[English] 日本語
Yorodumi
- PDB-6qzc: HLA-DR1 with the QAR Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qzc
TitleHLA-DR1 with the QAR Peptide
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • M1-208-222-QAR-Peptide
KeywordsIMMUNE SYSTEM / HLA-DR1 / CD4 / T-cell / Influenza / Matrix / Conserved
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsGreenshields-Watson, A. / Rizkallah, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell Rep / Year: 2020
Title: CD4+T Cells Recognize Conserved Influenza A Epitopes through Shared Patterns of V-Gene Usage and Complementary Biochemical Features.
Authors: Greenshields-Watson, A. / Attaf, M. / MacLachlan, B.J. / Whalley, T. / Rius, C. / Wall, A. / Lloyd, A. / Hughes, H. / Strange, K.E. / Mason, G.H. / Schauenburg, A.J. / Hulin-Curtis, S.L. / ...Authors: Greenshields-Watson, A. / Attaf, M. / MacLachlan, B.J. / Whalley, T. / Rius, C. / Wall, A. / Lloyd, A. / Hughes, H. / Strange, K.E. / Mason, G.H. / Schauenburg, A.J. / Hulin-Curtis, S.L. / Geary, J. / Chen, Y. / Lauder, S.N. / Smart, K. / Vijaykrishna, D. / Grau, M.L. / Shugay, M. / Andrews, R. / Dolton, G. / Rizkallah, P.J. / Gallimore, A.M. / Sewell, A.K. / Godkin, A.J. / Cole, D.K.
History
DepositionMar 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: HLA class II histocompatibility antigen, DR alpha chain
BBB: HLA class II histocompatibility antigen, DRB1-1 beta chain
CCC: M1-208-222-QAR-Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,51210
Polymers44,9703
Non-polymers5437
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-42 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.060, 116.080, 43.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AAABBB

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 20913.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR1


Mass: 22227.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04229

-
Protein/peptide , 1 types, 1 molecules CCC

#3: Protein/peptide M1-208-222-QAR-Peptide


Mass: 1828.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus

-
Non-polymers , 5 types, 227 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6 / Details: 0.1 M Na Cacodylate, 0.2 M NH4 SO4, 20% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.64→71.16 Å / Num. obs: 56957 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.3
Reflection shellResolution: 1.64→1.68 Å / Rmerge(I) obs: 1.912 / Num. unique obs: 4141 / CC1/2: 0.518 / Rpim(I) all: 0.753

