-0.00210.40810.04420.3097-4.114-26.8058.536
302.05310.42010.10522.08721.40074.1636-0.1304-0.07260.1903-0.00540.072-0.0154-0.17540.04940.02970.43930.0133-0.02870.3265-0.01140.3687-8.631-5.056-33.279
311.00371.04081.68091.65380.8464.1581-0.06490.07810.2219-0.08020.1194-0.0391-0.21840.00660.03070.41750.03920.02140.3753-0.00840.3577-6.333-4.284-28.591
326.1743-1.0808-0.51771.3932.38694.4154-0.3585-0.5613-0.24410.08170.3401-0.561.01130.245-0.2230.55320.08410.0450.57680.01850.52258.987-20.936.619
337.1728-5.16381.11098.2015-2.54515.14830.1073-0.12630.1150.4010.0878-0.1682-0.19210.2557-0.08490.35790.00430.04920.2724-0.08460.31366.048-14.391-0.993
347.7691-2.83881.60756.8584-1.75986.9020.55110.83560.3454-0.2178-0.5217-0.55720.37710.2452-0.19770.3921-0.18580.19790.4162-0.07420.278610.149-10.489-9.203
354.3169-1.67560.3432.881-0.35982.30080.2766-0.03540.194-0.2386-0.2648-0.2788-0.07220.3702-0.03260.4519-0.04380.03770.3778-0.00610.336810.543-14.412-2.549
367.6591.75380.2530.74330.05411.0260.48660.3797-0.055-0.1153-0.64710.3537-0.2021-0.364-0.06580.42040.04460.02840.7913-0.09420.6061-91.512-11.117-46.786
374.18741.45012.34192.59391.031.32210.2437-0.2332-0.05130.1798-0.30510.31990.3766-0.36550.01960.3587-0.0697-0.02650.5802-0.03810.4708-90.807-17.786-48.215
384.32420.5602-1.85383.3361-0.84241.17190.2396-0.1229-0.3064-0.0504-0.15430.5938-0.1382-0.03970.10570.7134-0.198-0.14320.6568-0.01210.6004-93.216-28.268-51.157
392.06780.30461.01524.0768-0.05143.01-0.002-0.2324-0.5647-0.20630.103-0.08960.7397-0.4519-0.13710.4154-0.05730.01880.54650.00750.3861-78.004-20.327-49.814
401.65990.20340.38461.3225-0.28732.867-0.2083-0.18770.02060.49390.1279-0.0794-0.23150.0059-0.01220.4102-0.04390.0860.5767-0.05530.5276-68.877-9.419-47.054
414.16320.5832-1.571.0994-1.00142.0605-0.0582-0.1806-0.35040.35780.1371-0.02850.1422-0.0008-0.04510.437-0.08130.00720.44220.07610.4599-66.007-18.019-36.222
429.9417-2.19454.76382.1332-1.69292.7609-0.084-0.25421.7523-0.0205-0.3228-0.5625-0.21060.28760.38160.3951-0.07880.07520.4231-0.07060.5544-57.536-9.694-37.854
430.85180.3560.96763.6838-2.75375.462-0.06610.02060.43-0.830.0573-0.37830.1158-0.6294-0.19690.54670.00990.05090.6866-0.08350.4769-70.781-8.205-59.1
441.81141.7951-0.75942.8388-0.41094.85020.090.2302-0.0015-0.06170.17910.05620.5061-1.1479-0.17820.4773-0.153-0.13090.78830.05140.6685-84.689-18.85-49.363
450.26990.4342-0.99254.05271.12675.89120.3745-2.1593-1.0126-0.492-0.0255-0.35580.3208-1.0145-0.36250.5932-0.1934-0.07861.22020.2960.7486-99.519-28.361-39.697
460.3264-0.8707-0.94522.482.83243.2669-0.0707-0.04520.2808-0.06210.4183-0.4155-0.17961.2019-0.64140.47190.0707-0.07360.54340.02330.4737-39.829-28.564-51.664
