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- PDB-9f40: Crystal structure of the NTD domain from S. cerevisia Niemann-Pic... -

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Basic information

Entry
Database: PDB / ID: 9f40
TitleCrystal structure of the NTD domain from S. cerevisia Niemann-Pick type C protein NCR1 with ergosterol bound
ComponentsNPC intracellular sterol transporter 1-related protein 1
KeywordsMEMBRANE PROTEIN / ergosterol / vacuole / NCR1 / Niemann-Pick type C protein
Function / homology
Function and homology information


Intestinal lipid absorption / LDL clearance / sterol binding / sterol transport / sphingolipid metabolic process / fungal-type vacuole membrane / transmembrane transporter activity / endoplasmic reticulum / membrane
Similarity search - Function
Niemann-Pick C1, N-terminal / : / Niemann-Pick C1 N terminus / NPC1, middle luminal domain / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Acriflavin resistance protein / AcrB/AcrD/AcrF family
Similarity search - Domain/homology
ACETONITRILE / ERGOSTEROL / DI(HYDROXYETHYL)ETHER / NPC intracellular sterol transporter 1-related protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsNel, L. / Olesen, E. / Frain, K.M. / Pedersen, B.P.
Funding support Denmark, European Union, 3items
OrganizationGrant numberCountry
Danish Council for Independent Research0135-00032B Denmark
The Carlsberg FoundationCF19-0127 Denmark
European Research Council (ERC)637372European Union
CitationJournal: Life Sci Alliance / Year: 2025
Title: Structural and biochemical analysis of ligand binding in yeast Niemann-Pick type C1-related protein.
Authors: Nel, L. / Thaysen, K. / Jamecna, D. / Olesen, E. / Szomek, M. / Langer, J. / Frain, K.M. / Hoglinger, D. / Wustner, D. / Pedersen, B.P.
History
DepositionApr 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 6, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NPC intracellular sterol transporter 1-related protein 1
B: NPC intracellular sterol transporter 1-related protein 1
C: NPC intracellular sterol transporter 1-related protein 1
D: NPC intracellular sterol transporter 1-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,16079
Polymers111,2394
Non-polymers16,92175
Water3,495194
1
A: NPC intracellular sterol transporter 1-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,32019
Polymers27,8101
Non-polymers4,51018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NPC intracellular sterol transporter 1-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,86819
Polymers27,8101
Non-polymers4,05818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NPC intracellular sterol transporter 1-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,17124
Polymers27,8101
Non-polymers4,36123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NPC intracellular sterol transporter 1-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,80117
Polymers27,8101
Non-polymers3,99216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.760, 109.580, 151.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-303-

SO4

21A-402-

HOH

31B-429-

HOH

41D-414-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 20 through 241 or resid 300 through 403))
d_2ens_1(chain "B" and (resid 20 through 241 or resid 300 through 403))
d_3ens_1(chain "C" and (resid 20 through 241 or resid 300 through 403))
d_4ens_1(chain "D" and (resid 20 through 241 or resid 300 through 403))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11THRTHRHISHISAA20 - 24120 - 241
d_12ERGERGERGERGAQ301
d_13NAGNAGNAGNAGEE1
d_14NAGNAGNAGNAGEE2
d_15BMABMABMABMAEE3
d_16MANMANMANMANEE7
d_21THRTHRHISHISBB20 - 24120 - 241
d_22ERGERGERGERGBFA301
d_23NAGNAGNAGNAGHH1
d_24NAGNAGNAGNAGHH2
d_25BMABMABMABMAHH3
d_26MANMANMANMANHH4
d_31THRTHRHISHISCC20 - 24120 - 241
d_32ERGERGERGERGCUA301
d_33NAGNAGNAGNAGKK1
d_34NAGNAGNAGNAGKK2
d_35BMABMABMABMAKK3
d_36MANMANMANMANKK4
d_41THRTHRHISHISDD20 - 24120 - 241
d_42ERGERGERGERGDOB301
d_43NAGNAGNAGNAGNN1
d_44NAGNAGNAGNAGNN2
d_45BMABMABMABMANN3
d_46MANMANMANMANNN7

