[English] 日本語
Yorodumi
- PDB-4pjd: Structure of human MR1-5-OP-RU in complex with human MAIT C-C10 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pjd
TitleStructure of human MR1-5-OP-RU in complex with human MAIT C-C10 TCR
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR-alpha
  • TCR-beta
KeywordsIMMUNE SYSTEM / MR1 / TCR / Immune complex / 5-OP-RU
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 / : ...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
Chem-2LJ / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.78 Å
AuthorsBirkinshaw, R.W. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2014
Title: A molecular basis underpinning the T cell receptor heterogeneity of mucosal-associated invariant T cells.
Authors: Eckle, S.B. / Birkinshaw, R.W. / Kostenko, L. / Corbett, A.J. / McWilliam, H.E. / Reantragoon, R. / Chen, Z. / Gherardin, N.A. / Beddoe, T. / Liu, L. / Patel, O. / Meehan, B. / Fairlie, D.P. ...Authors: Eckle, S.B. / Birkinshaw, R.W. / Kostenko, L. / Corbett, A.J. / McWilliam, H.E. / Reantragoon, R. / Chen, Z. / Gherardin, N.A. / Beddoe, T. / Liu, L. / Patel, O. / Meehan, B. / Fairlie, D.P. / Villadangos, J.A. / Godfrey, D.I. / Kjer-Nielsen, L. / McCluskey, J. / Rossjohn, J.
History
DepositionMay 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: TCR-alpha
F: TCR-beta
G: TCR-alpha
H: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,82511
Polymers188,1008
Non-polymers7253
Water11,349630
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
E: TCR-alpha
F: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4586
Polymers94,0504
Non-polymers4082
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
G: TCR-alpha
H: TCR-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3665
Polymers94,0504
Non-polymers3161
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.290, 70.520, 144.160
Angle α, β, γ (deg.)90.00, 104.50, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 4 types, 8 molecules ACBDEGFH

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31711.670 Da / Num. of mol.: 2 / Fragment: UNP residues 23-292 / Mutation: C262S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein 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 (E. coli) / References: UniProt: P61769
#3: Protein TCR-alpha


Mass: 22889.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein TCR-beta


Mass: 27569.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 3 types, 633 molecules

#5: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O6
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Bis-tris propane, sodium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.78→40.1 Å / Num. obs: 53280 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 49.07 Å2 / Net I/σ(I): 7

