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- PDB-7l0n: Circulating SARS-CoV-2 spike N439K variants maintain fitness whil... -

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Basic information

Entry
Database: PDB / ID: 7l0n
TitleCirculating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Components
  • (Monoclonal antibody S304 Fab ...) x 2
  • (Monoclonal antibody S309 Fab ...) x 2
  • Angiotensin-converting enzyme 2
  • Spike protein S1
KeywordsVIRAL PROTEIN/HYDROLASE / COVID-19 / SARS-CoV-2 / variant RBD / viral protein-receptor complex / VIRAL PROTEIN / VIRAL PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy ...positive regulation of amino acid transport / angiotensin-converting enzyme 2 / positive regulation of L-proline import across plasma membrane / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / angiotensin-mediated drinking behavior / positive regulation of gap junction assembly / regulation of systemic arterial blood pressure by renin-angiotensin / tryptophan transport / regulation of cardiac conduction / maternal process involved in female pregnancy / peptidyl-dipeptidase activity / regulation of vasoconstriction / transporter activator activity / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase activity / angiotensin maturation / Attachment and Entry / receptor-mediated endocytosis of virus by host cell / metallocarboxypeptidase activity / viral life cycle / positive regulation of cardiac muscle contraction / regulation of cytokine production / blood vessel diameter maintenance / negative regulation of smooth muscle cell proliferation / brush border membrane / negative regulation of ERK1 and ERK2 cascade / positive regulation of reactive oxygen species metabolic process / metallopeptidase activity / endocytic vesicle membrane / regulation of cell population proliferation / virus receptor activity / regulation of inflammatory response / endopeptidase activity / symbiont-mediated disruption of host tissue / Maturation of spike protein / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / viral translation / symbiont-mediated-mediated suppression of host tetherin activity / Potential therapeutics for SARS / 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 / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / cell surface / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane
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, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / 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 / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / Spike glycoprotein / Angiotensin-converting enzyme 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.78 Å
AuthorsSnell, G. / Czudnochowski, N. / Dillen, J. / Nix, J.C. / Croll, T.I. / Corti, D.
CitationJournal: Cell / Year: 2021
Title: Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.
Authors: Thomson, E.C. / Rosen, L.E. / Shepherd, J.G. / Spreafico, R. / da Silva Filipe, A. / Wojcechowskyj, J.A. / Davis, C. / Piccoli, L. / Pascall, D.J. / Dillen, J. / Lytras, S. / Czudnochowski, ...Authors: Thomson, E.C. / Rosen, L.E. / Shepherd, J.G. / Spreafico, R. / da Silva Filipe, A. / Wojcechowskyj, J.A. / Davis, C. / Piccoli, L. / Pascall, D.J. / Dillen, J. / Lytras, S. / Czudnochowski, N. / Shah, R. / Meury, M. / Jesudason, N. / De Marco, A. / Li, K. / Bassi, J. / O'Toole, A. / Pinto, D. / Colquhoun, R.M. / Culap, K. / Jackson, B. / Zatta, F. / Rambaut, A. / Jaconi, S. / Sreenu, V.B. / Nix, J. / Zhang, I. / Jarrett, R.F. / Glass, W.G. / Beltramello, M. / Nomikou, K. / Pizzuto, M. / Tong, L. / Cameroni, E. / Croll, T.I. / Johnson, N. / Di Iulio, J. / Wickenhagen, A. / Ceschi, A. / Harbison, A.M. / Mair, D. / Ferrari, P. / Smollett, K. / Sallusto, F. / Carmichael, S. / Garzoni, C. / Nichols, J. / Galli, M. / Hughes, J. / Riva, A. / Ho, A. / Schiuma, M. / Semple, M.G. / Openshaw, P.J.M. / Fadda, E. / Baillie, J.K. / Chodera, J.D. / Rihn, S.J. / Lycett, S.J. / Virgin, H.W. / Telenti, A. / Corti, D. / Robertson, D.L. / Snell, G.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Monoclonal antibody S309 Fab light chain
A: Monoclonal antibody S309 Fab heavy chain
D: Monoclonal antibody S309 Fab light chain
C: Monoclonal antibody S309 Fab heavy chain
L: Monoclonal antibody S304 Fab light chain
H: Monoclonal antibody S304 Fab heavy chain
N: Monoclonal antibody S304 Fab light chain
M: Monoclonal antibody S304 Fab heavy chain
E: Angiotensin-converting enzyme 2
F: Angiotensin-converting enzyme 2
R: Spike protein S1
S: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,02464
Polymers373,99012
Non-polymers6,03452
Water4,179232
1
B: Monoclonal antibody S309 Fab light chain
A: Monoclonal antibody S309 Fab heavy chain
L: Monoclonal antibody S304 Fab light chain
H: Monoclonal antibody S304 Fab heavy chain
E: Angiotensin-converting enzyme 2
R: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,80227
Polymers186,9956
Non-polymers2,80721
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Monoclonal antibody S309 Fab light chain
C: Monoclonal antibody S309 Fab heavy chain
N: Monoclonal antibody S304 Fab light chain
M: Monoclonal antibody S304 Fab heavy chain
F: Angiotensin-converting enzyme 2
S: Spike protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,22137
Polymers186,9956
Non-polymers3,22631
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.980, 186.580, 194.520
Angle α, β, γ (deg.)90.000, 96.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules EFRS

