[English] 日本語
Yorodumi
- PDB-8vqr: Crystal structure of chimeric SARS-CoV-2 RBD complexed with chime... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vqr
TitleCrystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric raccoon dog ACE2
Components
  • Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsHYDROLASE/VIRAL PROTEIN / SARS2 / CELL INVASION / HYDROLASE-VIRAL PROTEIN complex / HYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction ...Hydrolases; Acting on peptide bonds (peptidases) / positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / angiotensin-mediated drinking behavior / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / regulation of systemic arterial blood pressure by renin-angiotensin / positive regulation of gap junction assembly / tryptophan transport / regulation of cardiac conduction / regulation of vasoconstriction / peptidyl-dipeptidase activity / maternal process involved in female pregnancy / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / regulation of transmembrane transporter activity / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / metallopeptidase activity / positive regulation of reactive oxygen species metabolic process / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / Potential therapeutics for SARS / 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 / cilium / symbiont-mediated suppression of host innate immune response / apical plasma membrane / receptor ligand activity / membrane raft / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / symbiont 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 / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / metal ion binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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 ...Collectrin domain / Renal amino acid transporter / Collectrin-like domain profile. / Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature. / 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
Angiotensin-converting enzyme / Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesNyctereutes procyonoides (raccoon dog)
Homo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.565 Å
AuthorsHsueh, F.-C. / Shi, K. / Aihara, H. / Li, F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089728 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110700 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Plos Pathog. / Year: 2024
Title: Structural basis for raccoon dog receptor recognition by SARS-CoV-2.
Authors: Hsueh, F.C. / Shi, K. / Mendoza, A. / Bu, F. / Zhang, W. / Aihara, H. / Li, F.
History
DepositionJan 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 13, 2024Group: 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 / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2
B: Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2
E: Spike protein S1
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,47519
Polymers192,3664
Non-polymers5,10915
Water28816
1
A: Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2
E: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7789
Polymers96,1832
Non-polymers2,5957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2
F: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,69710
Polymers96,1832
Non-polymers2,5148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.961, 118.107, 112.233
Angle α, β, γ (deg.)90.00, 92.89, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 4 molecules ABEF

#1: Protein Angiotensin-converting enzyme,Processed angiotensin-converting enzyme 2


Mass: 70028.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nyctereutes procyonoides (raccoon dog), (gene. exp.) Homo sapiens (human)
Gene: ACE2, NYPRO_LOCUS14582, ACE2, UNQ868/PRO1885 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: B4XEP4, UniProt: Q9BYF1, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Spike protein S1


Mass: 26154.381 Da / Num. of mol.: 2 / Fragment: receptor-binding domain
Mutation: Q321V, T323S, E324G, S325D, I326V, A348P, N354E, R357K, A372T, S373F, P384A, T393S, I402V, R403K, E406D, K417V, T430M, I434L, S438T, N439R, L441I, S443A, V445S, G446T, L452K, H519N, K529L, N532D, V534I, N536S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: S, 2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTC2

-
Sugars , 7 types, 9 molecules

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


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


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-2-3/a4-b1_a6-e1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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.: 2
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
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#11: 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.: 2
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 , 4 types, 22 molecules

