[English] 日本語
Yorodumi
- PDB-5u2v: Structure of human MR1-HMB in complex with human MAIT A-F7 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u2v
TitleStructure of human MR1-HMB in complex with human MAIT A-F7 TCR
Components
  • (MAIT T-cell receptor ...) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / T-cell Receptor Complex
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 / early endosome lumen / positive regulation of receptor binding ...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 / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / 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 / membrane / identical protein binding / 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
2-hydroxy-5-methoxybenzaldehyde / PROLINE / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKeller, A.N. / Rossjohn, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE140100011 Australia
National Health and Medical Research Council (NHMRC, Australia)AF50 Australia
CitationJournal: Nat. Immunol. / Year: 2017
Title: Drugs and drug-like molecules can modulate the function of mucosal-associated invariant T cells.
Authors: Keller, A.N. / Eckle, S.B. / Xu, W. / Liu, L. / Hughes, V.A. / Mak, J.Y. / Meehan, B.S. / Pediongco, T. / Birkinshaw, R.W. / Chen, Z. / Wang, H. / D'Souza, C. / Kjer-Nielsen, L. / Gherardin, ...Authors: Keller, A.N. / Eckle, S.B. / Xu, W. / Liu, L. / Hughes, V.A. / Mak, J.Y. / Meehan, B.S. / Pediongco, T. / Birkinshaw, R.W. / Chen, Z. / Wang, H. / D'Souza, C. / Kjer-Nielsen, L. / Gherardin, N.A. / Godfrey, D.I. / Kostenko, L. / Corbett, A.J. / Purcell, A.W. / Fairlie, D.P. / McCluskey, J. / Rossjohn, J.
History
DepositionDec 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)187,91713
Polymers187,3138
Non-polymers6045
Water19,2401068
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: MAIT T-cell receptor alpha chain
H: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0167
Polymers93,6564
Non-polymers3593
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: MAIT T-cell receptor alpha chain
F: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9016
Polymers93,6564
Non-polymers2442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.232, 69.730, 142.400
Angle α, β, γ (deg.)90.000, 104.360, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#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
Source method: isolated from a genetically manipulated source
Details: Fragment: extracellular domain, residues 23-292 / Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 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 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769

-
MAIT T-cell receptor ... , 2 types, 4 molecules GEHF

#3: Protein MAIT T-cell receptor alpha chain


Mass: 22650.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAV/TRAC / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein MAIT T-cell receptor beta chain


Mass: 27546.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRBV/TRBC / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

-
Non-polymers , 4 types, 1073 molecules

#5: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical ChemComp-7WQ / 2-hydroxy-5-methoxybenzaldehyde / 2-Hydroxy-5-methoxybenzaldehyde


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1068 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.69 % / Mosaicity: 0.7 °
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: BTP, PEG 3350, NaAc

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.2→52.369 Å / Num. obs: 104386 / % possible obs: 99.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 29.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.508 / CC1/2: 0.86 / % possible all: 97.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimless0.3.6data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t


