[English] 日本語
Yorodumi
- PDB-5u16: Structure of human MR1-2-OH-1-NA in complex with human MAIT A-F7 TCR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u16
TitleStructure of human MR1-2-OH-1-NA in complex with human MAIT A-F7 TCR
Components
  • (MAIT T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / T-cell Receptor
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 / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / 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 / 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 / external side of plasma membrane / Golgi 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 / 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
2-hydroxynaphthalene-1-carbaldehyde / 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 Å
AuthorsKeller, A.N. / Birkinshaw, R.W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE140100011 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
DepositionNov 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: MAIT T-cell receptor alpha chain
F: MAIT T-cell receptor beta chain
G: MAIT T-cell receptor alpha chain
H: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,29321
Polymers187,3138
Non-polymers98013
Water21,9241217
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)94,10710
Polymers93,6564
Non-polymers4506
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-74 kcal/mol
Surface area37050 Å2
MethodPISA
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)94,18611
Polymers93,6564
Non-polymers5307
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-72 kcal/mol
Surface area36070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.440, 69.850, 143.120
Angle α, β, γ (deg.)90.000, 104.350, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
13chain E
23chain G
14chain F
24chain H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETVALVALchain AAA0 - 2691 - 270
21ARGARGVALVALchain CCC1 - 2692 - 270
12ILEILEASPASPchain BBB1 - 961 - 96
22ILEILEMETMETchain DDD1 - 991 - 99
13GLYGLYPROPROchain EEE1 - 1981 - 198
23GLYGLYPROPROchain GGG1 - 2001 - 200
14GLYGLYGLYGLYchain FFF3 - 2423 - 242
24ASNASNARGARGchain HHH1 - 2431 - 243

NCS ensembles :
ID
1
2
3
4

-
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: Residue K43 is covalently bound to the compound 2-hydroxy-1-napthaldehyde through a Schiff-base bond.
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


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 EGFH

#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 , 5 types, 1230 molecules

#5: Chemical ChemComp-7WO / 2-hydroxynaphthalene-1-carbaldehyde


Mass: 172.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1217 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
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→69.327 Å / Num. obs: 139855 / % possible obs: 99.8 % / Redundancy: 3.7 % / Net I/σ(I): 1.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.66 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t


