[English] 日本語
Yorodumi
- PDB-4pje: Structure of human MR1-Ac-6-FP in complex with human MAIT B-B10 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pje
TitleStructure of human MR1-Ac-6-FP in complex with human MAIT B-B10 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 / 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 ...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 / 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 / DAP12 interactions / negative regulation of receptor binding / 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 / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / defense response to Gram-negative bacterium / 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 / external side of plasma membrane / Golgi 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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 / ACETATE ION / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 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.pdbx_dist_value / _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
Remark 0 : statistics at the very beginning when nothing is done yet

-
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)189,75926
Polymers188,2268
Non-polymers1,53318
Water26,3561463
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)95,17017
Polymers94,1134
Non-polymers1,05713
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)94,5899
Polymers94,1134
Non-polymers4765
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.040, 72.460, 143.360
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: 22879.352 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: 27642.717 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 , 6 types, 1481 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: 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
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1463 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.96 %
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: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.95→46.9 Å / Num. obs: 155088 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 29.88 Å2 / Net I/σ(I): 11

-
Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 1.95→28.55 Å / Cor.coef. Fo:Fc: 0.9525 / Cor.coef. Fo:Fc free: 0.9427 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.132 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.117
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 7803 5.03 %RANDOM
Rwork0.171 ---
obs0.1724 155058 97.75 %-
Displacement parametersBiso mean: 37.11 Å2
Baniso -1Baniso -2Baniso -3
1-3.6763 Å20 Å20.5217 Å2
2---7.7037 Å20 Å2
3---4.0274 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: 1 / Resolution: 1.95→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12651 0 1560 1463 15674
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113101HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0317825HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4362SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes341HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1933HARMONIC5
X-RAY DIFFRACTIONt_it13101HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.87
X-RAY DIFFRACTIONt_other_torsion16.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1650SEMIHARMONIC5
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_contact15676SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2161 575 5.05 %
Rwork0.1947 10812 -
all0.1958 11387 -
obs--97.75 %
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)
10.796-0.3011-0.30331.2230.27230.89970.03910.1310.0663-0.0345-0.03560.1291-0.0697-0.0211-0.0035-0.0272-0.0039-0.0009-0.0045-0.0029-0.0587-78.372220.178821.7015
21.1774-0.0303-0.28372.537-0.56180.56610.0357-0.0327-0.08480.2246-0.113-0.15530.0210.08370.0772-0.008-0.0160.0008-0.0046-0.0101-0.0959-70.56612.889432.18
31.48580.5108-0.6321.5734-0.0220.97490.0255-0.2211-0.090.0728-0.0520.13260.0674-0.00130.0264-0.03130.01630.0416-0.0420.0107-0.0209-94.293829.088352.6233
41.42420.36820.02960.65940.73911.44040.0630.15230.1214-0.085-0.18790.2532-0.1029-0.20580.1249-0.0323-0.00570.0151-0.0634-0.00470.0494-100.425721.872437.5464
52.6783-1.0355-0.45832.23270.54430.5404-0.00890.5260.1687-0.2952-0.07580.2752-0.1446-0.08850.0847-0.02640.0205-0.0381-0.01580.01820.0011-100.462122.235728.663
66.0257-2.6179-0.72163.80070.48181.6901-0.10510.13350.2387-0.13080.05890.3566-0.2478-0.2720.0461-0.03870.0141-0.0239-0.0521-0.007-0.0205-99.733124.079333.0227
