[English] 日本語
Yorodumi
- PDB-6am5: Crystal structure of DMF5 TCR bound to HLA-A2 presenting syntheti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6am5
TitleCrystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide SMLGIGIVPV
Components
  • Beta-2-microglobulin
  • DMF5 TCR alpha chain
  • DMF5 TCR beta chain
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • SER-MET-LEU-GLY-ILE-GLY-ILE-VAL-PRO-VAL
KeywordsIMMUNE SYSTEM / TCR / MHC
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.394 Å
AuthorsRiley, T.P. / Baker, B.M.
CitationJournal: To Be Published
Title: Crystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide SMLGIGIVPV
Authors: Riley, T.P. / Baker, B.M.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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, A-2 alpha chain
B: Beta-2-microglobulin
C: SER-MET-LEU-GLY-ILE-GLY-ILE-VAL-PRO-VAL
D: DMF5 TCR alpha chain
E: DMF5 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)92,1865
Polymers92,1865
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-55 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.106, 49.900, 92.455
Angle α, β, γ (deg.)90.00, 95.72, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein DMF5 TCR alpha chain


Mass: 20828.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein DMF5 TCR beta chain


Mass: 26637.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Protein/peptide / Non-polymers , 2 types, 213 molecules C

#3: Protein/peptide SER-MET-LEU-GLY-ILE-GLY-ILE-VAL-PRO-VAL


Mass: 985.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 13% PEG3350, 0.25 M magnesium chloride, 0.1 M Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 40458 / % possible obs: 98 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.94 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.037 / Rrim(I) all: 0.072 / Χ2: 1.119 / Net I/σ(I): 8.7 / Num. measured all: 152065
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.70.53319930.8520.3220.6240.6398.5
2.44-2.493.80.45420390.9080.2690.5290.62598.5
2.49-2.533.90.41919900.8970.2460.4860.61998.6
2.53-2.593.80.34919840.9320.2060.4050.65798.5
2.59-2.643.90.2920740.9530.1710.3370.64898.5
2.64-2.73.80.25719570.9550.1530.2990.78198.5
2.7-2.773.90.20820520.9710.1230.2420.75598.7
2.77-2.853.80.17220190.9750.1020.20.82898.7
2.85-2.933.80.14520220.9790.0870.1690.84298.8
2.93-3.023.80.11620270.9860.0690.1350.89999
3.02-3.133.80.09920180.990.0590.1160.9898.9
3.13-3.263.80.08520380.9920.0510.0991.11699
3.26-3.413.80.07220460.9920.0440.0841.13898.9
3.41-3.583.60.06620110.9930.0410.0781.3297.5
3.58-3.813.50.05819510.9940.0360.0691.48594
3.81-4.13.30.05319440.990.0340.0631.81594.2
4.1-4.523.80.04720560.9960.0280.0551.9199
4.52-5.173.80.04220530.9960.0260.051.92698.8
5.17-6.513.80.04220940.9970.0250.0491.78798.6
6.51-503.60.03620900.9970.0220.0431.86295.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
HKL-2000data collection
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.394→38.754 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 1919 4.95 %
Rwork0.2011 --
obs0.2033 38731 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.394→38.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 0 212 6696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026658
