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- PDB-4n0c: 42F3 TCR pCPE3/H-2Ld complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4n0c
Title42F3 TCR pCPE3/H-2Ld complex
Components
  • 42F3 VmCh alpha
  • 42F3 VmCh beta
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • pCPE3
KeywordsIMMUNE SYSTEM / Ig / TCR / MHC / antigen
Function / homology
Function and homology information


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 / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...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 / 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 / T cell receptor complex / 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 / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / 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 / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / antibacterial humoral response / protein-folding chaperone binding / adaptive immune response / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / plasma membrane
Similarity search - Function
Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor beta, variable 13-1 / T-cell receptor alpha chain V region PHDS58 / H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBirnbaum, M.E. / Adams, J.J. / Garcia, K.C.
CitationJournal: Nat. Immunol. / Year: 2016
Title: Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.
Authors: Adams, J.J. / Narayanan, S. / Birnbaum, M.E. / Sidhu, S.S. / Blevins, S.J. / Gee, M.H. / Sibener, L.V. / Baker, B.M. / Kranz, D.M. / Garcia, K.C.
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, L-D alpha chain
B: pCPE3
C: 42F3 VmCh alpha
D: 42F3 VmCh beta
E: H-2 class I histocompatibility antigen, L-D alpha chain
F: pCPE3
G: 42F3 VmCh alpha
H: 42F3 VmCh beta


Theoretical massNumber of molelcules
Total (without water)145,5818
Polymers145,5818
Non-polymers00
Water0
1
A: H-2 class I histocompatibility antigen, L-D alpha chain
B: pCPE3
C: 42F3 VmCh alpha
D: 42F3 VmCh beta


Theoretical massNumber of molelcules
Total (without water)72,7914
Polymers72,7914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: H-2 class I histocompatibility antigen, L-D alpha chain
F: pCPE3
G: 42F3 VmCh alpha
H: 42F3 VmCh beta


Theoretical massNumber of molelcules
Total (without water)72,7914
Polymers72,7914
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.450, 102.450, 325.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 21115.303 Da / Num. of mol.: 2 / Fragment: UNP residues 25-203 / Mutation: F8Y, V12T, P15R, I23T, N30D, A49V, K131R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Escherichia coli (E. coli) / References: UniProt: P01897
#2: Protein/peptide pCPE3


Mass: 1043.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
#3: Antibody 42F3 VmCh alpha


Mass: 23383.928 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: UniProt: P01738*PLUS
#4: Protein 42F3 VmCh beta


Mass: 27248.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: UniProt: A0A075B5I3*PLUS

