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- PDB-7ly3: Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab -

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Basic information

Entry
Database: PDB / ID: 7ly3
TitleCrystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab
Components
  • S2M28 Fab Heavy Chain
  • S2M28 Fab Light Chain
  • Spike protein S1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Antibody / VIRAL PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Translation of structural proteins / Maturation of spike protein / Virion Assembly and Release / suppression by virus of host tetherin activity / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding ...Translation of structural proteins / Maturation of spike protein / Virion Assembly and Release / suppression by virus of host tetherin activity / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endoplasmic reticulum-Golgi intermediate compartment / viral translation / host cell surface receptor binding / endocytosis involved in viral entry into host cell / endocytic vesicle membrane / fusion of virus membrane with host plasma membrane / viral protein processing / suppression by virus of host type I interferon-mediated signaling pathway / fusion of virus membrane with host endosome membrane / viral envelope / viral entry into host cell / : / endoplasmic reticulum lumen / host cell plasma membrane / virion membrane / integral component of membrane / identical protein binding
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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike receptor binding domain superfamily, coronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / : ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein, betacoronavirus / Spike receptor binding domain superfamily, coronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / : / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Spike glycoprotein S2 superfamily, coronavirus / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus
Similarity search - Domain/homology
Xylitol / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMcCallum, M. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
History
DepositionMar 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
B: Spike protein S1
D: S2M28 Fab Heavy Chain
C: S2M28 Fab Light Chain
E: S2M28 Fab Light Chain
F: S2M28 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,33926
Polymers168,2096
Non-polymers7,13020
Water0
1
A: Spike protein S1
D: S2M28 Fab Heavy Chain
C: S2M28 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,92513
Polymers84,1043
Non-polymers3,82110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spike protein S1
E: S2M28 Fab Light Chain
F: S2M28 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,41413
Polymers84,1043
Non-polymers3,30910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)66.444, 125.457, 365.946
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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
11(chain A and (resid 12 through 40 or (resid 41...
21(chain B and (resid 12 through 31 or (resid 32...
12(chain C and ((resid 3 and (name N or name...
22(chain E and (resid 3 through 56 or (resid 57...
13(chain D and (resid 1 through 217 or (resid 218...
23(chain F and (resid 1 through 64 or (resid 65...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 12 through 40 or (resid 41...A12 - 40
121(chain A and (resid 12 through 40 or (resid 41...A41
131(chain A and (resid 12 through 40 or (resid 41...A12 - 1902
141(chain A and (resid 12 through 40 or (resid 41...A12 - 1902
151(chain A and (resid 12 through 40 or (resid 41...A12 - 1902
161(chain A and (resid 12 through 40 or (resid 41...A12 - 1902
211(chain B and (resid 12 through 31 or (resid 32...B12 - 31
221(chain B and (resid 12 through 31 or (resid 32...B32
231(chain B and (resid 12 through 31 or (resid 32...B11 - 303
241(chain B and (resid 12 through 31 or (resid 32...B11 - 303
251(chain B and (resid 12 through 31 or (resid 32...B11 - 303
261(chain B and (resid 12 through 31 or (resid 32...B11 - 303
112(chain C and ((resid 3 and (name N or name...C3
122(chain C and ((resid 3 and (name N or name...C2 - 212
132(chain C and ((resid 3 and (name N or name...C2 - 212
142(chain C and ((resid 3 and (name N or name...C2 - 212
152(chain C and ((resid 3 and (name N or name...C2 - 212
212(chain E and (resid 3 through 56 or (resid 57...E3 - 56
222(chain E and (resid 3 through 56 or (resid 57...E57
232(chain E and (resid 3 through 56 or (resid 57...E3 - 212
242(chain E and (resid 3 through 56 or (resid 57...E3 - 212
252(chain E and (resid 3 through 56 or (resid 57...E3 - 212
262(chain E and (resid 3 through 56 or (resid 57...E3 - 212
113(chain D and (resid 1 through 217 or (resid 218...D1 - 217
123(chain D and (resid 1 through 217 or (resid 218...D218
133(chain D and (resid 1 through 217 or (resid 218...D1 - 221
213(chain F and (resid 1 through 64 or (resid 65...F1 - 64
223(chain F and (resid 1 through 64 or (resid 65...F65
233(chain F and (resid 1 through 64 or (resid 65...F1 - 221
243(chain F and (resid 1 through 64 or (resid 65...F1 - 221
253(chain F and (resid 1 through 64 or (resid 65...F1 - 221
263(chain F and (resid 1 through 64 or (resid 65...F1 - 221