X-RAY DIFFRACTIONf_angle_d0.5759046
X-RAY DIFFRACTIONf_dihedral_angle_d18.2462427
X-RAY DIFFRACTIONf_chiral_restr0.049953
X-RAY DIFFRACTIONf_plane_restr0.0031185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3941-2.4540.30631190.26652227X-RAY DIFFRACTION81
2.454-2.52030.30541260.25652436X-RAY DIFFRACTION87
2.5203-2.59450.30281280.24292480X-RAY DIFFRACTION89
2.5945-2.67820.32471330.23852542X-RAY DIFFRACTION91
2.6782-2.77390.30461390.22422598X-RAY DIFFRACTION93
2.7739-2.88490.22811380.21962604X-RAY DIFFRACTION95
2.8849-3.01620.27731360.21772718X-RAY DIFFRACTION97
3.0162-3.17510.271400.22042728X-RAY DIFFRACTION98
3.1751-3.37390.26631430.20772740X-RAY DIFFRACTION98
3.3739-3.63430.24351370.20142604X-RAY DIFFRACTION93
3.6343-3.99970.19411400.18242685X-RAY DIFFRACTION95
3.9997-4.57760.22231450.1582804X-RAY DIFFRACTION99
4.5776-5.76430.19481460.16532797X-RAY DIFFRACTION99
5.7643-38.75920.21181490.19512849X-RAY DIFFRACTION97
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)
12.0186-0.25690.48491.83710.38471.83540.13440.33280.3396-0.0367-0.0260.1320.02230.1978-0.0130.12130.00040.0095-0.0081-0.05080.2341-39.0177-14.9235-2.9002
21.6568-0.23991.51490.75430.11582.68440.15331.05390.6789-0.31990.0620.1424-0.38790.2799-0.09080.38120.05370.09560.66990.34180.5069-41.9601-10.9005-26.9342
30.6807-1.12950.6311.9668-0.76621.28010.02440.86951.5115-0.22990.0294-0.0504-0.98910.06370.20570.84920.02560.02090.82710.63691.2068-51.51050.3959-32.2063
41.5882-1.0989-0.47213.31361.69555.77010.07560.07830.48070.11870.1678-0.0531-0.12980.0620.01370.08920.0293-0.03530.14490.14980.4348-58.6734-9.1835-13.4275
52.6620.64491.76121.71390.52481.17170.00351.19510.0332-1.25490.10310.05190.14060.002-0.14730.59210.03480.00930.96930.05810.1747-57.1557-20.7814-36.1397
63.2420.12150.62133.95781.18893.36650.23510.67260.0856-0.56730.0980.13130.00870.0953-0.19510.21290.0586-0.03460.2720.08680.2034-56.5305-16.9454-21.6553
75.56443.62825.8636.14266.39568.70220.1153-0.03980.25040.2018-0.00370.16220.4917-0.3033-0.270.1669-0.0246-0.00160.14280.1060.2623-61.783-18.4948-12.5962
85.1282-0.65231.76275.01610.96956.11950.25110.3683-0.3605-0.1685-0.05670.38410.8929-0.4427-0.30040.2906-0.074-0.12940.23310.04510.2972-63.9175-26.8166-19.9403
94.16220.28121.83583.95731.47635.31730.11120.45080.078-0.14820.2122-0.21450.18320.1861-0.36690.14960.03820.01430.09860.08870.2245-52.0836-16.335-15.4595
104.10670.45420.552.31830.2721.41670.2531.0053-0.0361-1.0419-0.1830.9110.0416-0.9753-0.07020.7871-0.0016-0.32160.98340.0610.5424-69.4123-21.8035-34.3118
112.82840.02841.2313.37411.75075.79540.01620.14530.24150.0744-0.16350.50370.2208-0.4854-0.01720.1125-0.0138-0.01580.22370.14660.3643-66.9824-14.7859-13.1312
123.4303-1.12210.28374.81141.87015.08960.21140.87230.4283-0.9693-0.12970.235-0.328-0.07210.18050.3780.0529-0.18320.50950.29220.4459-65.5778-12.4994-27.4542
132.19460.85110.11821.6821-0.1360.95170.1030.075-0.11960.1348-0.0995-0.0009-0.04820.0676-0.08130.1228-0.03830.01390.0133-0.11570.3255-33.5998-16.58151.6079
142.2104-0.4203-0.30850.3736-0.43070.867-0.03890.1886-0.4036-0.0303-0.1012-0.14180.3310.5922-0.62040.41370.3717-0.0380.6754-0.26540.3829-7.176-32.73882.7483
151.0473-0.3255-0.79640.3940.16690.62060.10030.0939-0.0180.0125-0.0954-0.11170.1020.7216-0.2540.11280.2480.19270.6942-0.18380.1743-11.8773-24.8952-0.4877