472.4841-0.0737-0.6143.4323.09075.29970.0388-0.0594-0.23150.2167-0.10950.08480.5189-0.09040.03490.3342-0.0167-0.00890.27910.01950.4158-51.072-28.087-53.608
481.7644-1.0323-0.86730.98321.06411.0566-0.18570.08560.0226-0.0610.04830.06420.1117-0.03620.03820.40310.0232-0.0330.3361-0.03030.3926-41.766-26.898-57.307
494.6204-0.3677-0.79752.0584-0.64272.23390.2767-0.0625-0.0197-0.0825-0.18020.08380.06230.0149-0.09930.3991-0.0221-0.05040.3417-0.03410.2624-21.323-22.421-74.942
503.3321.059-0.73612.91380.45591.8230.3680.19530.16260.0418-0.09940.08790.09110.1986-0.13090.35190.0597-0.04250.4108-0.00090.346-25.82-21.517-74.945
518.22294.6701-1.42027.3648-2.27982.9133-0.25660.2562-0.3189-0.7746-0.0047-0.50770.30020.11560.29210.42070.04630.03640.4736-0.03720.351-16.16-29.388-77.652
524.15110.5692-1.34181.8906-0.26753.57560.0521-0.12850.4356-0.01480.1614-0.1608-0.0504-0.0411-0.2210.2842-0.00230.02460.2169-0.02630.4177-47.825-4.864-52.864
532.7537-0.0739-2.95990.98580.46143.28960.3357-0.10710.3630.0385-0.04060.1647-0.2846-0.0821-0.20490.3037-0.02130.02920.2789-0.02440.4663-42.934-4.66-54.508
548.75545.49282.18033.56212.16975.9979-0.30691.2657-2.2176-0.88020.3875-0.92390.36510.3331-0.62380.69490.05180.00330.6475-0.19790.927-23.889-21.999-86.958
557.61491.40841.71523.74681.27214.6202-0.31120.21210.1919-1.04680.18940.5343-0.3643-0.15950.15470.451-0.0043-0.04270.34390.1580.4073-32.36-12.059-80.243
563.3256-0.1555-1.452.8891-1.05783.1186-0.20860.15950.3168-0.4625-0.02770.3002-0.1536-0.28840.14480.4278-0.0222-0.05260.28690.02990.4098-32.551-15.116-82.134
572.64491.71240.78582.0685-0.53193.96980.05310.90330.2448-1.1308-0.34550.1644-0.7093-0.10480.29980.6675-0.075-0.00180.64330.16590.4466-27.398-10.462-89.63
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN I AND RESID 334:370 )I334 - 370
2X-RAY DIFFRACTION2( CHAIN I AND RESID 371:409 )I371 - 409
3X-RAY DIFFRACTION3( CHAIN I AND RESID 410:506 )I410 - 506
4X-RAY DIFFRACTION4( CHAIN I AND RESID 507:529 )I507 - 529
5X-RAY DIFFRACTION5( CHAIN L AND RESID 1:25 )L1 - 25
6X-RAY DIFFRACTION6( CHAIN L AND RESID 26:139 )L26 - 139
7X-RAY DIFFRACTION7( CHAIN L AND RESID 140:150 )L140 - 150
8X-RAY DIFFRACTION8( CHAIN L AND RESID 151:213 )L151 - 213
9X-RAY DIFFRACTION9( CHAIN H AND RESID 1:53 )H1 - 53
10X-RAY DIFFRACTION10( CHAIN H AND RESID 54:92 )H54 - 92
11X-RAY DIFFRACTION11( CHAIN H AND RESID 93:123 )H93 - 123
12X-RAY DIFFRACTION12( CHAIN H AND RESID 124:138 )H124 - 138
13X-RAY DIFFRACTION13( CHAIN H AND RESID 139:161 )H139 - 161
14X-RAY DIFFRACTION14( CHAIN H AND RESID 162:213 )H162 - 213