#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#12: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris (pH 8-8.5), 18-22% PEG 6000, 100 mM NaCl and ethylene glycol (0.5-2%)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.565→112.091 Å / Num. obs: 42428 / % possible obs: 62.8 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.028 / Rrim(I) all: 0.057 / Net I/σ(I): 9.8 / Num. measured all: 166083
Reflection shellResolution: 2.565→2.838 Å / % possible obs: 12.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.733 / Num. measured all: 8531 / Num. unique obs: 2121 / Rpim(I) all: 0.42 / Rrim(I) all: 0.847 / Net I/σ(I) obs: 1.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.565→58.41 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2642 2202 5.19 %
Rwork0.2138 --
obs0.2165 42417 62.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.565→58.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12781 0 329 16 13126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d13.0514934
X-RAY DIFFRACTIONf_chiral_restr0.0611991
X-RAY DIFFRACTIONf_plane_restr0.0032329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.565-2.620.661250.394395X-RAY DIFFRACTION2
2.62-2.680.3945210.4171333X-RAY DIFFRACTION8
2.68-2.750.4807340.3761578X-RAY DIFFRACTION15
2.75-2.820.3831340.3725815X-RAY DIFFRACTION20
2.82-2.910.2543350.35891054X-RAY DIFFRACTION26
2.91-30.3378730.35051413X-RAY DIFFRACTION35
3-3.110.38641120.35051908X-RAY DIFFRACTION48
3.11-3.230.36821280.33592735X-RAY DIFFRACTION68
3.23-3.380.37882030.28943324X-RAY DIFFRACTION83
3.38-3.560.35282310.26293863X-RAY DIFFRACTION98
3.56-3.780.30562430.23373989X-RAY DIFFRACTION100
3.78-4.070.24862810.1983942X-RAY DIFFRACTION100
4.07-4.480.23052350.1793977X-RAY DIFFRACTION99
4.48-5.130.2141540.17284075X-RAY DIFFRACTION100
5.13-6.460.25171860.20864032X-RAY DIFFRACTION100
6.46-58.410.22012270.18484082X-RAY DIFFRACTION99
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)
12.06670.2023-0.45510.49470.74041.3977-0.2668-0.2403-0.4531-0.0041-0.5185-0.6810.56870.3147-0.09180.7521-0.03910.07020.84560.49040.809119.4563-21.020259.331
23.11110.8152-1.64091.8629-1.26812.0223-0.36520.0425-0.3811-0.18080.1232-0.28770.60660.0329-0.03360.17090.05340.02970.44360.10390.365639.6971-3.143843.3632
32.1417-0.3043-1.4212.3581-2.06813.17250.4006-0.19480.83361.2623-0.6375-0.908-1.24530.6470.89950.7742-0.3685-0.37171.00420.53330.932918.97757.353757.9132
42.14010.9816-0.85461.3107-1.33191.4377-0.28870.84450.2229-0.54340.33030.08210.3136-0.6209-0.27710.21070.07620.02260.53830.28450.416830.1019-0.576338.2787
52.07550.67220.29081.1548-0.7390.7972-0.02630.94740.0005-0.82150.35890.15230.5924-0.5847-0.29641.27260.12190.06821.24470.2580.5495-1.368434.392-16.0326
61.68430.74790.51962.7407-2.23842.6930.01330.70370.7372-0.16170.30660.4841-0.8012-0.774-0.27670.60270.15750.02950.89260.37020.6731-25.903334.27245.0448
71.3003-0.1849-0.15651.7755-0.30271.2197-0.09950.6433-0.3627-0.63360.20280.11290.0336-0.22210.08890.19480.01260.21880.3949-0.03190.1258-14.86617.11439.5709
82.0344-0.5082-0.3592.18440.75941.42670.00260.23170.467-0.3992-0.1006-0.1128-0.482-0.25720.11030.18840.1667-0.03910.43980.09250.30932.893537.080410.4756
91.80590.5454-0.81721.7023-0.71971.396-0.19250.4243-0.2218-0.43810.2171-0.04660.3754-0.3384-0.01040.29970.00780.07660.38140.03090.1862-8.218718.16829.1529
104.8663-2.3863-1.81768.94473.35647.0610.1797-0.5297-0.04530.1135-0.1711.1329-1.5592-1.4461-0.00830.73930.12150.02830.95180.03880.3563-15.0836-9.936983.3919