Resolution: 2.2→52.369 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.83
RfactorNum. reflection% reflection
Rfree0.2213 5207 4.99 %
Rwork0.1788 --
obs0.1809 104332 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.16 Å2 / Biso mean: 37.4384 Å2 / Biso min: 12.53 Å2
Refinement stepCycle: final / Resolution: 2.2→52.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12780 0 39 1068 13887
Biso mean--39.7 40.43 -
Num. residues----1598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113181
X-RAY DIFFRACTIONf_angle_d1.36417920
X-RAY DIFFRACTIONf_chiral_restr0.2171891
X-RAY DIFFRACTIONf_plane_restr0.0062336
X-RAY DIFFRACTIONf_dihedral_angle_d18.0354770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2250.29631540.24573265341997
2.225-2.25120.29111810.24313204338598
2.2512-2.27860.28681720.23513251342398
2.2786-2.30750.28821830.22623213339699
2.3075-2.33780.29881850.22993262344799
2.3378-2.36990.28341870.219632863473100
2.3699-2.40370.2571610.213633333494100
2.4037-2.43960.26081920.20532053397100
2.4396-2.47770.25881550.214933323487100
2.4777-2.51830.29011660.213532903456100
2.5183-2.56180.27481630.214132913454100
2.5618-2.60840.27721550.209633053460100
2.6084-2.65850.29121690.206933073476100
2.6585-2.71280.2741670.204133023469100
2.7128-2.77180.23561740.206633363510100
2.7718-2.83620.28181800.207332943474100
2.8362-2.90720.25341690.209533083477100
2.9072-2.98580.26551590.195633103469100
2.9858-3.07360.22331660.186533443510100
3.0736-3.17280.21351900.177332953485100
3.1728-3.28620.20041860.180332603446100
3.2862-3.41770.2321820.181333103492100
3.4177-3.57320.20571920.163733043496100
3.5732-3.76160.2021600.157633493509100
3.7616-3.99720.19121720.159533103482100
3.9972-4.30570.17981680.142533643532100
4.3057-4.73870.15291920.12733373529100
4.7387-5.42380.18371900.139933343524100
5.4238-6.8310.20311690.17733853554100
6.831-52.38390.18851680.16853439360799
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)
11.10440.17360.00711.6793-0.34371.75050.06540.2496-0.0204-0.1301-0.08440.1144-0.0257-0.04540.0230.17330.0091-0.00280.2377-0.0350.2127-4.491262.2967159.3002
21.3742-0.110.06431.5779-0.54940.86970.05420.0217-0.05880.0858-0.0893-0.03920.02230.09520.03120.2182-0.02390.00270.2588-0.02050.19673.3254.5399169.6611
31.38290.1432-0.0661.05260.25460.9420.0027-0.1151-0.14520.0219-0.08-0.0007-0.0091-0.04870.08930.2610.00990.00990.1633-0.00650.254-19.977471.4203189.6192
42-8.36162222-0.3298-0.4774-0.02040.8193-2.2683-5.128-0.82121.68632.62940.7915-0.2890.24430.6325-0.04550.9387-29.226176.8497202.7776
51.5367-0.2854-0.19962.0826-0.12731.4717-0.0860.1309-0.09430.1245-0.1080.0854-0.01720.05220.20640.1445-0.0002-0.00890.1758-0.00490.1829-23.5657.9721173.344
62.349-0.49750.58860.3002-0.45721.0061-0.1038-0.09850.72940.0388-0.24560.5216-0.8735-0.68630.40020.44170.1147-0.00860.3214-0.10350.5435-32.118679.4992177.6188
71.455-0.2323-0.3121.2262-0.06830.9628-0.07080.2710.0994-0.326-0.06390.1642-0.2044-0.15480.09860.26110.0273-0.04950.2028-0.0210.2065-25.701963.9387167.6642
83.690.9155-2.78115.73531.02875.8737-0.040.6093-0.0866-0.9883-0.24120.20690.1027-0.41110.21870.38930.0464-0.11140.42260.02020.3386-37.924967.7428162.5761
93.2177-3.96221.55685.0072-2.39652.5106-0.13960.96190.1111-0.1946-0.14860.1135-0.7476-0.56660.29650.4474-0.0002-0.09210.4916-0.03370.4299-26.823971.2682160.7763
101.7905-1.54360.54821.6547-0.38290.21120.13470.0430.1655-0.32-0.1111-0.032-0.0620.1063-0.01470.28910.00780.02750.2282-0.05080.2549-12.35859.4645168.4159
