[English] 日本語
Yorodumi
- PDB-6ghn: HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P9-Phe. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ghn
TitleHLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P9-Phe.
Components
  • ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, E alpha chain variant
KeywordsIMMUNE SYSTEM / Complex / Histocompatibility antigen
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production ...trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / enoyl-[acyl-carrier-protein] reductase (NADH) / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / antigen processing and presentation / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / NAD+ binding / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / T cell receptor binding / peptidoglycan-based cell wall / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / fatty acid binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / NAD(P)-binding domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin / Enoyl-[acyl-carrier-protein] reductase [NADH] / HLA class I histocompatibility antigen, E alpha chain variant
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacteriaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.542 Å
AuthorsWalters, L.C. / Gillespie, G.M. / McMichael, A.J. / Rozbesky, D. / Jones, E.Y. / Harlos, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1133649 United States
CitationJournal: Nat Commun / Year: 2018
Title: Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding.
Authors: Walters, L.C. / Harlos, K. / Brackenridge, S. / Rozbesky, D. / Barrett, J.R. / Jain, V. / Walter, T.S. / O'Callaghan, C.A. / Borrow, P. / Toebes, M. / Hansen, S.G. / Sacha, J. / Abdulhaqq, S. ...Authors: Walters, L.C. / Harlos, K. / Brackenridge, S. / Rozbesky, D. / Barrett, J.R. / Jain, V. / Walter, T.S. / O'Callaghan, C.A. / Borrow, P. / Toebes, M. / Hansen, S.G. / Sacha, J. / Abdulhaqq, S. / Greene, J.M. / Fruh, K. / Marshall, E. / Picker, L.J. / Jones, E.Y. / McMichael, A.J. / Gillespie, G.M.
History
DepositionMay 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, E alpha chain variant
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, E alpha chain variant
D: Beta-2-microglobulin
P: ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
Q: ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1758
Polymers88,9836
Non-polymers1922
Water4,378243
1
A: HLA class I histocompatibility antigen, E alpha chain variant
B: Beta-2-microglobulin
P: ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5874
Polymers44,4913
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-34 kcal/mol
Surface area19400 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, E alpha chain variant
D: Beta-2-microglobulin
Q: ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5874
Polymers44,4913
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-37 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.453, 64.681, 97.308
Angle α, β, γ (deg.)107.03, 93.89, 106.84
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein HLA class I histocompatibility antigen, E alpha chain variant


Mass: 31597.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS / References: UniProt: Q59EE1, UniProt: P13747*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS / References: UniProt: P61769
#3: Protein/peptide ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE


Mass: 1014.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacteriaceae (bacteria) / References: UniProt: P9WGR1*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Ammonium Sulphate, 0.1 M HEPES, pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.54→58.5 Å / Num. obs: 26488 / % possible obs: 97.7 % / Redundancy: 4.9 % / CC1/2: 0.98 / Rmerge(I) obs: 0.21 / Net I/σ(I): 5.2
Reflection shellResolution: 2.54→2.59 Å / Num. unique obs: 1053 / CC1/2: 0.57 / % possible all: 77.5