NCS oper:
IDCodeMatrixVector
1given(-0.999694761285, -0.0247047974019, -0.000239260086604), (0.0245772247192, -0.993451860706, -0.111576702252), (0.00251878644568, -0.111548525072, 0.993755796093)165.124534929, 271.199589121, 15.0068553579
2given(0.999639570891, 0.0266823285233, -0.00296338538953), (-0.0261584194166, 0.992899596287, 0.116043650347), (0.00603865895852, -0.11592430736, 0.993239693911)43.5025154398, 2.79643540701, 16.7253393833
3given(-0.99999969131, 0.00047132480028, -0.000628675191999), (-0.000475355139979, -0.999979238927, 0.00642617717731), (-0.000625633323353, 0.0064264740376, 0.99997915429)208.788424944, 273.797240428, 0.793304894209

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NPC intracellular sterol transporter 1-related protein 1 / Niemann-Pick type C-related protein 1


Mass: 27809.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NCR1, YPL006W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12200

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Sugars , 7 types, 12 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_f2-g1WURCSPDB2Glycan 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-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c6-d1_d3-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}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.: 3
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)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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-D-Manp]{}}}}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

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Non-polymers , 6 types, 257 molecules

#9: Chemical
ChemComp-ERG / ERGOSTEROL


Mass: 396.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C28H44O / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: SO4
#11: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 29
Source method: isolated from a genetically manipulated source
Formula: Zn
#12: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#13: Chemical
ChemComp-CCN / ACETONITRILE


Mass: 41.052 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C2H3N
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50mM ZnSO4, 42% PEG 200, 4% v/v acetonitrile and 100mM MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.44→47.18 Å / Num. obs: 58262 / % possible obs: 99.9 % / Redundancy: 7.47 % / Biso Wilson estimate: 74.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.094 / Net I/σ(I): 12.19
Reflection shellResolution: 2.44→2.59 Å / Rmerge(I) obs: 1.514 / Num. unique obs: 9257 / CC1/2: 0.619 / Rrim(I) all: 1.628

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→45.05 Å / SU ML: 0.4178 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2572 2096 3.61 %
Rwork0.2143 56007 -
obs0.2159 58103 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.82 Å2
Refinement stepCycle: LAST / Resolution: 2.44→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6936 0 1033 194 8163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00368078
X-RAY DIFFRACTIONf_angle_d0.660110899
X-RAY DIFFRACTIONf_chiral_restr0.04351336
X-RAY DIFFRACTIONf_plane_restr0.00321304
X-RAY DIFFRACTIONf_dihedral_angle_d12.80663260
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.00773348616
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.04168851412
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.541384656542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.50.43631370.39483686X-RAY DIFFRACTION99.82
2.5-2.560.42231370.3363675X-RAY DIFFRACTION99.95
2.56-2.630.3111380.30273681X-RAY DIFFRACTION99.92
2.63-2.710.30061370.28653702X-RAY DIFFRACTION99.92
2.71-2.790.32971390.28353706X-RAY DIFFRACTION99.92
2.79-2.890.3011390.28933705X-RAY DIFFRACTION99.95
2.89-3.010.34671380.28073701X-RAY DIFFRACTION99.79
3.01-3.150.31581390.26233708X-RAY DIFFRACTION99.9
3.15-3.310.26511400.243740X-RAY DIFFRACTION99.85
3.31-3.520.29291400.23043731X-RAY DIFFRACTION99.97
3.52-3.790.26921400.20363746X-RAY DIFFRACTION99.92
3.79-4.170.19671400.17153745X-RAY DIFFRACTION99.95
4.17-4.770.19041420.16463793X-RAY DIFFRACTION99.82
4.77-6.010.20481420.18473814X-RAY DIFFRACTION99.85
6.01-45.050.29041480.21313874X-RAY DIFFRACTION97.13
Refinement TLS params.Method: refined / Origin x: 104.345318123 Å / Origin y: 136.733230677 Å / Origin z: 21.4033352199 Å
111213212223313233
T0.755945016761 Å20.0399200183082 Å20.0163191922566 Å2-0.428521057521 Å2-0.0361460690916 Å2--0.44265970951 Å2
L1.55238940269 °20.180122811457 °2-0.0196337432933 °2-0.275162639792 °20.00412730006085 °2--0.310284823703 °2
S0.046116350453 Å °-0.267547330808 Å °0.231403896664 Å °-0.0852820369008 Å °-0.0168543862869 Å °-0.0177967188663 Å °-0.0639327117748 Å °-0.000854515783757 Å °-0.0266735098735 Å °
Refinement TLS groupSelection details: all

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  • 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

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