113.1562-2.25810.22913.34140.26521.39530.04590.1260.2011-0.41350.08750.0312-0.3935-0.1266-0.0870.31360.0094-0.00690.24150.01320.1873-24.5969.5877167.9729
122.511-0.6491-0.4472.9131.14222.98570.0994-0.24450.25930.3658-0.64240.9460.3249-0.38370.47870.4290.0697-0.05820.4864-0.05670.6891-42.118473.4413173.5686
131.7527-0.8591-0.49191.76260.41721.1108-0.00880.3777-0.1677-0.3544-0.2510.5117-0.1223-0.18810.24410.2469-0.0117-0.06920.3197-0.07990.3488-30.796156.3877166.3864
141.77230.04920.26793.84831.78863.84820.2349-0.37130.4280.7110.05370.2766-0.1043-0.2204-0.26830.32520.02320.05910.3228-0.05830.4034-34.923765.6598176.5588
151.94490.4982-0.34861.1283-0.01781.38060.0010.0997-0.00490.0621-0.0205-0.03930.05330.15650.01520.199-0.0138-0.01170.24650.03540.180929.122461.0196159.8395
161.7781-0.1467-1.46740.45730.20181.14930.05980.0322-0.0556-0.1114-0.0135-0.10560.06230.1413-0.05410.2197-0.0066-0.00990.3730.00910.216241.532759.2073146.9367
172.7266-0.34080.59041.64-0.31643.49120.012-0.33160.09530.12420.0996-0.1687-0.10120.2164-0.06350.38560.01630.02770.4817-0.02350.444651.947960.2304141.2656
182.7138-0.0540.04051.11830.90990.92130.1413-0.10530.421-0.15450.1331-0.4672-0.2310.628-0.27940.4801-0.07860.05280.55540.00950.530259.338563.9112136.8045
192.22060.1781-0.77221.1673-0.01691.5608-0.07630.27750.0136-0.251-0.0190.11810.0758-0.24290.08920.2813-0.0347-0.03360.36570.0270.213114.239960.1006139.1444
201.72660.0515-0.47782.2937-1.10622.39250.00990.01420.05680.09850.13590.1975-0.134-0.498-0.15850.2895-0.0516-0.02020.36810.03670.242916.369459.7697142.0161
212.4410.3352-1.63550.8566-0.33682.66570.31010.33910.4251-0.12640.0710.10130.0451-0.096-0.27660.41690.00780.02090.40660.04850.285728.956365.6405123.8
222.96970.24281.06721.0551-0.47392.20540.41990.1224-0.6007-0.1814-0.0169-0.05080.45740.3261-0.34190.43320.0661-0.04450.3243-0.05590.313147.420353.3539130.5736
231.73120.6416-1.38492.9375-0.00312.04450.6340.4687-0.1026-0.83850.11660.22830.53610.0591-0.75480.61260.0278-0.02550.5075-0.11950.285435.89855.3895118.0673
241.4643-0.23060.31251.5530.20991.32030.02910.12920.1089-0.11590.024-0.0646-0.01220.1167-0.05310.1808-0.03140.01750.23210.01040.216950.372376.0912222.7376
250.9876-0.0833-0.10992.14080.06810.3694-0.0056-0.08690.10070.03580.01610.1102-0.0224-0.0252-0.00690.1945-0.01030.00750.20320.00070.222237.866979.8343233.5919
261.1774-0.11090.35690.82490.11821.09750.09340.0147-0.17350.13090.1216-0.2890.15730.2528-0.21190.22480.0239-0.04440.3042-0.0230.29362.218868.3121241.3008
271.11310.61750.7081.1703-0.16441.5698-0.0251-0.25770.38220.2748-0.00550.0242-0.3197-0.30930.03250.33140.1078-0.03740.4468-0.12150.397566.88578.7442254.9732
283.3059-1.39950.86212.6458-0.67831.6684-0.3924-0.0090.46840.48870.0929-0.2742-0.32860.20770.23770.3025-0.0272-0.00610.3336-0.08270.427362.85290.61237.5229
290.77571.15140.42981.95021.38682.5787-0.6782-0.56990.13710.1868-0.0518-1.4184-0.1761.12340.63140.31310.034-0.15980.67560.05410.750383.056278.4947240.1263
302.8074-0.17490.6890.23530.19160.89180.03570.17220.5049-0.22650.0511-0.3784-0.24540.4251-0.03930.2576-0.07450.02110.44210.01540.493968.134787.8501231.5178
312.582-0.96120.68695.2550.19574.07650.43050.09520.2077-0.44380.33110.2151-0.48390.322-0.63240.404-0.21250.02170.91070.21220.987279.900793.175227.2314
326.9185-0.51180.83934.3461.9212.7471-0.04130.72780.0737-0.90340.2195-0.0501-0.09570.2265-0.24010.4657-0.10320.06970.6895-0.07350.670673.361283.7939223.8928
