[English] 日本語
Yorodumi
- PDB-9c42: Structure of human MR1-ellagic acid in complex with human MAIT A-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c42
TitleStructure of human MR1-ellagic acid in complex with human MAIT A-F7 TCR
Components
  • Beta-2-microglobulin
  • MAIT T-cell receptor beta chain
  • Major histocompatibility complex class I-related gene protein
  • TRA@ protein
KeywordsIMMUNE SYSTEM / T-cell receptor / MHC-like / Inhibitor / Antigen-presenting molecule
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 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 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 / 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 / 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 / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / adaptive immune response / 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 / 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 / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...: / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETIC ACID / Chem-REF / Beta-2-microglobulin / TRA@ protein / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsWang, C.J.H. / Le Nours, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2008981 Australia
CitationJournal: To Be Published
Title: Ellagic acid metabolism as a source of dietary MR1 ligands
Authors: Wang, C.J.H. / Tang, J.S. / Stephens, R. / Faulkner, S. / Gell, K. / Li, Y. / Cait, A. / Rossjohn, J. / Le Nours, J. / Gasser, O.
History
DepositionJun 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list

-
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: TRA@ protein
E: MAIT T-cell receptor beta chain
F: Beta-2-microglobulin
G: TRA@ protein
H: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,26520
Polymers188,1008
Non-polymers1,16512
Water2,648147
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: TRA@ protein
H: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4819
Polymers94,0504
Non-polymers4315
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-81 kcal/mol
Surface area35900 Å2
MethodPISA
2
C: Major histocompatibility complex class I-related gene protein
D: TRA@ protein
E: MAIT T-cell receptor beta chain
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,78411
Polymers94,0504
Non-polymers7347
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-55 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.810, 70.352, 143.434
Angle α, β, γ (deg.)90.00, 104.09, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

-
Protein , 4 types, 8 molecules ACBFDGEH

#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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / 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 BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein TRA@ protein


Mass: 22781.268 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA@ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6P4G7
#4: Protein MAIT T-cell receptor beta chain


Mass: 27677.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 6 types, 159 molecules

#5: Chemical ChemComp-REF / 2,3,7,8-tetrahydroxychromeno[5,4,3-cde]chromene-5,10-dione / Ellagic acid, 4,4',5,5',6,6'-Hexahydroxydiphenic acid 2,6,2',6'-dilactone