161.7905-0.1095-0.29441.1578-0.94591.3410.1969-0.07720.24060.0108-0.3455-0.3139-0.08981.00270.0020.09540.02690.02870.6217-0.07730.2151-11.8818-21.91156.0654
172.6104-1.04170.56851.0219-0.25110.6566-0.2327-0.3538-0.42650.5028-0.083-0.1356-0.09111.19310.10150.51820.1465-0.05181.39730.25410.35215.288-37.547423.4569
186.5192-0.50810.13344.11490.00272.1376-0.23260.6331-1.06670.0938-0.1853-0.20570.19671.43230.43460.930.1039-0.031.7062-0.22080.73019.5731-44.800418.3082
195.59630.0079-0.18454.468-0.51552.2707-0.3640.0945-0.20.30890.0038-0.3352-0.45061.48080.38880.7774-0.103-0.06951.31290.08170.34396.7456-35.613225.4914
208.4536-0.1837-0.19674.12860.77891.9782-0.42790.2206-1.63290.0287-0.07260.01160.60621.40250.45410.92890.24630.39281.6264-0.14951.035313.0428-51.662324.1952
213.8963-1.51040.43744.06-0.30833.0980.2167-0.5227-0.56590.37750.09360.24550.37340.3965-0.2340.26250.0226-0.04160.1356-0.13250.1442-26.7516-33.424618.4912
222.6898-0.55270.58753.2118-0.03152.34820.2714-0.219-0.45620.0570.02570.42680.44020.1838-0.20070.22140.0078-0.05910.1314-0.06150.2054-29.5512-32.82114.4956
235.9653-2.47683.98821.9398-1.73896.74560.4949-0.4463-1.0774-0.07770.0160.38540.69850.4087-0.35230.67580.0871-0.10760.54820.16810.413-18.7125-49.332427.9612
242.7934-0.3251.12921.0865-0.45233.41930.08290.1162-0.2459-0.0589-0.0806-0.1961-0.39871.1698-0.13780.65890.0149-0.03251.33580.09050.12760.7118-38.415833.6247
256.60372.92550.61272.7159-1.07914.55320.2011-1.0816-0.96760.4466-0.11370.74460.4155-0.376-0.37030.73570.04380.0091.07430.19670.5824-21.8313-48.716336.886
261.2946-0.02321.32321.5349-0.22325.5933-0.1993-0.15060.02750.29110.0221-0.3512-0.2891.13120.13120.7518-0.0225-0.00831.21910.06810.12691.9052-38.312244.1007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 162 )
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 198 )
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 275 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 12 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 31 )
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 42 )
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 52 )
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 72 )
10X-RAY DIFFRACTION10chain 'B' and (resid 73 through 78 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 91 )
12X-RAY DIFFRACTION12chain 'B' and (resid 92 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 10 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 13 )
15X-RAY DIFFRACTION15chain 'D' and (resid 14 through 31 )
16X-RAY DIFFRACTION16chain 'D' and (resid 32 through 96 )
17X-RAY DIFFRACTION17chain 'D' and (resid 97 through 135 )
18X-RAY DIFFRACTION18chain 'D' and (resid 136 through 150 )
19X-RAY DIFFRACTION19chain 'D' and (resid 151 through 175 )
20X-RAY DIFFRACTION20chain 'D' and (resid 176 through 190 )
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 49 )
22X-RAY DIFFRACTION22chain 'E' and (resid 50 through 106 )
23X-RAY DIFFRACTION23chain 'E' and (resid 107 through 121 )
24X-RAY DIFFRACTION24chain 'E' and (resid 122 through 212 )
25X-RAY DIFFRACTION25chain 'E' and (resid 213 through 230 )
26X-RAY DIFFRACTION26chain 'E' and (resid 231 through 242 )

+
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