333.79960.1166-0.55441.0235-0.44761.14240.17820.26260.191-0.1201-0.0495-0.0812-0.16370.2775-0.06890.1753-0.001-0.01730.20870.00180.271455.05182.7301232.088
343.01680.1162-0.18050.4518-0.53760.6163-0.4085-0.04040.13590.03820.1941-0.529-0.17220.67410.12610.2457-0.04460.0210.6463-0.01720.560776.042585.0125233.2152
352.8396-0.43330.69311.3188-0.3061.29840.02430.00621.36210.0255-0.0995-0.5268-0.56010.57360.12170.4452-0.0918-0.00640.46220.08560.742567.373197.0532231.4418
363.039-0.8396-1.45143.01671.23270.9497-0.45010.05970.80380.62750.06620.3014-0.1549-0.05880.33810.4669-0.1639-0.0850.5586-0.09840.777174.902493.3536238.545
370.54730.87450.39351.38810.69160.6435-0.00870.0565-0.2169-0.00840.0723-0.11830.11780.0623-0.0620.2218-0.0267-0.01220.20650.02590.246324.175653.7479220.9288
381.0112-0.1274-0.54171.29980.03250.30340.00860.16360.0225-0.08310.21120.2048-0.0081-0.1801-0.23070.1823-0.054-0.00540.16730.02940.234722.815563.0459218.965
394.57760.52562.92791.14620.66173.19480.1332-0.6514-0.0370.1807-0.11890.13250.0846-0.4323-0.06880.1981-0.0420.0430.1830.0320.257521.108458.1559228.7467
403.55071.1050.61991.03580.09240.8328-0.0491-0.1548-0.0175-0.0930.03910.2120.0678-0.09470.06010.2209-0.0153-0.01020.19710.01210.232216.024657.548217.9895
412.23671.20511.16830.74260.65010.70320.0251-0.2215-0.0587-0.0193-0.0293-0.0279-0.0324-0.042-0.01310.1829-0.0196-0.01730.17520.02790.167114.236251.6541212.7999
420.52310.3751-0.93050.3658-0.76955.14990.12670.15470.0546-0.36590.1320.30190.0194-0.162-0.23140.4239-0.031-0.01380.21170.00690.2952-1.177544.9273189.0613
431.8648-0.4075-1.17121.83061.43454.6767-0.0901-0.1404-0.2319-0.0292-0.0426-0.03970.43780.88770.1320.2630.05370.01070.29740.07210.32095.478838.7755203.2689
443.6275-1.3074-1.33833.19490.90363.53020.2488-0.31510.3939-0.1834-0.0395-0.2686-0.3441-0.035-0.20280.3033-0.0435-0.01950.2167-0.00680.24281.848650.9173203.7067
452.0479-0.04120.03620.2752-0.40461.1382-0.20880.0299-0.2514-0.34250.13340.14580.240.12390.02330.3742-0.04330.04680.16320.00390.33591.081140.8808195.6206
463.9622-1.08340.44592.3572-1.13411.6740.2712-0.1061-0.4539-0.3947-0.00380.2980.4482-0.196-0.23750.3946-0.0367-0.01750.25830.08790.3509-4.230135.2602202.0155
471.32510.47540.5531.56950.8171.0131-0.04010.27070.0731-0.17780.0039-0.0177-0.19610.16390.02370.2408-0.0506-0.00480.27440.03290.18534.296665.6146201.5946
481.10720.3815-1.10042.63090.69881.5595-0.10930.0210.2260.1846-0.07530.2025-0.20240.20490.20340.2331-0.0202-0.04270.18250.04220.224730.062870.7936214.667
492.1711.47671.80971.35630.73592.21640.16880.2764-0.29120.12790.1195-0.28680.34610.6-0.150.27470.0103-0.02250.3173-0.02440.282926.021852.8546187.4106
501.7452-0.4305-0.40640.9753-0.71651.51190.134-0.0669-0.0255-0.0582-0.0480.1121-0.1182-0.0019-0.08930.2622-0.023-0.01160.1612-0.00770.23651.997352.5907193.0189
512.25850.4856-1.03991.6088-0.2083.27350.0353-0.4349-0.29160.0084-0.0937-0.15140.0810.53320.06510.2869-0.0512-0.03640.25350.02420.253611.878951.3889195.2561
521.92120.6889-1.05620.6-0.07541.15550.13160.0580.3209-0.10630.02550.1429-0.223-0.0338-0.14540.2938-0.02770.00320.21460.02770.2464-1.17757.4755192.6232
531.8743-0.1682-0.69230.809-0.05521.95170.0555-0.0742-0.0357-0.034-0.0367-0.00730.01210.1555-0.0040.2587-0.02-0.04360.18780.0320.173315.150357.4972181.1291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 83 )A0 - 83
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 171 )A84 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 269 )A172 - 269
