[English] 日本語
Yorodumi
- PDB-4pjh: Structure of human MR1-Ac-6-FP in complex with human MAIT B-G8 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pjh
TitleStructure of human MR1-Ac-6-FP in complex with human MAIT B-G8 TCR
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • TCR-alpha
  • TCR-beta
KeywordsIMMUNE SYSTEM / MR1 / TCR / Immune complex / Ac-6-FP
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 / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / defense response to Gram-negative bacterium / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-30W / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
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)188,72618
Polymers187,8008
Non-polymers92710
Water27,7611541
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)94,38610
Polymers93,9004
Non-polymers4866
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)94,3408
Polymers93,9004
Non-polymers4404
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)217.736, 71.481, 143.799
Angle α, β, γ (deg.)90.00, 104.59, 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: 22893.377 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: 27415.436 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 , 4 types, 1551 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-30W / N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide / Acetyl 6-formylpterin


Mass: 233.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7N5O3
#7: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1541 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
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: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 144612 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 29.39 Å2 / Net I/σ(I): 10

-
Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 2→29.28 Å / Cor.coef. Fo:Fc: 0.9466 / Cor.coef. Fo:Fc free: 0.9352 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 7250 5.02 %RANDOM
Rwork0.1685 ---
obs0.17 144558 99.9 %-
Displacement parametersBiso mean: 37.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.4648 Å20 Å2-0.78 Å2
2---9.5847 Å20 Å2
3---7.1199 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: 1 / Resolution: 2→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12525 0 1601 1541 15667
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112935HARMONIC2
X-RAY DIFFRACTIONt_angle_deg117604HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5757SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes319HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1916HARMONIC5
X-RAY DIFFRACTIONt_it12935HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.03
X-RAY DIFFRACTIONt_other_torsion2.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1646SEMIHARMONIC5
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_contact15438SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2333 525 4.94 %
Rwork0.1895 10104 -
all0.1916 10629 -
obs--99.9 %
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)
11.62760.3033-0.07240.85070.02031.1323-0.0395-0.04840.0651-0.0338-0.0034-0.01470.06360.16460.0429-0.12940.0103-0.0114-0.04030.035-0.1298-45.162628.576919.8748
22.10170.3568-0.6830.40870.230.9076-0.0815-0.0789-0.11120.0445-0.0481-0.05260.16170.24020.1297-0.00250.0355-0.01080.09690.0316-0.0153-41.983424.394623.7052
35.6237-1.1732-2.42750.73110.56251.4740.0913-0.01730.2025-0.0404-0.0271-0.24510.05440.2868-0.0641-0.16310.05250.00490.05580.0371-0.0844-30.099927.01237.2722
46.8844-1.51043.21312.9147-1.00066.1391-0.2305-0.29491.09960.0710.0983-0.25980.08640.46140.1322-0.18610.0613-0.0023-0.0257-0.04380.1532-20.431728.30341.0083
52.55922.52780.50652.71440.84780.1258-0.0146-0.00690.0780.0446-0.044-0.0497-0.02520.14310.0586-0.37250.031-0.12490.0694-0.11420.3581-9.61331.04692.7659
61.74670.1402-0.90971.3635-0.27381.4936-0.02450.12730.0571-0.0648-0.0646-0.01820.1554-0.07180.08910.0081-0.0302-0.0002-0.04160.011-0.0644-59.178227.53170.9684
72.02210.8184-2.31590.8945-0.75373.56710.0884-0.07490.1584-0.03820.02310.12680.11320.0342-0.1115-0.0252-0.00060.0315-0.0890.0056-0.0554-49.947227.0342-2.0729
84.0786-1.17863.07971.4338-1.31483.94040.49810.3132-0.3969-0.1597-0.1509-0.11990.68440.6419-0.34720.02280.1569-0.0005-0.0901-0.0277-0.096-27.041420.249-6.9103
92.8988-1.4564-1.51775.10553.23086.50410.01280.2862-0.298-0.22970.21120.05270.320.1153-0.22410.00670.0527-0.0063-0.2276-0.0402-0.1577-38.430521.792-19.1049