Mass: 302.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6O8 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H4O2
#8: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, bis-tris propane, sodium acetate / PH range: 6.1 - 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2024
RadiationMonochromator: Channel-cut Si(111) liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.69→47.83 Å / Num. obs: 57901 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 47.9 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.084 / Rrim(I) all: 0.2 / Net I/σ(I): 7
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.168 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4476 / CC1/2: 0.599 / Rpim(I) all: 0.608 / Rrim(I) all: 1.32 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSBUILT=20220110data reduction
Aimless0.2.1data scaling
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→47.78 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 2958 5.11 %
Rwork0.1935 --
obs0.1961 57863 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12374 0 85 147 12606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912898
X-RAY DIFFRACTIONf_angle_d1.15817622
X-RAY DIFFRACTIONf_dihedral_angle_d19.6894487
X-RAY DIFFRACTIONf_chiral_restr0.0631907
X-RAY DIFFRACTIONf_plane_restr0.0082274
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.740.3631200.30632490X-RAY DIFFRACTION96
2.74-2.780.39891460.30022633X-RAY DIFFRACTION100
2.78-2.840.34971230.27762631X-RAY DIFFRACTION100
2.84-2.890.32391460.26522563X-RAY DIFFRACTION100
2.89-2.950.32451580.26332608X-RAY DIFFRACTION100
2.95-3.010.31811250.24632632X-RAY DIFFRACTION100
3.01-3.080.26281330.24332615X-RAY DIFFRACTION100
3.08-3.160.2871500.23612607X-RAY DIFFRACTION100
3.16-3.250.29821470.23892585X-RAY DIFFRACTION100
3.25-3.340.28431370.22282644X-RAY DIFFRACTION100
3.34-3.450.27681540.20572559X-RAY DIFFRACTION99
3.45-3.570.26531320.19322625X-RAY DIFFRACTION99
3.57-3.720.2211370.18392589X-RAY DIFFRACTION99
3.72-3.880.27951330.18192628X-RAY DIFFRACTION99
3.88-4.090.21291380.17322597X-RAY DIFFRACTION99
4.09-4.340.19471490.14992627X-RAY DIFFRACTION100
4.34-4.680.17781320.13862634X-RAY DIFFRACTION100
4.68-5.150.1941360.14542644X-RAY DIFFRACTION99
5.15-5.890.24361570.17452621X-RAY DIFFRACTION100
5.9-7.420.24931550.20262635X-RAY DIFFRACTION99
7.42-47.780.20991500.18532738X-RAY DIFFRACTION99
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)
11.8511-0.64120.48812.72540.92312.2812-0.00370.06930.1612-0.26680.1544-0.3271-0.01840.3745-0.13180.2344-0.05920.04630.35340.01990.329750.892277.3325224.5446
22.2097-1.97030.30945.7536-1.35512.01270.0016-0.1933-0.15430.18370.05650.29020.0148-0.1286-0.07680.211-0.0366-0.02750.3216-0.00050.270238.704480.6124235.3891
32.83250.02271.37691.33910.25322.4437-0.1232-0.28420.28580.2780.227-0.2227-0.06970.2251-0.06470.33560.1021-0.05220.4776-0.05850.540564.775474.464247.7566
40.34110.7463-0.52443.70610.95572.9302-0.0968-0.74380.45980.54210.0471-0.2635-0.381-0.30420.07630.48720.1374-0.16770.8364-0.18510.629670.38179.7214262.0302
55.22770.9454-2.1082.46931.73855.095-0.23550.24230.57860.4434-0.1123-0.8494-0.24440.47420.32150.2782-0.0811-0.07050.48480.0360.589370.234987.8667239.7982
62.0177-0.55810.51141.33991.54321.93060.0753-0.09881.1459-0.3472-0.0027-1.0028-0.23660.7724-0.0770.3069-0.07910.05940.61660.08780.674968.941888.8317233.3555
76.94691.5627-0.61312.0062-1.67966.92230.29080.75391.126-0.3448-0.2510.1018-0.25260.5174-0.07720.435-0.18750.04071.1553-0.09780.775877.623489.5987228.0441
82.35961.83361.19452.7166-0.3461.82680.03110.278-0.5522-0.23290.0702-0.40360.08230.8044-0.11790.2545-0.01180.01520.537-0.02880.406164.484883.8667233.4794
92.66221.21461.23651.02291.02572.0536-0.32171.05910.89880.08950.151-0.3208-0.33930.90290.17630.4248-0.14830.00150.81740.15251.096873.652895.892234.4788
106.50811.9178-4.61413.9351.43445.58320.0589-0.5825-0.05630.3995-0.17530.245-0.39150.90120.09180.4628-0.1721-0.23170.55310.00061.063476.084593.811240.5874
111.83570.3285-0.72583.2206-0.55212.1824-0.10330.36650.1266-0.08770.08230.3006-0.1305-0.04910.04180.2328-0.0107-0.04210.36330.01360.4108-4.213862.9104161.035