#5: Protein Angiotensin-converting enzyme 2 / ACE-related carboxypeptidase / Angiotensin-converting enzyme homolog / ACEH / Metalloprotease MPROT15


Mass: 69153.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACE2, UNQ868/PRO1885 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q9BYF1, angiotensin-converting enzyme 2
#6: Protein Spike protein S1 / S glycoprotein / E2 / Peplomer protein / Spike glycoprotein


Mass: 22963.859 Da / Num. of mol.: 2 / Fragment: Binding domain
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 , 4 types, 8 molecules BDACLNHM

#1: Antibody Monoclonal antibody S309 Fab light chain


Mass: 23204.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Monoclonal antibody S309 Fab heavy chain


Mass: 24573.471 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 Monoclonal antibody S304 Fab light chain


Mass: 23369.947 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Monoclonal antibody S304 Fab heavy chain


Mass: 23729.389 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 , 3 types, 11 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-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: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][b-D-Manp]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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.: 1
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
#15: 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.: 9 / 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

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Non-polymers , 8 types, 273 molecules

#9: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#11: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#12: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#13: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#14: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#16: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.09 M Buffer System 3 pH 8.5 contains Tris (base); BICINE 27% Precipitant Mix 2 contains Ethylene glycol and PEG8000 0.1 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→48.95 Å / Num. obs: 131453 / % possible obs: 94.8 % / Redundancy: 7.2 % / CC1/2: 0.97 / Rmerge(I) obs: 0.506 / Rpim(I) all: 0.202 / Rrim(I) all: 0.545 / Net I/σ(I): 3.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.78-2.834.73.263173368120.181.6413.6710.599.8
15.23-48.97.10.160748570.9940.0410.1089.896.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M0j, 7jx3

6m0j

7jx3


Resolution: 2.78→48.9 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.836 / SU B: 31.038 / SU ML: 0.539 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.067 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3247 6375 5 %RANDOM
Rwork0.2904 ---
obs0.2921 122372 92.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 194.15 Å2 / Biso mean: 86.099 Å2 / Biso min: 18.99 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å2-0 Å20.79 Å2
2--4.32 Å20 Å2
3----2.53 Å2
Refinement stepCycle: final / Resolution: 2.78→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25898 0 347 232 26477
Biso mean--107.2 49.17 -
Num. residues----3304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01226919
X-RAY DIFFRACTIONr_angle_refined_deg0.6681.65236609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36153286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54323.181302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49154258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6615111
X-RAY DIFFRACTIONr_chiral_restr0.0560.23490
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0220534
LS refinement shellResolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 390 -
Rwork0.423 7386 -
all-7776 -
obs--76.78 %

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