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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: 3.39 Å3/Da / Density % sol: 63.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 17% PEG 3350 and 100mM BiS-TRIS, pH 6.6 and 200mM magnesium nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.68→88.72 Å / Num. all: 56842 / Num. obs: 56729 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.68→2.76 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→59.987 Å / σ(F): 1.91 / Phase error: 24.63 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 4231 5.02 %random
Rwork0.1915 ---
obs0.1954 44888 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→59.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9790 0 0 0 9790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610057
X-RAY DIFFRACTIONf_angle_d0.96713651
X-RAY DIFFRACTIONf_dihedral_angle_d14.5133586
X-RAY DIFFRACTIONf_chiral_restr0.0391419
X-RAY DIFFRACTIONf_plane_restr0.0051788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9005-2.95050.4242170.38673969X-RAY DIFFRACTION94
2.9505-3.00410.38492080.35474060X-RAY DIFFRACTION94
3.0041-3.06190.34512020.32433888X-RAY DIFFRACTION94
3.0619-3.12430.34272140.31043991X-RAY DIFFRACTION93
3.1243-3.19230.34272040.29784037X-RAY DIFFRACTION95
3.1923-3.26650.26372070.26863966X-RAY DIFFRACTION94
3.2665-3.34810.38282100.24834022X-RAY DIFFRACTION94
3.3481-3.43860.29892170.23433976X-RAY DIFFRACTION94
3.4386-3.53980.28252030.21934010X-RAY DIFFRACTION95
3.5398-3.6540.23662180.21724014X-RAY DIFFRACTION95
3.654-3.78450.26512160.2014000X-RAY DIFFRACTION94
3.7845-3.93590.25972070.18823989X-RAY DIFFRACTION94
3.9359-4.11490.24462100.18014028X-RAY DIFFRACTION95
4.1149-4.33170.22892060.15743980X-RAY DIFFRACTION95
4.3317-4.60280.17772070.1454042X-RAY DIFFRACTION95
4.6028-4.95770.21011940.14253975X-RAY DIFFRACTION95
4.9577-5.45570.21392020.14924037X-RAY DIFFRACTION95
5.4557-6.2430.21382160.16214007X-RAY DIFFRACTION95
6.243-7.85760.24032230.16094019X-RAY DIFFRACTION94
7.8576-42.80670.21792290.15173961X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5021-0.06550.33560.2684-0.33120.3398-0.32760.8047-0.4041-0.0112-0.1458-0.56010.37370.10510.15680.8337-0.46410.10090.8118-0.05150.56854.015177.0148312.2081
21.1036-0.21210.0311.6295-0.70961.2033-0.14470.2828-0.0752-0.47550.1149-0.09910.00130.21590.10040.5815-0.13970.01290.445-0.13360.58535.486579.9822313.6549
30.5781-0.3616-1.01360.27550.49922.1735-0.14710.5295-0.165-0.07750.1658-0.2238-0.4206-0.8307-0.02390.5723-0.2854-0.16490.62450.20620.9052-7.768294.2268317.8013
40.5826-0.63280.35320.9909-0.12230.4195-0.6146-0.128-0.2492-0.28460.2578-0.0507-0.08360.36540.2330.3852-0.17580.0720.57780.01210.49334.396492.0508316.0651
50.1023-0.0037-0.21142.59660.07911.75740.20930.11230.05950.27050.0946-0.4086-0.35170.11110.48140.429-0.0858-0.05790.06810.18491.08756.2585.3984321.7397
62.99850.80670.68730.7061-0.98282.96910.3878-0.40580.22570.3943-0.66680.00290.54480.92780.00440.5778-0.0782-0.06070.58680.05740.579920.4328108.9333339.2671
71.31540.0837-1.50940.68360.5442.3272-0.58480.11120.0241-0.33880.17260.14820.73140.09530.41420.44890.0381-0.08510.35140.04290.659917.401299.9718330.9188
81.68010.61210.34550.79370.05241.09460.1478-0.25740.2132-0.0855-0.2395-0.10240.1413-0.73830.06170.3568-0.0851-0.06230.28610.06840.407411.4238105.2797335.2254
91.5018-0.06070.35630.72950.35741.28790.25730.0832-0.13350.226-0.16770.0077-0.42160.086-0.3580.44920.05080.06060.54410.42240.466917.850892.4256332.8181
100.2569-0.1842-0.0340.72751.04551.78090.2022-0.4760.0553-0.42850.4789-0.3484-0.9535-0.2494-0.44950.5953-0.12990.26990.90710.19010.876720.6315116.436365.1125
111.9626-0.40390.57620.6051-0.25611.5084-0.18810.44870.1716-0.62820.2221-0.8268-0.97410.68380.00090.9861-0.34940.09770.5408-0.12771.064415.1826112.496362.3776
120.8965-0.56591.40141.1092-0.3182.6303-0.2167-0.5737-0.0852-0.194-0.3959-0.4354-0.46830.21650.37861.3313-0.24970.3710.69630.18270.694815.5236114.7184363.5778
132.23720.511-0.20315.3791.15072.9109-0.33730.0471-0.47311.18480.5711-0.85930.197-0.679-0.7030.6805-0.2154-0.08650.94860.25090.685329.7275118.7639370.5362
140.4410.5567-0.01571.6945-0.87321.47530.1169-0.2274-0.62450.166-0.0416-0.41520.44140.37910.04820.28970.07480.03740.41530.01440.63914.853782.2103344.24
151.51381.00010.03871.65290.51911.5750.3416-0.4243-0.66120.03840.0471-0.13710.47760.5897-0.21780.18780.05360.01750.4374-0.0420.537819.377587.831355.006
161.2018-0.2908-0.35281.27-0.2151.42560.0335-0.18510.3992-0.64030.0885-0.0095-0.64770.4123-0.09830.6052-0.1758-0.1160.6030.10580.655714.9421106.0246370.9107