123.24451.21931.79885.3227-0.35742.3520.0125-0.1622-0.03890.4871-0.2169-0.1218-0.0097-0.01510.19980.2475-0.03330.06060.3840.01150.24131.158151.1858171.6796
132.8039-0.7242-1.5610.62260.65941.9422-0.0098-0.2430.08530.071-0.0207-0.0419-0.21530.1917-0.01160.3539-0.0757-0.04330.32220.01780.2927-10.891470.19183.4636
145.27480.7181-0.79754.0578-1.75065.6290.2252-0.48790.01290.529-0.0735-0.2515-0.1709-0.0597-0.10840.38520.0783-0.04560.2899-0.07610.3956-19.271973.5084195.5218
153.609-0.0812-0.9541.41850.73652.20880.01540.20870.08820.03370.0684-0.1313-0.00540.0944-0.08590.294-0.092-0.01120.48240.10130.353530.257861.5592160.3246
166.4731-1.0644-4.12571.02041.32213.61690.3566-0.44240.2005-0.13070.222-0.3145-0.11230.4602-0.5840.3448-0.0656-0.03030.57130.0220.526146.683263.0646144.9858
177.9028-0.40181.3082.38421.78062.85140.2572-0.34340.17770.0040.2124-0.56720.05970.3356-0.51630.3973-0.02990.01130.7471-0.01930.542756.796962.0997139.0022
183.7601-0.284-1.61042.9437-1.07184.6566-0.08110.4187-0.0075-0.41830.01360.16910.2701-0.53650.08720.3214-0.1126-0.0630.57470.05790.289915.08261.7052139.9231
192.389-0.96271.08111.71770.62131.38350.22180.18580.0041-0.0549-0.03450.0163-0.044-0.3003-0.27250.3043-0.13490.01390.4250.03220.337322.958361.0749138.3848
206.934-1.95973.00412.7835-1.88143.82190.48530.4813-1.0581-0.35080.09750.35920.43720.1416-0.5920.4108-0.0309-0.05840.4333-0.01850.417544.640655.062129.0733
212.0078-2.42663.02352.00840.0512.00870.64650.1827-0.2498-0.79650.2496-1.05520.76980.388-0.84510.4661-0.0054-0.00110.3632-0.08630.5148-19.260649.5243171.7551
225.01062.24950.65142.7618-1.85073.6872-0.23190.13860.75490.276-0.06790.2941-0.6107-0.41160.30840.36090.1192-0.07380.3509-0.06270.3164-29.247473.3437178.1339
232.20081.06170.39524.8201-0.0322.4707-0.49160.44780.50340.01940.4379-0.2701-0.41310.41980.05270.3293-0.0087-0.10680.4665-0.02970.2822-25.010668.9092173.0936
249.4102-7.5141-1.17528.14071.48574.93840.37651.1286-0.0135-0.4047-0.6247-0.2032-0.3894-0.110.18110.2689-0.0269-0.04230.39690.01050.3841-26.239160.8583165.6982
252.0019-0.33871.95045.7831-1.1873.3454-1.05171.13981.8086-0.88520.54480.5435-0.1885-0.24380.48210.45480.0529-0.13570.71120.09170.527-31.761670.5903163.6515
266.4191-2.93722.75854.8382-3.25977.5239-0.25440.0750.4351-0.23660.1584-0.21740.4314-0.24830.15230.2672-0.0157-0.01310.3399-0.04790.3781-12.140760.2126170.2486
277.0802-5.7318-1.75212.03073.05246.66960.05710.20480.5165-1.22390.2826-0.313-0.5268-0.5539-0.35890.3691-0.0867-0.11050.4572-0.03960.5547-24.622270.5427169.5254
280.97440.61060.29120.38370.18160.08180.50860.54590.2714-0.731-0.78171.1198-0.4139-0.91490.28180.47040.2529-0.09790.6882-0.12820.8504-41.551574.7891174.8384
294.1771-3.208-0.86798.13840.84622.07920.17710.3579-0.3958-1.188-0.30350.7256-0.0668-0.33040.10990.2749-0.0112-0.08760.5026-0.07930.3975-30.783757.2296168.0457
309.2304-3.3508-2.69648.07332.60554.11130.2082-0.27310.78950.0958-0.30640.0774-0.1829-0.15110.09320.2898-0.03660.01980.5079-0.06120.2684-34.609266.2048177.2827
3122.000222.00011.10620.4861-1.47143.72810.272-0.1960.68511.03570.5066-0.29840.9870.36060.11710.9998-0.24140.9262-35.68769.6004186.6859
326.4993-2.7974-1.52832.16150.10291.5639-0.1666-0.5278-0.2021-0.02780.098-0.0768-0.15440.29070.07190.4133-0.0669-0.01670.25110.04810.274821.016150.2776220.7822
335.48852.11394.66853.75231.87095.47540.3530.365-0.60650.0860.0178-0.17360.32010.5455-0.38270.2729-0.0089-0.04850.29870.01750.312426.601558.2186221.7501
341.2182-0.16681.18750.75180.50571.7732-0.3120.08280.75220.22130.02720.052-0.3860.03530.32840.4091-0.07530.00060.30020.02310.446322.323464.6078227.4474
356.01491.41443.15081.00351.51683.03340.01880.0035-0.30740.08860.0243-0.17880.1637-0.0909-0.05530.4051-0.104-0.04390.22360.04680.33423.794757.0435230.6137
362.01272.90953.81653.50071.14225.81420.07910.38560.6031-0.2320.02360.370.0464-0.4249-0.15170.34780.0023-0.0450.25910.07450.350417.368658.1508219.6745
376.36661.76251.632.7970.65852.85860.0364-0.1604-0.2837-0.1411-0.0161-0.2929-0.5220.1246-0.00880.3667-0.0329-0.00770.36180.01230.218128.267757.1859218.5053