NCS ensembles:
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.948841942798, -0.0135187128683, -0.315461902595), (0.00807504147932, -0.999795195955, 0.0185569353625), (-0.315648160603, 0.0150602306531, 0.948756780298)29.278558801, 19.3403153213, 3.70647989365
2given(-0.949129251261, -0.229836903326, -0.215240940043), (0.0984705552933, -0.865909737398, 0.490411945634), (-0.299093988809, 0.444269427881, 0.844492428213)19.5769930924, 3.09952658949, 20.9236028154
3given(-0.968356689393, 0.137372605122, -0.208360479625), (-0.216811407454, -0.876544096512, 0.429724633304), (-0.123604756, 0.461301652102, 0.878591287268)29.9308510479, 6.82986131684, 15.3413983811

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Spike protein S1


Mass: 37705.730 Da / Num. of mol.: 2
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

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Antibody , 2 types, 4 molecules DFCE

#2: Antibody S2M28 Fab Heavy Chain


Mass: 23778.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody S2M28 Fab Light Chain


Mass: 22619.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 5 types, 16 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 4
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
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[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_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / 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
#9: Sugar ChemComp-XYL / Xylitol / D-Xylitol / Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O5

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Non-polymers , 2 types, 4 molecules

#8: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically
#10: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.63 Å3/Da / Density % sol: 73.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 10 mM HEPES-HCl pH 8.0 750 mM NaCl 0.1 M Ammonium Sulfate 0.05 M Sodium Citrate pH 4.75 12.5 % PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 3→49.42 Å / Num. obs: 62479 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 83.5 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 12.6
Reflection shellResolution: 3→3.1 Å / Mean I/σ(I) obs: 1.39 / Num. unique obs: 6095 / Rpim(I) all: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 7LY2
Resolution: 3→49.42 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1185 5 %
Rwork0.2085 116934 -
Obs0.2088 62479 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.66 Å2 / Biso mean: 93.8569 Å2 / Biso min: 51 Å2
Refinement stepCycle: final / Resolution: 3→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10827 0 465 0 11292
Biso mean--150.19 --
Num. residues----1429
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefinement-IDRmsType
11A0X-RAY DIFFRACTION5.165TORSIONAL
12B0X-RAY DIFFRACTION5.165TORSIONAL
21C1834X-RAY DIFFRACTION5.165TORSIONAL
22E1834X-RAY DIFFRACTION5.165TORSIONAL
31D1968X-RAY DIFFRACTION5.165TORSIONAL
32F1968X-RAY DIFFRACTION5.165TORSIONAL
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3-3.140.35211490.334414568
3.14-3.30.34591480.30214678
3.3-3.510.28871500.259714623
3.51-3.780.24181510.226214515
3.78-4.160.24381460.204114701
4.16-4.760.16931470.158214632
4.76-60.18141500.180314616
6-49.420.24661440.200214601
Refinement TLS params.