-
Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2.78→40.1 Å / Cor.coef. Fo:Fc: 0.9058 / Cor.coef. Fo:Fc free: 0.8567 / SU R Cruickshank DPI: 1.302 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.884 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.309
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 2703 5.07 %RANDOM
Rwork0.1675 ---
obs0.1705 53269 99.78 %-
Displacement parametersBiso mean: 31.65 Å2
Baniso -1Baniso -2Baniso -3
1-2.6598 Å20 Å20.4892 Å2
2---14.7794 Å20 Å2
3---12.1196 Å2
Refine analyzeLuzzati coordinate error obs: 0.304 Å
Refinement stepCycle: 1 / Resolution: 2.78→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12226 0 50 630 12906
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112629HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1917222HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4070SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes288HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1875HARMONIC5
X-RAY DIFFRACTIONt_it12629HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.06
X-RAY DIFFRACTIONt_other_torsion20.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1633SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13860SEMIHARMONIC4
LS refinement shellResolution: 2.78→2.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 195 5.07 %
Rwork0.2133 3654 -
all0.2179 3849 -
obs--99.78 %
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)
11.05710.52030.34411.15990.23552.0701-0.00870.0212-0.0670.0776-0.02820.0214-0.15930.00980.0369-0.13080.0387-0.0004-0.00610.0178-0.0995-5.451164.8877161.9858
21.1654-0.3894-0.95842.8832-0.9810.241-0.1601-0.08580.13470.26330.08540.21830.0771-0.00770.0747-0.05360.0134-0.01220.0336-0.0241-0.116-3.281457.7096172.2138
34.04543.5249-0.17575.0403-0.08862.0917-0.0098-0.0606-0.37260.17430.0273-0.34490.40940.3297-0.0175-0.05840.0045-0.0536-0.0433-0.0169-0.13322.947648.5057172.451
4-0.01190.9205-0.01111.6043-0.32820.26420.1213-0.24550.3348-0.16180.1276-0.0225-0.19490.0491-0.2488-0.0394-0.0072-0.09180.06080.0349-0.103-6.034372.0975179.0296
53.0847-1.5398-0.69743.8010.8955-0.567-0.0863-0.0392-0.2640.42470.09740.1405-0.12230.05-0.0111-0.00150.0232-0.0127-0.04480.0516-0.0136-20.857872.5923194.1849
63.1848-0.4773-0.50783.13980.84211.80310.02510.24380.0866-0.2437-0.12610.2496-0.1804-0.35330.101-0.11390.041-0.0470.0284-0.023-0.0973-28.391567.0644172.0671
71.06510.1964-0.31082.31880.15621.23250.0396-0.06090.2050.09290.01930.12220.048-0.0764-0.0589-0.09180.0713-0.05010.0941-0.0209-0.0228-48.24845.0926192.5281
83.20761.6295-0.00463.99520.55840.7076-0.01840.07420.0386-0.1470.1115-0.24220.0690.0958-0.0931-0.16270.0466-0.0081-0.01380.0062-0.0925-35.15645.7206181.9636
9-0.1981-1.13680.35742.2227-2.22790.19810.1915-0.2031-0.37630.020.08870.27820.2072-0.0662-0.2803-0.07270.0154-0.07090.0311-0.0353-0.0556-54.778929.9721180.758
102.7002-1.20970.96771.3546-0.98793.5829-0.14930.22120.3996-0.09580.1664-0.0582-0.1190.1174-0.0171-0.133-0.0967-0.08850.03760.06120.0141-67.717546.3914163.161
114.94340.192-0.04661.74230.40313.1723-0.0392-0.34090.7469-0.1544-0.01210.4367-0.2887-0.62820.0513-0.24270.1372-0.0785-0.00230.01020.0425-68.553255.7694183.4025
122.6049-0.5249-1.58480.210.38851.83310.05120.0378-0.006-0.03630.0188-0.10560.27040.2186-0.07-0.1235-0.0006-0.0588-0.00020.0216-0.113632.146464.1659157.5811
136.1857-0.47113.69901.25438.0599-0.0609-0.43660.49230.18740.0783-0.00990.2996-0.2851-0.0174-0.23810.1165-0.02110.1155-0.0828-0.075650.299764.283142.6591
141.7784-0.95271.44124.5717-0.22411.3098-0.24770.34380.5733-0.21480.2607-0.7211-0.01380.3999-0.0131-0.11290.0735-0.04410.20930.07050.224657.362966.7688138.1974
151.78070.8197-1.15961.4265-1.96245.143-0.04140.2412-0.1327-0.089-0.1529-0.12680.12370.04690.1943-0.0390.0143-0.03670.0701-0.0091-0.079215.355761.0073139.1831