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DLH

1dlh


Resolution: 1.64→71.156 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.607 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2399 2819 4.954 %
Rwork0.2018 --
all0.204 --
obs-56904 99.797 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.371 Å2
Baniso -1Baniso -2Baniso -3
1--1.414 Å20 Å20 Å2
2---1.492 Å20 Å2
3---2.906 Å2
Refinement stepCycle: LAST / Resolution: 1.64→71.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3135 0 34 220 3389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133258
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172898
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.6564428
X-RAY DIFFRACTIONr_angle_other_deg1.3491.5716705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg23.3355.593405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51821.828186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97115498
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg11.96153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9541523
X-RAY DIFFRACTIONr_chiral_restr0.0790.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024187
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02744
X-RAY DIFFRACTIONr_nbd_refined0.2050.2506
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.22699
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21496
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21593
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.222
X-RAY DIFFRACTIONr_nbd_other0.2120.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.211
X-RAY DIFFRACTIONr_mcbond_it1.0631.8321549
X-RAY DIFFRACTIONr_mcbond_other1.0631.8311548
X-RAY DIFFRACTIONr_mcangle_it1.6852.7371934
X-RAY DIFFRACTIONr_mcangle_other1.6852.7381935
X-RAY DIFFRACTIONr_scbond_it1.472.0821708
X-RAY DIFFRACTIONr_scbond_other1.4672.0521705
X-RAY DIFFRACTIONr_scangle_it2.2633.0312494
X-RAY DIFFRACTIONr_scangle_other2.2572.9832489
X-RAY DIFFRACTIONr_lrange_it6.92721.7793427
X-RAY DIFFRACTIONr_lrange_other6.86621.3823393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.64-1.6830.4441730.40539670.40641520.3440.39599.7110.409
1.683-1.7290.3951920.38638640.38640680.1650.15199.7050.384
1.729-1.7790.3791930.35837070.35939160.4370.48699.59140.35
1.779-1.8330.3382020.3336230.33138370.6370.64299.68730.316
1.833-1.8940.2861890.28935330.28937320.7670.75899.7320.269
1.894-1.960.3051730.26134240.26336020.8370.8499.86120.238
1.96-2.0340.251730.22832680.2334550.8850.88799.59480.205
2.034-2.1170.2321820.20831630.20933490.9120.92299.88060.188
2.117-2.2110.251620.1930690.19332380.9110.93399.78380.174
2.211-2.3190.2391540.18929350.19130940.9260.93799.83840.175
2.319-2.4440.2371630.19427740.19629400.9250.93499.8980.178
2.444-2.5920.2211500.19626450.19727950.9370.9331000.187
2.592-2.7710.2491140.1925030.19326190.9250.94199.92360.183
2.771-2.9920.2451120.1823410.18224540.9330.95399.95930.18
2.992-3.2770.221260.18621370.18822650.9370.95499.91170.193
3.277-3.6630.194980.1819850.18120840.9590.96199.9520.195
3.663-4.2280.242930.17317340.17618300.9410.96199.83610.196
4.228-5.1740.166770.14515050.14615820.9740.9771000.176
5.174-7.2980.265630.19611990.19912660.9380.96299.6840.228
7.298-71.1560.22300.1877090.1897420.9670.9699.59570.234
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)
17.71081.19380.27241.49190.18013.86960.06980.29760.3618-0.34110.02290.1009-0.1514-0.2361-0.09270.2523-0.0266-0.02880.2204-0.03310.220566.050229.7028-12.131
24.09390.5172-1.87211.23530.09580.9512-0.01530.0496-0.0683-0.03310.0024-0.04540.0027-0.02720.01290.0163-0.0094-0.04930.0515-0.00750.199781.092930.2392-2.1034