101.5718-0.45020.40631.37220.00250.654-0.0484-0.0558-0.02840.00650.01970.023-0.0284-0.00830.0287-0.07460.04290.0190.0006-0.0211-0.100113.03821.136156.2481
113.4806-1.27281.49572.4901-1.96751.9418-0.02510.36020.2475-0.2083-0.1407-0.06790.08110.16730.1657-0.03020.06430.03570.0439-0.0285-0.079515.653422.750547.961
123.3953-1.23880.5180.72010.06930.391-0.0716-0.14210.0821-0.02750.0633-0.0696-0.0417-0.08440.0083-0.01080.0490.00990.1109-0.0263-0.014514.518821.720159.0857
132.3696-0.6521-0.80340.95620.1755.7850.00070.3941-0.18860.097-0.1136-0.02240.3108-0.26760.113-0.065-0.02050.0214-0.066-0.0885-0.107736.495110.154175.8612
143.384-1.0496-1.07934.0617-0.20531.86490.00490.2715-0.58580.2911-0.01140.03850.50860.09220.00650.1462-0.04880.0491-0.0401-0.12280.072839.2254-0.130178.5757
151.7698-0.25720.67081.849-1.22272.0752-0.1167-0.38060.09860.10220.0212-0.0159-0.2938-0.3020.0955-0.09020.1117-0.00680.1759-0.0692-0.14882.219230.705675.1749
16-0.2342-0.11331.53861.5761-1.96814.43790.0567-0.06470.0326-0.1152-0.01080.1853-0.0365-0.3453-0.0459-0.10040.08490.01440.0918-0.0299-0.11049.665425.767477.0541
172.5471-0.4125-1.14950.81210.5132.48060.11910.3548-0.0413-0.0544-0.0306-0.0836-0.1065-0.1984-0.0884-0.06110.02490.0099-0.0284-0.0393-0.096434.9417.953183.3678
183.22630.0768-0.98372.27890.27512.68110.04740.5745-0.0341-0.0508-0.04480.1643-0.0562-0.4685-0.0026-0.0640.0326-0.01370.0012-0.0676-0.139330.596417.643580.8889
194.66781.0894-2.2340.05450.06661.56080.16650.31440.0103-0.0207-0.0361-0.0481-0.1609-0.2362-0.13040.01530.03280.00160.0197-0.00710.002728.013724.463592.3682
200.78630.0592-0.2131.52920.08731.17930.00730.0910.0326-0.0498-0.03160.1279-0.0761-0.03110.0243-0.0165-0.01160.0122-0.0349-0.0321-0.0196-78.125727.298322.1773
210.93890.1828-0.10942.2939-0.03380.86840.0462-0.0391-0.0750.2052-0.0719-0.05940.08710.1190.0257-0.0048-0.01190.0142-0.0517-0.0223-0.0753-70.075320.52532.2699
222.69031.0651-1.74061.6595-0.89822.2115-0.0415-0.2179-0.0777-0.00560.04510.17910.0106-0.0757-0.0036-0.05390.02130.0489-0.06410.0129-0.0306-94.558337.827751.0538
232.6472-0.62750.02062.4857-0.38772.8998-0.0586-0.3039-0.22390.15990.08610.23990.1394-0.0327-0.02740.00940.02790.0705-0.05270.01620.0208-93.245131.701252.1518
240.9740.09780.49262.33550.56790.19040.0391-0.3753-0.12390.208-0.05670.18850.104-0.08550.0176-0.00520.01390.06150.07780.0384-0.016-92.968937.535156.5163
251.9908-0.6183-0.54562.30180.89221.64320.00250.29960.0321-0.2732-0.13920.4023-0.1898-0.34690.1367-0.07190.0151-0.0271-0.069-0.0235-0.0053-100.916129.171632.5611
261.66740.01810.04541.2196-0.22141.2396-0.0689-0.37350.16720.0670.13130.05610.0509-0.1161-0.0623-0.11210.0719-0.01420.0918-0.0415-0.0763-12.757141.759354.0599
271.64930.3913-0.25522.2490.38430.82020.0018-0.07980.2091-0.15950.0263-0.2113-0.01690.076-0.0281-0.06410.0189-0.00740.0034-0.0264-0.0305-0.567444.803343.4943
283.9339-0.85021.94320.5822-0.55071.42010.0408-0.07180.0557-0.05650.04090.08960.144-0.1636-0.0817-0.03680.0012-0.04080.02390.0293-0.061-24.140633.08136.3183
292.8015-0.42661.06251.20220.44933.0035-0.13180.18920.524-0.1731-0.0461-0.0958-0.48430.19790.1779-0.0981-0.0514-0.0742-0.01190.1118-0.0258-30.677144.100623.7103
305.63530.53831.05621.71860.33742.1855-0.1904-0.5010.9296-0.0739-0.02130.4537-0.2669-0.47770.2117-0.21950.0924-0.0694-0.021-0.07610.0496-31.82254.044143.8461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{E|2 - 52}
2X-RAY DIFFRACTION2{E|53 - 91}
3X-RAY DIFFRACTION3{E|92 - 135}
4X-RAY DIFFRACTION4{E|136 - 187}
5X-RAY DIFFRACTION5{E|188 - 199}
6X-RAY DIFFRACTION6{F|3 - 93}
7X-RAY DIFFRACTION7{F|94 - 121}
8X-RAY DIFFRACTION8{F|122 - 212}
9X-RAY DIFFRACTION9{F|213 - 241}
10X-RAY DIFFRACTION10{G|2 - 52}
11X-RAY DIFFRACTION11{G|53 - 75}
12X-RAY DIFFRACTION12{G|76 - 108}
13X-RAY DIFFRACTION13{G|109 - 175}
14X-RAY DIFFRACTION14{G|176 - 199}
15X-RAY DIFFRACTION15{H|3 - 86}
16X-RAY DIFFRACTION16{H|87 - 121}
17X-RAY DIFFRACTION17{H|122 - 159}
18X-RAY DIFFRACTION18{H|160 - 199}
19X-RAY DIFFRACTION19{H|200 - 241}
20X-RAY DIFFRACTION20{A|1 - 84}
21X-RAY DIFFRACTION21{A|85 - 171}
22X-RAY DIFFRACTION22{A|172 - 216}
23X-RAY DIFFRACTION23{A|217 - 237}
24X-RAY DIFFRACTION24{A|238 - 269}
25X-RAY DIFFRACTION25{B|0 - 98}
26X-RAY DIFFRACTION26{C|1 - 84}
27X-RAY DIFFRACTION27{C|85 - 158}
28X-RAY DIFFRACTION28{C|159 - 196}
29X-RAY DIFFRACTION29{C|197 - 269}
30X-RAY DIFFRACTION30{D|0 - 97}

+
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