161.59460.1377-1.30850.25630.08171.7102-0.12860.24190.1222-0.22060.1079-0.0849-0.1131-0.16460.0207-0.1208-0.063-0.03490.05720.034-0.138112.635265.4263143.8867
17-1.3652-2.73282.45480.2290.93211.42840.03030.13730.231-0.1150.294-0.0495-0.28380.0447-0.3244-0.0906-0.0916-0.01010.07750.0862-0.162727.586869.0023126.1091
183.6292-1.85293.22041.4886-1.97224.53060.19960.0439-0.2349-0.10930.0664-0.15830.76440.4187-0.2660.01930.1190.04610.0240.0145-0.104845.554758.4733133.4641
191.9235-1.6397-1.27188.77093.95631.1798-0.02140.1126-0.1486-0.32640.10220.12880.3468-0.039-0.0808-0.0052-0.01510.0463-0.0458-0.0012-0.226833.267357.9551122.5624
20-0.1284-2.5979-0.075701.42162.50550.0074-0.0594-0.1809-0.29630.1201-0.20790.2295-0.1755-0.1275-0.02460.0412-0.0547-0.0284-0.04360.0166-18.999616.4749197.6423
212.2487-0.46210.86181.4772-0.28571.49480.0238-0.0618-0.3295-0.08560.10430.23380.1868-0.2006-0.1281-0.09220.0666-0.07350.0095-0.0028-0.0609-24.922626.6146195.3337
224.4465-1.53011.0171.3609-0.36552.8569-0.02930.21320.3254-0.0399-0.1091-0.1878-0.146-0.17110.1384-0.0410.0730.012-0.0088-0.0128-0.0049-18.406724.8746191.8451
234.3939-1.28974.29530.2778-1.242.66070.00820.0938-0.1298-0.09340.0609-0.04290.0349-0.1072-0.0691-0.0605-0.001-0.03910.05570.0014-0.0172-13.396418.8678203.6764
24-0.46212.03052.38820-2.07752.0719-0.0132-0.1948-0.38030.1422-0.0441-0.08870.21470.00380.0573-0.0734-0.00460.086-0.1501-0.044-0.03681.681812.3284227.3053
253.7663-0.0723-0.992700.04159.7335-0.0160.48950.0338-0.2336-0.07530.15950.3223-0.50690.0913-0.09380.07270.0304-0.0903-0.0964-0.0199-2.535312.4059212.8004
261.7254-0.08010.13072.2967-2.08345.8846-0.08780.1042-0.30460.3458-0.0034-0.18480.3842-0.08110.0912-0.03880.00280.0029-0.0403-0.04980.03121.49256.0534217.5719
27-0.062-1.02411.75420.2532-1.73265.68710.0321-0.18440.23920.2527-0.1810.1113-0.38720.0510.1489-0.0130.0891-0.05240.0796-0.0369-0.0425-29.821634.4378216.4259
281.97210.06440.64441.2233-0.98662.4618-0.0636-0.2924-0.10290.10650.1071-0.0230.1091-0.306-0.0436-0.05030.1226-0.00160.0661-0.0316-0.0722-34.511532.7504211.3996
290.6602-2.7088-1.27350-0.3519-0.0228-0.1050.2216-0.2666-0.26390.07370.08830.3249-0.14360.0313-0.1099-0.0769-0.0185-0.06920.0542-0.108-24.655720.7458229.0174
304.1718-0.3273-1.22432.6343-0.28781.97070.09760.5250.0319-0.0292-0.06110.1206-0.0162-0.2814-0.03650.0335-0.0101-0.04910.0016-0.0072-0.1539-4.947719.5378222.4745
310.45970.2625-0.58840.4880.27310.32150.07740.0863-0.0020.0637-0.0735-0.0971-0.0362-0.1582-0.004-0.01240.0337-0.02710.0801-0.0018-0.0243-6.223425.169228.8998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|0 - 84}
2X-RAY DIFFRACTION2{A|85 - 114}
3X-RAY DIFFRACTION3{A|115 - 146}
4X-RAY DIFFRACTION4{A|147 - 195}
5X-RAY DIFFRACTION5{A|217 - 269}
6X-RAY DIFFRACTION6{B|1 - 96}
7X-RAY DIFFRACTION7{C|0 - 100}
8X-RAY DIFFRACTION8{C|101 - 158}
9X-RAY DIFFRACTION9{C|159 - 182}
10X-RAY DIFFRACTION10{C|183 - 269}
11X-RAY DIFFRACTION11{D|1 - 96}
12X-RAY DIFFRACTION12{E|2 - 135}
13X-RAY DIFFRACTION13{E|136 - 165}
14X-RAY DIFFRACTION14{E|166 - 198}
15X-RAY DIFFRACTION15{F|3 - 37}
16X-RAY DIFFRACTION16{F|38 - 107}
17X-RAY DIFFRACTION17{F|108 - 122}
18X-RAY DIFFRACTION18{F|123 - 201}
19X-RAY DIFFRACTION19{F|202 - 237}
20X-RAY DIFFRACTION20{G|2 - 17}
21X-RAY DIFFRACTION21{G|18 - 52}
22X-RAY DIFFRACTION22{G|53 - 91}
23X-RAY DIFFRACTION23{G|92 - 120}
24X-RAY DIFFRACTION24{G|121 - 135}
25X-RAY DIFFRACTION25{G|136 - 165}
26X-RAY DIFFRACTION26{G|166 - 198}
27X-RAY DIFFRACTION27{H|3 - 37}
28X-RAY DIFFRACTION28{H|38 - 107}
29X-RAY DIFFRACTION29{H|108 - 122}
30X-RAY DIFFRACTION30{H|123 - 186}
31X-RAY DIFFRACTION31{H|187 - 241}

+
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