35.9036-1.36541.55152.027-2.06792.7876-0.1589-0.2046-0.1920.31210.1061-0.0665-0.01130.08370.05280.24470.0362-0.02240.1842-0.00670.14177.959829.76388.4574
47.8795-0.2653-2.8461.4378-0.0012.1458-0.048-0.3367-0.54370.11430.04090.01170.2303-0.01040.00710.082-0.0206-0.05940.0673-0.01920.20781.935123.83921.0993
54.5787-4.0445-3.51056.96183.22113.42460.33420.5222-0.1581-0.6367-0.2222-0.0185-0.193-0.1434-0.1120.06790.0361-0.02420.1713-0.09260.103790.812539.6-10.0235
64.1693-1.4079-1.58673.00044.1695.9092-0.0926-0.13310.23490.0136-0.12670.2042-0.0846-0.20190.21930.22790.03150.02550.22410.02010.258465.624758.686.6564
72.4738-0.992-1.31372.81661.44532.43180.0565-0.04610.06610.1270.05350.0699-0.0091-0.1381-0.110.01150.00480.00820.03890.03550.111680.560846.67741.6446
87.2833-2.9247-2.69985.57322.93483.80930.15110.12480.4596-0.05840.00080.094-0.3432-0.1907-0.15190.05990.0109-0.00480.03570.03480.133284.01156.84740.9322
98.90892.58031.27582.3260.13841.5616-0.0990.4458-0.266-0.20140.11970.07170.1436-0.2069-0.02080.0921-0.0094-0.02450.1255-0.06530.112582.410428.9337-11.2425
1010.86654.51720.26172.1563-0.36484.3088-0.30470.875-0.2274-0.41340.25260.05140.5254-0.08930.0520.3778-0.0342-0.06130.3409-0.2140.255783.559721.8659-20.7619
1110.1877-0.415-0.1561.66970.16821.6853-0.20060.3483-0.7355-0.11960.05880.13340.4365-0.08260.14180.3733-0.05760.01690.226-0.19960.379585.417613.1032-16.6937
123.5606-3.67840.057810.54951.07470.28030.13550.1594-0.5183-0.60590.04740.28960.0382-0.1553-0.18290.1752-0.2653-0.12240.50920.11730.393665.795322.0433-6.2435
131.34481.9223-0.48487.0837-1.13060.77390.1604-0.1060.04150.1666-0.19910.0118-0.1839-0.01410.03870.16430.03970.00280.22420.01720.149459.031853.6873-1.5628
147.4013-0.7294.81473.7914-5.10698.9087-0.78810.7978-0.23850.00790.5194-0.3058-0.4629-0.17280.26870.770.07990.10690.4938-0.00710.435364.951871.1278-11.3126
151.4807-2.79921.326110.7476-3.57682.42890.15040.1608-0.1313-0.5913-0.1372-0.2189-0.1986-0.3867-0.01320.18430.18990.010.29890.01480.159958.46852.1932-8.5778
1613.9593-4.6306-3.31581.71190.74851.61070.4391.13280.028-0.2102-0.40740.0157-0.2115-0.2867-0.03150.49620.2235-0.02260.52310.09780.244455.654359.9647-16.5684
171.0005-2.4060.90788.2747-5.01064.63170.02090.1655-0.0558-0.0533-0.0716-0.081-0.1514-0.04510.05070.1348-0.00710.02410.21-0.00650.171366.643546.6366-5.0332
183.0275-2.1447-0.13346.6975-0.97511.67590.14760.17760.2851-0.5548-0.21780.0582-0.2734-0.2560.07030.19680.1985-0.030.40890.01070.113552.177559.1311-8.5186
190.003-0.0394-0.01911.270.45850.3944-0.0331-0.01650.00680.7056-0.11660.03040.2110.29330.14970.4851-0.0595-0.03640.63240.04030.351665.460317.86418.2976
207.865-1.3214-5.93344.89211.02964.4787-0.256-0.0177-0.25840.01370.0694-0.08570.21450.01220.18660.2069-0.0332-0.04310.1759-0.01640.226976.147518.2243-2.6924
2115.7478-2.6523-12.34151.36441.806610.3234-0.09790.3489-0.5147-0.1009-0.10090.05670.14230.09740.19880.22730.013-0.03540.2624-0.09210.250690.68816.1011-10.9528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA3 - 7
2X-RAY DIFFRACTION2ALLAAA8 - 34
3X-RAY DIFFRACTION3ALLAAA35 - 45
4X-RAY DIFFRACTION4ALLAAA46 - 74
5X-RAY DIFFRACTION5ALLAAA75 - 93
6X-RAY DIFFRACTION6ALLAAA94 - 101
7X-RAY DIFFRACTION7ALLAAA102 - 155
8X-RAY DIFFRACTION8ALLAAA156 - 182
9X-RAY DIFFRACTION9ALLBBB0 - 34
10X-RAY DIFFRACTION10ALLBBB35 - 53
11X-RAY DIFFRACTION11ALLBBB54 - 71
12X-RAY DIFFRACTION12ALLBBB72 - 93
13X-RAY DIFFRACTION13ALLBBB94 - 105
14X-RAY DIFFRACTION14ALLBBB106 - 113
15X-RAY DIFFRACTION15ALLBBB114 - 132
16X-RAY DIFFRACTION16ALLBBB133 - 145
17X-RAY DIFFRACTION17ALLBBB146 - 159
18X-RAY DIFFRACTION18ALLBBB160 - 190
19X-RAY DIFFRACTION19ALLCCC3 - 7
20X-RAY DIFFRACTION20ALLCCC8 - 12
21X-RAY DIFFRACTION21ALLCCC13 - 18

+
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