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 301 )A301
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 11 )B1 - 11
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 19 )B12 - 19
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 41 )B20 - 41
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 46 )B42 - 46
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 51 )B47 - 51
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 61 )B52 - 61
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 71 )B62 - 71
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 77 )B72 - 77
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 90 )B78 - 90
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 99 )B91 - 99
15X-RAY DIFFRACTION15chain 'G' and (resid 1 through 75 )G1 - 75
16X-RAY DIFFRACTION16chain 'G' and (resid 76 through 135 )G76 - 135
17X-RAY DIFFRACTION17chain 'G' and (resid 136 through 165 )G136 - 165
18X-RAY DIFFRACTION18chain 'G' and (resid 166 through 199 )G166 - 199
19X-RAY DIFFRACTION19chain 'H' and (resid 3 through 73 )H3 - 73
20X-RAY DIFFRACTION20chain 'H' and (resid 74 through 109 )H74 - 109
21X-RAY DIFFRACTION21chain 'H' and (resid 110 through 124 )H110 - 124
22X-RAY DIFFRACTION22chain 'H' and (resid 125 through 215 )H125 - 215
23X-RAY DIFFRACTION23chain 'H' and (resid 216 through 244 )H216 - 244
24X-RAY DIFFRACTION24chain 'C' and (resid 0 through 83 )C0 - 83
25X-RAY DIFFRACTION25chain 'C' and (resid 84 through 158 )C84 - 158
26X-RAY DIFFRACTION26chain 'C' and (resid 159 through 203 )C159 - 203
27X-RAY DIFFRACTION27chain 'C' and (resid 204 through 269 )C204 - 269
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 11 )D1 - 11
29X-RAY DIFFRACTION29chain 'D' and (resid 12 through 19 )D12 - 19
30X-RAY DIFFRACTION30chain 'D' and (resid 20 through 41 )D20 - 41
31X-RAY DIFFRACTION31chain 'D' and (resid 42 through 46 )D42 - 46
32X-RAY DIFFRACTION32chain 'D' and (resid 47 through 51 )D47 - 51
33X-RAY DIFFRACTION33chain 'D' and (resid 52 through 61 )D52 - 61
34X-RAY DIFFRACTION34chain 'D' and (resid 62 through 77 )D62 - 77
35X-RAY DIFFRACTION35chain 'D' and (resid 78 through 90 )D78 - 90
36X-RAY DIFFRACTION36chain 'D' and (resid 91 through 96 )D91 - 96
37X-RAY DIFFRACTION37chain 'E' and (resid 1 through 37 )E1 - 37
38X-RAY DIFFRACTION38chain 'E' and (resid 38 through 52 )E38 - 52
39X-RAY DIFFRACTION39chain 'E' and (resid 53 through 75 )E53 - 75
40X-RAY DIFFRACTION40chain 'E' and (resid 76 through 91 )E76 - 91
41X-RAY DIFFRACTION41chain 'E' and (resid 92 through 120 )E92 - 120
42X-RAY DIFFRACTION42chain 'E' and (resid 121 through 135 )E121 - 135
43X-RAY DIFFRACTION43chain 'E' and (resid 136 through 150 )E136 - 150
44X-RAY DIFFRACTION44chain 'E' and (resid 151 through 165 )E151 - 165
45X-RAY DIFFRACTION45chain 'E' and (resid 166 through 185 )E166 - 185
46X-RAY DIFFRACTION46chain 'E' and (resid 186 through 200 )E186 - 200
47X-RAY DIFFRACTION47chain 'F' and (resid 3 through 94 )F3 - 94
48X-RAY DIFFRACTION48chain 'F' and (resid 95 through 109 )F95 - 109
49X-RAY DIFFRACTION49chain 'F' and (resid 110 through 124 )F110 - 124
50X-RAY DIFFRACTION50chain 'F' and (resid 125 through 162 )F125 - 162
51X-RAY DIFFRACTION51chain 'F' and (resid 163 through 188 )F163 - 188
52X-RAY DIFFRACTION52chain 'F' and (resid 189 through 215 )F189 - 215
53X-RAY DIFFRACTION53chain 'F' and (resid 216 through 244 )F216 - 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