15X-RAY DIFFRACTION15( CHAIN A AND RESID 331:349 )A331 - 349
16X-RAY DIFFRACTION16( CHAIN A AND RESID 350:364 )A350 - 364
17X-RAY DIFFRACTION17( CHAIN A AND RESID 365:393 )A365 - 393
18X-RAY DIFFRACTION18( CHAIN A AND RESID 394:421 )A394 - 421
19X-RAY DIFFRACTION19( CHAIN A AND RESID 422:459 )A422 - 459
20X-RAY DIFFRACTION20( CHAIN A AND RESID 460:494 )A460 - 494
21X-RAY DIFFRACTION21( CHAIN A AND RESID 495:516 )A495 - 516
22X-RAY DIFFRACTION22( CHAIN A AND RESID 517:529 )A517 - 529
23X-RAY DIFFRACTION23( CHAIN B AND RESID 1:13 )B1 - 13
24X-RAY DIFFRACTION24( CHAIN B AND RESID 14:25 )B14 - 25
25X-RAY DIFFRACTION25( CHAIN B AND RESID 26:90 )B26 - 90
26X-RAY DIFFRACTION26( CHAIN B AND RESID 91:139 )B91 - 139
27X-RAY DIFFRACTION27( CHAIN B AND RESID 140:150 )B140 - 150
28X-RAY DIFFRACTION28( CHAIN B AND RESID 151:188 )B151 - 188
29X-RAY DIFFRACTION29( CHAIN B AND RESID 189:214 )B189 - 214
30X-RAY DIFFRACTION30( CHAIN C AND RESID 1:68 )C1 - 68
31X-RAY DIFFRACTION31( CHAIN C AND RESID 69:123 )C69 - 123
32X-RAY DIFFRACTION32( CHAIN C AND RESID 124:138 )C124 - 138
33X-RAY DIFFRACTION33( CHAIN C AND RESID 139:149 )C139 - 149
34X-RAY DIFFRACTION34( CHAIN C AND RESID 150:161 )C150 - 161
35X-RAY DIFFRACTION35( CHAIN C AND RESID 162:214 )C162 - 214
36X-RAY DIFFRACTION36( CHAIN D AND RESID 333:349 )D333 - 349
37X-RAY DIFFRACTION37( CHAIN D AND RESID 350:375 )D350 - 375
38X-RAY DIFFRACTION38( CHAIN D AND RESID 376:393 )D376 - 393
39X-RAY DIFFRACTION39( CHAIN D AND RESID 394:442 )D394 - 442
40X-RAY DIFFRACTION40( CHAIN D AND RESID 443:459 )D443 - 459
41X-RAY DIFFRACTION41( CHAIN D AND RESID 460:479 )D460 - 479
42X-RAY DIFFRACTION42( CHAIN D AND RESID 480:494 )D480 - 494
43X-RAY DIFFRACTION43( CHAIN D AND RESID 495:506 )D495 - 506
44X-RAY DIFFRACTION44( CHAIN D AND RESID 507:516 )D507 - 516
45X-RAY DIFFRACTION45( CHAIN D AND RESID 517:529 )D517 - 529
46X-RAY DIFFRACTION46( CHAIN E AND RESID 1:13 )E1 - 13
47X-RAY DIFFRACTION47( CHAIN E AND RESID 14:90 )E14 - 90
48X-RAY DIFFRACTION48( CHAIN E AND RESID 91:113 )E91 - 113
49X-RAY DIFFRACTION49( CHAIN E AND RESID 114:163 )E114 - 163
50X-RAY DIFFRACTION50( CHAIN E AND RESID 164:188 )E164 - 188
51X-RAY DIFFRACTION51( CHAIN E AND RESID 189:214 )E189 - 214
52X-RAY DIFFRACTION52( CHAIN F AND RESID 1:61 )F1 - 61
53X-RAY DIFFRACTION53( CHAIN F AND RESID 62:123 )F62 - 123
54X-RAY DIFFRACTION54( CHAIN F AND RESID 124:138 )F124 - 138
55X-RAY DIFFRACTION55( CHAIN F AND RESID 139:161 )F139 - 161
56X-RAY DIFFRACTION56( CHAIN F AND RESID 162:207 )F162 - 207
57X-RAY DIFFRACTION57( CHAIN F AND RESID 208:215 )F208 - 215

+
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