Method: refined / Refinement-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.7682-1.9022-0.55541.0306-1.34538.8774-0.03640.3482-0.31921.02460.26430.09220.3444-1.0434-0.25681.07340.03370.10550.4467-0.11360.7795-0.661-20.20164.907
26.2921-1.9314-2.79562.02774.17862.1146-0.2629-0.00080.13020.60370.54230.69890.07071.6916-0.22431.4321-0.0746-0.01050.38010.06080.78639.7139.46364.853
36.90471.27821.24032.82341.65026.36770.3842-0.55590.5150.4101-0.42850.3983-0.2888-0.1188-0.04791.35060.03130.11070.5506-0.01680.74320.802-3.24992.862
45.8240.4982-1.05395.2491-1.45974.4609-0.20960.1193-0.9094-0.19670.1433-0.2380.6958-0.0956-0.01251.48430.01660.22490.5382-0.03950.8105-1.33124.70191.568
53.27661.0274-0.79390.47311.10386.0622-0.0660.0316-0.2180.38020.0457-0.13980.74560.36950.00940.86020.13130.05020.3808-0.02270.64845.422-8.89869.972
62.26140.66280.21790.1194-1.03685.52870.05170.01110.1520.4573-0.03590.3555-0.5565-0.1167-0.01640.85330.03530.06520.3236-0.02730.76411.99829.49568.517
75.18471.388-2.33084.0468-3.012.58680.4893-0.72410.71261.3132-0.1720.5614-0.73890.3253-0.32091.74360.05760.18320.5898-0.13020.849-0.685-4.693100.008
81.66160.52820.00392.39410.38823.163-0.0572-0.3283-0.32191.06770.09830.27290.3514-0.1752-0.08231.74470.06240.20740.61740.06090.8793-1.80226.02798.608
91.22490.98340.22513.21411.35791.784-0.1884-0.4482-0.37150.16730.0762-0.2472-0.0555-0.25410.12681.29520.14550.15221.20420.11941.13246.846-3.78869.746
100.986-0.21010.05741.3765-1.33742.4416-0.2390.1345-0.13320.0839-0.11120.02990.59710.3750.32951.53150.09790.14031.0548-0.09921.08245.91324.1257.742
114.18411.0099-1.51311.2883-0.31294.68250.03670.0153-0.15860.04090.281-0.85910.80031.4021-0.29730.78650.371-0.06781.2128-0.31070.865828.077-24.10939.776
123.73561.30780.47721.9191-0.98617.56350.12450.42690.39010.1660.02490.6981-0.8964-1.0768-0.13350.56340.21420.0350.67120.00350.6912-9.18344.21832.145
133.83880.05770.23813.0940.90585.76920.03760.6252-0.52080.6002-0.20470.3420.9348-0.21280.16910.78240.10280.13080.6565-0.24720.73295.941-26.50137.678
145.76430.8629-0.90154.4836-0.42649.38230.09580.5460.45120.4488-0.1635-0.365-0.94431.44890.05160.655-0.0993-0.10960.67360.11910.55912.66245.33237.246
155.1636-0.85721.43292.962-1.09114.3991-0.48-0.36620.42080.09940.2471-0.0055-0.1413-0.040.24550.4240.03550.00451.1153-0.32780.895424.055-23.7141.323
164.534-1.7758-1.77924.49920.95113.4436-0.5239-0.6698-0.01750.17170.4804-0.02630.1452-0.08870.06230.39710.0587-0.04031.23170.11030.750.84328.737.336
172.45781.51221.85695.42330.66023.3573-0.26410.0475-0.452-0.13120.2773-0.24990.09270.17270.01910.43050.04830.01591.2689-0.26130.847414.432-36.5242.282
182.0586-0.6026-0.56663.85310.70496.8051-0.2336-0.05490.1803-0.18750.3905-0.0235-0.13420.1245-0.14630.3971-0.01470.01091.16660.08210.791610.50136.175-3.295
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 12:29 )A12 - 29
2X-RAY DIFFRACTION2( CHAIN B AND RESID 11:29 )B11 - 29
3X-RAY DIFFRACTION3( CHAIN A AND RESID 30:61 )A30 - 61
4X-RAY DIFFRACTION4( CHAIN B AND RESID 30:61 )B30 - 61
5X-RAY DIFFRACTION5( CHAIN A AND RESID 62:270 )A62 - 270
6X-RAY DIFFRACTION6( CHAIN B AND RESID 62:270 )B62 - 270
7X-RAY DIFFRACTION7( CHAIN A AND RESID 271:305 )A271 - 305
8X-RAY DIFFRACTION8( CHAIN B AND RESID 271:303 )B271 - 303
9X-RAY DIFFRACTION9( CHAIN A AND RESID 1701:1702 )A1701 - 1702
10X-RAY DIFFRACTION10( CHAIN B AND RESID 401:403 )B401 - 403
11X-RAY DIFFRACTION11( CHAIN C AND RESID 2:108 )C2 - 108
12X-RAY DIFFRACTION12( CHAIN E AND RESID 3:108 )E3 - 108
13X-RAY DIFFRACTION13( CHAIN D AND RESID 1:119 )D1 - 119
14X-RAY DIFFRACTION14( CHAIN F AND RESID 1:119 )F1 - 119
15X-RAY DIFFRACTION15( CHAIN C AND RESID 109:212 )C109 - 212
16X-RAY DIFFRACTION16( CHAIN E AND RESID 109:212 )E109 - 212
17X-RAY DIFFRACTION17( CHAIN D AND RESID 120:221 )D120 - 221
18X-RAY DIFFRACTION18( CHAIN F AND RESID 120:221 )F120 - 221

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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. See below links for details.
  • 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

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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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.

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

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