384.5260.9826-0.24442.5312-1.01453.31080.12480.172-0.0276-0.59170.15880.22910.2042-0.4601-0.32920.47120.0273-0.10070.27250.06030.4471-2.44745.5365199.2725
398.3575-0.3872-4.6914.2814-0.5957.7325-0.2433-0.7806-0.433-0.12540.0999-0.31670.99770.75480.12660.44680.0359-0.10360.2981-0.00270.42196.855340.3824203.0116
406.57110.6533-1.60691.7022-0.44585.11040.336-0.59170.5705-0.35020.2194-0.0966-0.5188-0.0206-0.53090.3817-0.03630.01430.30350.07420.39440.076252.3547205.7235
414.18440.8228-1.08041.40841.6577.898-0.17450.1101-0.8672-0.58770.2608-0.03741.65820.076-0.03620.74730.04120.01430.30950.02210.4971-1.916835.5997199.2148
422.9542-0.17231.40594.06322.83952.83090.04380.44320.0434-0.4302-0.0789-0.0567-0.36050.21730.01760.3505-0.05280.00130.41850.09630.240134.3666.4284204.3151
434.2661-0.6617-0.17095.3583.11281.84030.09490.32610.2814-0.09750.0442-0.21120.00640.2189-0.11790.4624-0.1068-0.11040.45260.12370.256534.281968.2604206.0364
443.54590.47291.39960.58121.62716.78120.1094-0.085-0.21780.46860.3408-0.28931.04180.8857-0.38080.57380.0727-0.16370.460.00290.420926.40353.9038189.1121
458.0722-0.9832-2.79551.29780.18172.6106-0.1334-0.0869-0.0846-0.12630.0080.036-0.16880.09490.1220.4017-0.036-0.06680.24730.02310.23742.825853.4325194.7787
466.6177-0.7687-1.67111.0653-0.1694.8294-0.4111-0.5493-0.20010.26610.1152-0.0509-0.00090.62820.40050.3373-0.0543-0.04660.30660.02090.340112.291952.1012196.8737
474.35750.3107-2.34630.7137-0.26692.68690.15830.21470.2685-0.1778-0.02860.1426-0.1240.0081-0.14970.37-0.0472-0.07630.23330.01840.27717.394758.4601188.8675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 158 )
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 270 )
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 19 )
6X-RAY DIFFRACTION6chain 'B' and (resid 20 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 71 )
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 90 )
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 97 )
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 84 )
12X-RAY DIFFRACTION12chain 'C' and (resid 85 through 146 )
13X-RAY DIFFRACTION13chain 'C' and (resid 147 through 237 )
14X-RAY DIFFRACTION14chain 'C' and (resid 238 through 270 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 91 )
16X-RAY DIFFRACTION16chain 'D' and (resid 92 through 150 )
17X-RAY DIFFRACTION17chain 'D' and (resid 151 through 199 )
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 94 )
19X-RAY DIFFRACTION19chain 'E' and (resid 95 through 124 )
20X-RAY DIFFRACTION20chain 'E' and (resid 125 through 243 )
21X-RAY DIFFRACTION21chain 'F' and (resid 0 through 5 )
22X-RAY DIFFRACTION22chain 'F' and (resid 6 through 19 )
23X-RAY DIFFRACTION23chain 'F' and (resid 20 through 30 )
24X-RAY DIFFRACTION24chain 'F' and (resid 31 through 41 )
25X-RAY DIFFRACTION25chain 'F' and (resid 42 through 51 )
26X-RAY DIFFRACTION26chain 'F' and (resid 52 through 61 )
27X-RAY DIFFRACTION27chain 'F' and (resid 62 through 71 )
28X-RAY DIFFRACTION28chain 'F' and (resid 72 through 77 )
29X-RAY DIFFRACTION29chain 'F' and (resid 78 through 90 )
30X-RAY DIFFRACTION30chain 'F' and (resid 91 through 98 )
31X-RAY DIFFRACTION31chain 'F' and (resid 99 through 99 )
32X-RAY DIFFRACTION32chain 'G' and (resid 1 through 17 )
33X-RAY DIFFRACTION33chain 'G' and (resid 18 through 42 )
34X-RAY DIFFRACTION34chain 'G' and (resid 43 through 59 )
35X-RAY DIFFRACTION35chain 'G' and (resid 60 through 75 )
36X-RAY DIFFRACTION36chain 'G' and (resid 76 through 91 )
37X-RAY DIFFRACTION37chain 'G' and (resid 92 through 108 )
38X-RAY DIFFRACTION38chain 'G' and (resid 109 through 135 )
39X-RAY DIFFRACTION39chain 'G' and (resid 136 through 156 )
40X-RAY DIFFRACTION40chain 'G' and (resid 157 through 175 )
41X-RAY DIFFRACTION41chain 'G' and (resid 176 through 201 )
42X-RAY DIFFRACTION42chain 'H' and (resid 1 through 63 )
43X-RAY DIFFRACTION43chain 'H' and (resid 64 through 109 )
44X-RAY DIFFRACTION44chain 'H' and (resid 110 through 124 )
45X-RAY DIFFRACTION45chain 'H' and (resid 125 through 162 )
46X-RAY DIFFRACTION46chain 'H' and (resid 163 through 188 )
47X-RAY DIFFRACTION47chain 'H' and (resid 189 through 244 )

+
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