172.8359-0.1101-1.07371.5639-0.13810.87840.31720.25470.3025-0.2686-0.1301-0.2009-0.44810.5771-0.2170.4933-0.0729-0.02390.58360.00850.373416.8487104.0206366.4266
181.87360.1095-0.04041.3406-1.5291.76330.05170.2305-0.32120.0799-0.1048-0.2005-0.74430.6401-0.09250.4078-0.2107-0.12810.6390.1370.35147.3704101.0521374.6484
191.0620.06670.26432.36321.36381.48180.1497-0.05010.1483-0.39530.4212-0.73720.02180.6344-0.49140.322-0.04450.05350.73370.1480.604218.057688.6218373.984
200.24030.12450.09230.3015-0.31280.7464-0.2022-0.0624-0.04710.10.1084-0.0605-0.2384-0.1224-0.80360.78780.25010.37710.81490.60460.5381-4.276383.524397.4842
210.93590.31750.62671.18-0.36451.59580.3090.0523-0.3858-0.17470.1992-0.02230.5448-0.2966-0.01770.9811-0.32-0.16270.69410.45960.5291-5.177470.7512388.4058
221.9159-0.43720.35791.8914-0.22420.8141-0.1931-0.7489-0.47350.3533-0.04690.45460.05830.22190.12190.5495-0.04090.1720.5940.08410.4574-6.314179.9695391.4089
230.994-0.2909-0.60091.70651.1253.12-0.1806-0.2991-0.0333-0.1789-0.11290.219-0.8460.40760.30780.6894-0.1564-0.08610.50660.06930.3397-2.104292.2037388.5116
240.5010.3350.15750.49610.41810.4038-0.30310.34790.4829-0.20490.41280.3455-0.3291-0.04510.16460.23170.01080.02510.55510.19770.7412-7.14285.2851383.8901
250.24810.25660.37440.3232-0.03161.5643-0.09610.07020.0222-0.0203-0.18550.3462-0.2623-1.32260.14060.40210.15280.09590.4599-0.11160.5819-17.2888103.6657368.9839
260.7811-0.06450.32710.1850.53011.31410.30950.0656-0.1742-0.2724-0.3618-0.13960.303-0.1113-0.00440.59950.15370.13010.3627-0.06810.5316-12.6908106.8193368.7244
270.17940.1017-0.73960.66430.42124.1731-0.2505-0.0080.21-0.0867-0.15180.3348-0.0181-0.85090.08340.93710.7641-0.10940.39-0.00090.8102-23.6412113.4547337.7168
281.03070.0699-0.20760.5074-0.35740.8990.2040.49340.46130.12790.01330.7071-0.4587-0.015-0.15430.46840.0171-0.05410.43670.17451.154-20.1883116.2858338.2959
290.5359-0.28620.81161.47880.03791.2881-0.1321-0.1102-0.53960.28410.12470.35280.0015-0.3638-0.01490.51650.04720.15540.5229-0.05750.3693-15.672182.0994361.2303
301.2241-0.92730.47131.5823-0.25021.1834-0.21270.3321-0.1894-0.12430.04410.2404-0.4096-0.07350.02490.43990.02230.10580.5215-0.21610.5567-20.154487.9557350.6479
310.85080.1485-0.49942.0932-0.36291.24830.44250.45210.1112-0.2764-0.28780.7707-0.1783-0.4173-0.21780.36340.1415-0.03240.71510.00830.4146-15.4257106.3647334.6742
320.6447-0.11160.12791.3489-0.00211.0962-0.09340.47710.270.03550.11720.7603-0.6101-0.4026-0.0190.48170.1838-0.04970.60930.00460.5034-17.0438104.3709339.0141
331.0439-0.3499-0.03761.9299-0.49630.5862-0.03340.16230.0928-0.34550.29120.96130.0190.2215-0.10590.3664-0.0677-0.10530.7888-0.19330.5129-15.389392.8281331.1709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 175 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 9 )
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 20 )
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 37 )
8X-RAY DIFFRACTION8chain 'C' and (resid 38 through 94 )
9X-RAY DIFFRACTION9chain 'C' and (resid 95 through 107 )
10X-RAY DIFFRACTION10chain 'C' and (resid 108 through 154 )
11X-RAY DIFFRACTION11chain 'C' and (resid 155 through 168 )
12X-RAY DIFFRACTION12chain 'C' and (resid 169 through 178 )
13X-RAY DIFFRACTION13chain 'C' and (resid 179 through 197 )
14X-RAY DIFFRACTION14chain 'D' and (resid 3 through 96 )
15X-RAY DIFFRACTION15chain 'D' and (resid 97 through 120 )
16X-RAY DIFFRACTION16chain 'D' and (resid 121 through 158 )
17X-RAY DIFFRACTION17chain 'D' and (resid 159 through 199 )
18X-RAY DIFFRACTION18chain 'D' and (resid 200 through 211 )
19X-RAY DIFFRACTION19chain 'D' and (resid 212 through 241 )
20X-RAY DIFFRACTION20chain 'E' and (resid 2 through 12 )
21X-RAY DIFFRACTION21chain 'E' and (resid 13 through 28 )
22X-RAY DIFFRACTION22chain 'E' and (resid 29 through 126 )
23X-RAY DIFFRACTION23chain 'E' and (resid 127 through 175 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1 through 9 )
25X-RAY DIFFRACTION25chain 'G' and (resid 0 through 43 )
26X-RAY DIFFRACTION26chain 'G' and (resid 44 through 120 )
27X-RAY DIFFRACTION27chain 'G' and (resid 121 through 162 )
28X-RAY DIFFRACTION28chain 'G' and (resid 163 through 200 )
29X-RAY DIFFRACTION29chain 'H' and (resid 3 through 96 )
30X-RAY DIFFRACTION30chain 'H' and (resid 97 through 120 )
31X-RAY DIFFRACTION31chain 'H' and (resid 121 through 158 )
32X-RAY DIFFRACTION32chain 'H' and (resid 159 through 199 )
33X-RAY DIFFRACTION33chain 'H' and (resid 200 through 241 )

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  • 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

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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

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