117.7919-2.70550.00154.16960.92368.7888-0.2744-0.05531.64071.09730.32750.7766-1.9205-2.4748-0.0741.37330.54430.11621.14420.33041.067-19.15761.811575.5646
120.3139-0.64220.77247.2946-0.9541.96590.24590.7810.08670.0612-0.2790.4912-1.1219-0.8528-0.24470.4852-0.0921-0.11060.94950.14770.3325-10.373-10.40572.0193
131.7284-0.20911.15422.0802-0.02322.6106-0.05050.3881-0.2119-0.3071-0.05930.46910.0791-0.8133-0.09170.5756-0.2087-0.19430.92870.02150.3135-7.0899-17.833669.5989
143.8367-1.5325-1.56084.8464-0.98894.0974-0.2440.4086-0.228-0.14-0.2149-0.0134-0.1452-0.13790.460.5093-0.2126-0.13010.56530.03290.2574-0.5941-17.54670.695
152.66364.42520.03557.46350.02790.0091-0.3318-0.06090.82690.4415-0.31862.3658-0.294-1.23580.42152.2699-0.21240.28362.4626-0.00981.3864-32.3476-6.326280.432
161.19980.34440.03522.7193-0.50475.93460.17730.08710.3725-0.1579-0.1452-0.6618-0.82240.72550.59551.2006-0.05230.67351.01250.51861.678335.108957.5261-11.2376
171.85750.1167-2.13570.28390.82568.31670.477-0.66770.0695-0.4878-0.4209-1.6408-0.42832.6747-0.09081.32110.04840.82081.44980.41112.149742.475756.9068-12.584
181.47363.0088-1.6447.8546-0.25567.49171.1252-1.17880.12851.1559-1.1792-0.1108-1.12510.24080.06561.34520.28540.44941.47160.33061.489135.945250.94381.6113
198.28155.1147-0.19413.1828-0.55427.7086-0.0182-0.03550.470.2385-0.21710.2706-0.74381.80650.21171.04480.13890.61851.20890.57651.739546.710245.7242-3.5107
200.5699-0.6903-0.25150.83230.29770.21140.13890.28530.1731-0.5631-0.2221-0.69340.18090.14320.33380.86650.34120.59580.6950.50741.083627.163343.6528-13.1594
213.6687-0.0267-0.86270.79340.49151.5986-0.42551.0478-0.2944-0.8635-0.0238-0.69030.2516-0.2711-0.42471.54240.28270.71411.17130.38231.10125.339939.2379-29.0449
223.71532.0078-2.32531.3672-1.33111.4746-0.04871.5499-0.0026-1.5014-0.2252-0.17770.8442-0.4934-0.01471.34170.46750.3421.03710.24340.703513.955841.7532-19.6817
230.1152-0.4384-0.72731.70012.74534.57750.3892-0.36340.2598-0.58450.0346-0.7486-0.63481.67630.06560.97710.19510.43731.29350.48721.0640.72850.7032-9.8626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 293 )
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 431 )
4X-RAY DIFFRACTION4chain 'A' and (resid 432 through 614 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 129 )
6X-RAY DIFFRACTION6chain 'B' and (resid 130 through 194 )
7X-RAY DIFFRACTION7chain 'B' and (resid 195 through 293 )
8X-RAY DIFFRACTION8chain 'B' and (resid 294 through 387 )
9X-RAY DIFFRACTION9chain 'B' and (resid 388 through 614 )
10X-RAY DIFFRACTION10chain 'E' and (resid 335 through 364 )
11X-RAY DIFFRACTION11chain 'E' and (resid 365 through 393 )
12X-RAY DIFFRACTION12chain 'E' and (resid 394 through 409 )
13X-RAY DIFFRACTION13chain 'E' and (resid 410 through 479 )
14X-RAY DIFFRACTION14chain 'E' and (resid 480 through 516 )
15X-RAY DIFFRACTION15chain 'E' and (resid 517 through 527 )
16X-RAY DIFFRACTION16chain 'F' and (resid 331 through 353 )
17X-RAY DIFFRACTION17chain 'F' and (resid 354 through 364 )
18X-RAY DIFFRACTION18chain 'F' and (resid 365 through 377 )
19X-RAY DIFFRACTION19chain 'F' and (resid 378 through 393 )
20X-RAY DIFFRACTION20chain 'F' and (resid 394 through 459 )
21X-RAY DIFFRACTION21chain 'F' and (resid 460 through 479 )
22X-RAY DIFFRACTION22chain 'F' and (resid 480 through 506 )
23X-RAY DIFFRACTION23chain 'F' and (resid 507 through 527 )

+
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