72.8344-0.1951-0.04422.09540.28450.9781-0.03060.1307-0.0703-0.2237-0.06770.49610.0059-0.24320.0983-0.0805-0.0144-0.0228-0.0452-0.03630.0532-106.483616.49633.2953
81.9146-0.45340.06541.3243-0.24951.2836-0.0823-0.35060.16720.07480.16630.06940.013-0.1835-0.084-0.08770.054-0.02230.0421-0.0281-0.0579-12.977734.005954.0467
92.00060.4429-0.0522.06350.04010.87020.0435-0.0050.2357-0.2861-0.0835-0.1697-0.04320.02880.04-0.05510.02070.0095-0.05480.0076-0.0308-0.661637.180743.1691
102.1684-0.57941.93780.1578-0.20612.049-0.14370.09690.2472-0.04890.00210.0091-0.1358-0.05070.1416-0.0434-0.0359-0.08890.01930.09210.001-28.476832.310328.3514
110.2403-3.7877-0.54981.9225-0.36722.0015-0.02740.10930.1688-0.26410.04890.2803-0.1113-0.5234-0.0215-0.11780.1108-0.07550.00720.0360.0238-31.923745.492139.0374
125.92420.2241.25941.576-0.14741.1926-0.0801-0.74750.7651-0.03440.00520.4522-0.1994-0.4910.0749-0.22250.0984-0.0361-0.0058-0.08070.0121-29.667145.300746.9367
135.5101-1.2921-1.612.6078-0.00811.1452-0.0697-0.190.4607-0.05660.01780.6992-0.2473-0.64440.0519-0.17040.1355-0.09690.1646-0.08350.1484-37.214546.015444.6179
140.5984-0.03490.70030.9344-1.39622.04980.031-0.03230.2505-0.15420.1553-0.0401-0.1598-0.1483-0.1863-0.12020.1952-0.1552-0.1566-0.09110.3101-30.326855.101642.838
151.90510.2488-0.14740.6168-0.06461.3808-0.0122-0.0285-0.02260.0271-0.0161-0.06330.08270.17130.0284-0.07360.0109-0.0143-0.00120.0482-0.0719-42.858919.714120.2395
168.6183-0.09670.95692.5571-0.19943.9932-0.1492-0.28851.04250.01630.103-0.3696-0.25060.50570.0462-0.13760.02240.0025-0.0346-0.02780.2284-18.041621.66490.0877
171.88250.1954-0.56891.1665-0.6871.5682-0.0240.1202-0.0151-0.0904-0.0136-0.01550.1113-0.08020.0377-0.038-0.02840.0023-0.05240.0181-0.1128-59.844320.08450.422
181.39590.0707-0.87570.00550.29171.0848-0.0380.13290.0152-0.12550.0544-0.01750.1998-0.128-0.0164-0.0165-0.01530.0096-0.0170.0259-0.0503-51.223420.4161-2.1699
194.5899-1.15481.71941.5564-0.81241.93770.15060.1213-0.7572-0.00110.0683-0.06850.22330.3047-0.2189-0.10560.07760.0259-0.1072-0.0258-0.0384-27.151713.1043-6.9833
203.6242-2.05790.44445.57530.77964.24680.0140.3562-0.4204-0.3370.2565-0.14730.18980.1362-0.2706-0.05540.00910.0425-0.0682-0.0946-0.0905-38.509114.5997-19.3441
212.3561-0.48750.36581.4494-0.22970.8438-0.00940.06670.0824-0.06590.0341-0.0037-0.03340.0289-0.0247-0.02310.02260.0076-0.0005-0.0053-0.056115.04313.975453.7306
224.3923-1.77692.60350.83-0.94651.48930.01340.2434-0.0184-0.0262-0.01910.03740.0650.07450.0056-0.01020.03110.01250.0174-0.018-0.056923.32959.069963.206
232.3571-0.1288-0.10241.23130.30863.1043-0.00220.1539-0.27380.1697-0.01170.01390.49550.02830.01390.045600.0187-0.0788-0.0471-0.063636.807-0.13677.383
242.1595-0.53270.2762.0104-0.93622.2594-0.1054-0.34630.07630.0130.0208-0.0174-0.147-0.18320.0847-0.06920.05-0.0090.0741-0.0342-0.11633.325822.296773.6355
251.5628-0.63381.05481.4255-1.52541.9739-0.0827-0.37020.18660.13630.04180.0336-0.2329-0.20180.0409-0.02930.0498-0.00660.0769-0.0566-0.04443.382424.306472.4524
260.0243-0.72071.20460-0.01763.10370.07630.07060.06310.02150.06080.14990.1172-0.5721-0.1371-0.1091-0.0286-0.00330.08280.0123-0.126211.635410.361589.3046
273.2536-0.4462-0.62010.94810.38212.1143-0.06410.1541-0.1083-0.044-0.0070.00690.0892-0.14080.0711-0.10460.0006-0.0134-0.0809-0.0414-0.156731.15999.645682.5191
280.74220.5098-0.46780.1824-0.31611.25210.07320.06630.1002-0.0041-0.011-0.0595-0.1344-0.1484-0.06220.03910.0182-0.01880.0534-0.04310.016830.825915.657488.9075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 83}
2X-RAY DIFFRACTION2{A|84 - 171}
3X-RAY DIFFRACTION3{A|172 - 269}
4X-RAY DIFFRACTION4{B|0 - 19}
5X-RAY DIFFRACTION5{B|20 - 56}
6X-RAY DIFFRACTION6{B|57 - 77}
7X-RAY DIFFRACTION7{B|78 - 98}
8X-RAY DIFFRACTION8{C|1 - 84}
9X-RAY DIFFRACTION9{C|85 - 158}
10X-RAY DIFFRACTION10{C|159 - 269}
11X-RAY DIFFRACTION11{D|0 - 19}
12X-RAY DIFFRACTION12{D|20 - 61}
13X-RAY DIFFRACTION13{D|62 - 83}
14X-RAY DIFFRACTION14{D|84 - 96}
15X-RAY DIFFRACTION15{E|2 - 116}
16X-RAY DIFFRACTION16{E|117 - 198}
17X-RAY DIFFRACTION17{F|3 - 86}
18X-RAY DIFFRACTION18{F|87 - 122}
19X-RAY DIFFRACTION19{F|123 - 213}
20X-RAY DIFFRACTION20{F|214 - 242}
21X-RAY DIFFRACTION21{G|2 - 91}
22X-RAY DIFFRACTION22{G|92 - 120}
23X-RAY DIFFRACTION23{G|121 - 198}
24X-RAY DIFFRACTION24{H|3 - 63}
25X-RAY DIFFRACTION25{H|64 - 107}
26X-RAY DIFFRACTION26{H|108 - 122}
27X-RAY DIFFRACTION27{H|123 - 186}
28X-RAY DIFFRACTION28{H|187 - 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://pdbjlvh1.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