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GH1

6gh1


Resolution: 2.542→58.498 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.64
RfactorNum. reflection% reflection
Rfree0.2642 1274 4.84 %
Rwork0.2183 --
obs0.2205 26305 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.542→58.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6231 0 10 245 6486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066424
X-RAY DIFFRACTIONf_angle_d0.8378728
X-RAY DIFFRACTIONf_dihedral_angle_d16.8543800
X-RAY DIFFRACTIONf_chiral_restr0.053893
X-RAY DIFFRACTIONf_plane_restr0.0061142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5418-2.64350.39361240.31722486X-RAY DIFFRACTION87
2.6435-2.76380.32381340.30652738X-RAY DIFFRACTION96
2.7638-2.90950.35481440.27412839X-RAY DIFFRACTION98
2.9095-3.09180.27721470.24692828X-RAY DIFFRACTION98
3.0918-3.33050.28381510.24112795X-RAY DIFFRACTION98
3.3305-3.66560.25051300.20362819X-RAY DIFFRACTION99
3.6656-4.19590.22621490.1742860X-RAY DIFFRACTION99
4.1959-5.28590.2231330.1692844X-RAY DIFFRACTION99
5.2859-58.51330.23321620.21242822X-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)
11.941-0.9959-0.57541.8327-0.59923.6758-0.02360.2435-0.3670.09460.06240.19720.156-0.497-0.04070.126-0.0216-0.02770.34290.03310.3266-10.46056.0756-5.3734
26.14380.8104-2.1841.4055-1.34733.7309-0.0405-0.2780.695900.31610.19450.00610.072-0.27590.10430.0156-0.02770.2073-0.00230.2281-9.389314.3541-14.4668
32.2978-0.3777-2.69941.1919-0.03055.09950.146-0.22470.30670.0418-0.0118-0.0803-0.34920.3347-0.14110.199-0.0169-0.08140.24920.04410.28314.9614.8111-7.1656
41.20712.0936-2.2523.6313-3.8224.09860.59210.09440.73220.63570.0170.2083-1.08130.043-0.55150.23240.00490.0460.44320.00230.33532.5624.9534-8.9108
52.3773-1.0350.49674.2304-0.77921.3811-0.1636-0.3496-0.3780.45630.21790.11180.08640.002-0.07430.35420.0522-0.01980.37550.00670.22261.331-4.144813.859
63.0798-0.34080.34852.52040.3931.3293-0.572-0.9965-0.27660.44550.5461-0.57740.08470.3097-0.04880.4470.1316-0.02770.48120.08130.39849.8731-10.685616.5224
72.64731.4525-1.59394.7488-0.63353.7714-0.0035-0.0783-0.03040.686-0.1235-0.01920.2680.09040.09520.33620.039-0.02970.2214-0.00190.28791.0105-12.83880.3157
84.56330.9984-1.42025.0113-0.3283.91690.00630.39410.10180.07260.20430.54280.596-0.1504-0.04920.21080.00750.03970.299-0.00340.2473-2.1205-11.6827-5.5862
94.6243-0.2047-0.78144.5059-0.38333.9461-0.25580.8078-0.62870.0377-0.28421.10190.7208-0.76270.18560.3915-0.13940.05010.4311-0.12630.4282-10.1044-18.4754-7.6906
102.7834-0.2021-1.09586.1821-1.88173.77270.3277-0.3372-0.26640.1236-0.5793-0.09920.41250.11270.20350.2424-0.0081-0.06810.25330.03330.161-2.6215-4.7312-3.3014
114.1605-2.2908-0.43573.572-0.68342.46210.1690.1426-0.20170.36760.43820.1038-0.71170.4387-0.64970.95820.25680.14770.5080.01470.4995-3.9206-30.1183.3329
122.4345-0.4908-0.02141.8907-3.62987.5689-0.18260.0642-0.1214-0.0445-0.2939-0.00150.8620.75890.44080.47040.0721-0.02140.2532-0.02830.36373.5965-18.0891-6.0301
132.0084-0.3277-0.1891.7293-0.11322.263-0.1078-0.19940.1876-0.04430.06120.1664-0.071-0.27350.06970.10080.02730.0040.23460.03160.3035-7.7073-30.9572-34.0262
141.5822-1.34322.38981.3731-0.64656.38470.31080.1347-0.2445-0.2298-0.04890.03880.72520.1437-0.23760.2032-0.0191-0.03660.2306-0.00250.30251.752-41.5334-40.3014
153.5832.5324-0.47994.117-1.54331.1036-0.54580.1568-0.2474-0.69420.1737-0.4639-0.15840.19160.34910.46670.01310.06940.3440.04650.24138.2242-11.5062-59.6834
168.1586-4.23273.8665.7163-1.10163.87330.1368-0.82560.1928-0.2860.0475-0.37060.2342-0.3073-0.13740.2676-0.0647-0.03040.2713-0.01510.21876.2437-13.9459-37.3199
170.8742-0.7778-0.90593.22131.13980.97420.20870.77870.5254-1.2159-0.1860.7622-0.4538-0.2494-0.08410.83220.0159-0.22790.30490.11640.5803-7.0871-0.9746-54.6522
182.8065-1.26270.63384.8398-2.18371.5016-0.1641-0.34640.01190.18140.13790.2962-0.6052-0.0295-0.00050.27150.0022-0.0680.2741-0.08180.2584-2.043-10.1301-37.9753
194.57982.7363-0.62794.8405-2.52742.2860.1284-1.18340.94310.7883-0.20451.177-0.3056-0.2836-0.03760.36910.1146-0.00560.4499-0.07730.4791-9.8587-3.4478-35.8013
201.94250.35050.30476.3463-0.64521.04880.28260.0967-0.0607-0.2378-0.27780.3598-0.1611-0.00250.00190.22440.04240.0040.31860.01150.1876-2.5513-17.0776-40.3337
210.0137-0.2080.09893.1123-1.36220.5964-0.1793-0.21891.2891-0.09450.1933-0.6134-0.47830.70080.00840.8865-0.1986-0.41470.3643-0.11731.003-3.98678.4008-46.8197
227.0563-5.12846.17889.01741.98111.9885-0.3903-0.48230.0118-0.2644-0.5115-0.156-1.4282-0.50450.72020.51690.0266-0.10350.2992-0.10930.4207-0.2976-3.3986-35.5389
236.7014-2.1679-3.7055.2726-1.48695.50360.6562-0.64870.76671.12380.3464-0.9526-1.46070.6887-0.72680.5946-0.1319-0.02770.27310.0140.31157.6266-9.0327-27.6077
246.04430.1659-0.90546.39750.46779.46330.31410.3371-0.0668-0.35560.0119-0.4027-0.37150.5077-0.34940.361-0.03580.0360.3333-0.03350.36093.7212-0.6812-44.8535
252.72850.3025-1.42191.5895-0.86893.42570.2035-0.16570.3865-0.07570.46360.0645-0.1856-0.2468-0.5197-0.5604-0.323-0.31490.2486-0.04830.5398-6.067819.12-9.9929
261.6902-0.20690.18493.1033-1.10856.0051-0.14150.0474-0.54820.05690.2380.07720.5648-0.4597-0.08360.1410.03350.05370.32150.05670.2593-6.0728-40.9282-33.4355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 138 )
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 274 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 20 )
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 78 )
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 103 )
14X-RAY DIFFRACTION14chain 'C' and (resid 104 through 174 )
15X-RAY DIFFRACTION15chain 'C' and (resid 175 through 274 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 12 )
17X-RAY DIFFRACTION17chain 'D' and (resid 13 through 20 )
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 42 )
19X-RAY DIFFRACTION19chain 'D' and (resid 43 through 52 )
20X-RAY DIFFRACTION20chain 'D' and (resid 53 through 72 )
21X-RAY DIFFRACTION21chain 'D' and (resid 73 through 78 )
22X-RAY DIFFRACTION22chain 'D' and (resid 79 through 84 )
23X-RAY DIFFRACTION23chain 'D' and (resid 85 through 91 )
24X-RAY DIFFRACTION24chain 'D' and (resid 92 through 100 )
25X-RAY DIFFRACTION25chain 'P' and (resid 1 through 9 )
26X-RAY DIFFRACTION26chain 'Q' and (resid 1 through 9 )

+
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