Resolution: 2→69.327 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2191 6975 4.99 %
Rwork0.173 --
obs0.1754 139754 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.87 Å2 / Biso mean: 34.3862 Å2 / Biso min: 10.71 Å2
Refinement stepCycle: final / Resolution: 2→69.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12776 0 60 1217 14053
Biso mean--33.39 36.79 -
Num. residues----1593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113217
X-RAY DIFFRACTIONf_angle_d1.22117927
X-RAY DIFFRACTIONf_chiral_restr0.0561892
X-RAY DIFFRACTIONf_plane_restr0.0072348
X-RAY DIFFRACTIONf_dihedral_angle_d13.9284772
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2399X-RAY DIFFRACTION8.863TORSIONAL
12C2399X-RAY DIFFRACTION8.863TORSIONAL
21B922X-RAY DIFFRACTION8.863TORSIONAL
22D922X-RAY DIFFRACTION8.863TORSIONAL
31E1604X-RAY DIFFRACTION8.863TORSIONAL
32G1604X-RAY DIFFRACTION8.863TORSIONAL
41F2181X-RAY DIFFRACTION8.863TORSIONAL
42H2181X-RAY DIFFRACTION8.863TORSIONAL
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 (%)
2-2.02270.31552460.282143464592100
2.0227-2.04650.31052390.282544104649100
2.0465-2.07150.31422220.257544094631100
2.0715-2.09770.28962190.247243954614100
2.0977-2.12530.29852370.232343844621100
2.1253-2.15440.29112000.231644524652100
2.1544-2.18520.24052460.21544724718100
2.1852-2.21780.2692200.20343324552100
2.2178-2.25250.24532410.201944374678100
2.2525-2.28940.26592440.20543474591100
2.2894-2.32890.25032410.207544764717100
2.3289-2.37130.2632290.201243774606100
2.3713-2.41690.28022360.197644234659100
2.4169-2.46620.24522120.192544404652100
2.4662-2.51980.22722280.186843974625100
2.5198-2.57840.23632450.178944184663100
2.5784-2.64290.2062310.174344054636100
2.6429-2.71440.22662270.175644044631100
2.7144-2.79430.2562390.189544344673100
2.7943-2.88450.24312560.18143524608100
2.8845-2.98760.23862190.16744644683100
2.9876-3.10720.20172330.163843764609100
3.1072-3.24860.19822230.160444534676100
3.2486-3.41990.21082260.15284424465099
3.4199-3.63410.18222500.146544394689100
3.6341-3.91470.19462280.148244434671100
3.9147-4.30860.17692360.13444440467699
4.3086-4.93190.14662250.118344974722100
4.9319-6.2130.17062320.141645174749100
6.213-69.3690.21122450.17284616486199
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)
11.6044-0.18340.03321.48080.67371.73470.02550.14020.1945-0.10610.0604-0.09930.01570.193-0.06660.1015-0.04640.00520.17210.00310.1733-5.040638.599516.0664
21.6864-0.0852-0.34284.3253-0.30021.0138-0.0022-0.07940.21040.125-0.02160.1297-0.0842-0.08210.0280.1096-0.0205-0.00530.1186-0.00470.1585-17.307841.745626.8358
35.44610.72513.54411.69410.42172.68110.22890.2203-0.4408-0.00190.1756-0.16220.33760.3846-0.43640.18760.0484-0.04140.2205-0.04920.17840.397424.541728.4365
41.33250.73550.08951.5999-0.26893.3676-0.0185-0.3770.49010.3692-0.0538-0.0785-0.5588-0.15880.06940.31570.1469-0.13230.5209-0.22460.425813.611841.616948.063
53.1769-2.96412.02433.46-2.67382.2359-0.2777-0.0920.81470.5350.1631-0.5584-0.39430.29170.17030.2709-0.0484-0.07540.3814-0.150.49427.650352.883530.6534
60.8346-0.15620.1491.67681.1280.8357-0.3733-0.2716-0.30050.222-0.1721-0.6671-0.02250.9624-0.1720.16460.0721-0.25370.7812-0.02740.912927.88240.692933.2357
72.41670.7374-0.15530.2763-0.18030.4197-0.0775-0.02990.0898-0.04380.2788-0.5858-0.06020.5307-0.04530.1653-0.0587-0.0830.4993-0.08390.573414.955246.283627.9049
84.30760.8509-0.58910.1861-0.09790.0809-0.22120.6060.4916-0.09010.0571-0.4192-0.35990.56570.02150.2137-0.1926-0.01060.49590.03720.566710.930853.984421.3552
92.08731.8385-2.12497.17561.36914.0506-0.01310.39940.5563-0.2230.26380.1439-0.43260.5356-0.16820.095-0.2354-0.02110.84110.19021.035124.926955.231520.1571
106.84823.1323-3.21682.10110.54468.3319-0.14590.6049-0.3038-0.7644-0.0609-1.12860.39270.49390.21210.293-0.0750.0830.7617-0.10580.640218.288345.279417.4229
119.593-4.019-6.54786.67713.08344.59560.0981-0.0310.2181-0.16110.2547-0.00460.1390.3545-0.3330.144-0.0295-0.03190.1937-0.01590.1769-0.329144.758425.6383
124.34021.2642-1.53690.9326-0.83270.8476-0.22440.74840.1405-0.09820.1571-0.58150.05720.57380.10180.1571-0.01450.03040.5353-0.10850.442415.534845.056524.239
131.65990.90590.12692.09090.72380.48630.1474-0.15150.17810.1530.0353-0.2726-0.10210.18220.24270.1011-0.1809-0.31291.1326-0.15591.220832.304252.023630.3507
140.60460.38780.75070.24720.47071.0467-0.07390.13350.9811-0.10270.0424-0.4943-0.74360.6023-0.09070.3541-0.1985-0.02510.45030.11570.987412.168259.310424.5203
152.98570.2114-2.20773.00720.55371.803-0.0344-0.27850.27630.6501-0.04780.1717-0.38260.673-0.03970.3585-0.1515-0.21940.5262-0.14560.82119.717855.47831.6939
161.15750.23190.00122.87410.10071.5415-0.00190.31140.062-0.1697-0.12190.279-0.0434-0.10070.10980.1381-0.0032-0.00670.3038-0.04240.1688-59.6823.9418-47.8806
171.19980.0294-0.12531.7901-0.70021.06380.09150.059-0.06120.1454-0.24840.0420.02340.07880.13840.1572-0.04220.00570.2316-0.0480.1263-51.723116.9823-37.2699
184.30263.4733-3.24453.6467-2.8253.7870.00540.0731-0.05680.0442-0.02580.1223-0.1218-0.11870.01570.22720.01860.01470.0771-0.03310.2183-75.584834.9364-18.9849
192.6376-0.13010.56333.51380.37572.98660.0048-0.3134-0.22270.3519-0.05480.15580.1943-0.27150.00660.22680.01830.03630.06980.01130.2501-75.17631.5743-14.655
204.2023-1.71340.34057.1309-0.7113.7567-0.01160.3607-0.06480.0956-0.1079-0.2348-0.01460.17510.11770.0993-0.0309-0.01390.1368-0.02870.1292-78.742620.1228-33.6674
211.5139-1.46751.43191.4273-1.38641.3496-0.0548-0.16660.9924-0.2046-0.15810.455-0.9769-0.6241-0.00620.37270.114-0.02720.2571-0.12220.5877-87.269641.7445-29.4243
224.2376-3.123-0.38414.57170.21332.17230.00750.59010.1198-0.5128-0.13250.2107-0.2718-0.02510.08310.21670.0016-0.05280.2087-0.04150.2281-80.872326.0783-39.3702
234.84471.7455-3.70156.8550.4523.4383-0.08551.2421-0.2458-0.94260.04030.9647-0.4969-1.16620.05430.37060.0393-0.19050.48140.06160.4317-93.099829.9665-44.4114
244.6709-5.67243.37947.4454-2.72925.9579-0.37011.62651.1671-0.90160.26150.3423-1.4895-0.56350.13530.62380.0566-0.16340.54580.13160.5063-82.343334.2562-46.4315
258.281-5.7262.28565.5299-3.76134.0116-0.29020.22650.20550.23190.2689-0.141-0.33940.33750.11550.2285-0.03140.00690.2345-0.11890.2353-67.326821.6679-38.2385
266.0129-6.7423-2.43157.8412.20544.23080.23040.73630.4129-0.5888-0.2625-0.0574-0.5449-0.0703-0.0130.2741-0.0299-0.04180.2089-0.01960.2797-79.773831.745-39.0737
272.39931.6664-2.77628.83813.85038.25050.22640.11890.57360.1528-0.44271.2278-0.3719-1.37550.16640.34130.1504-0.05160.5308-0.08250.7631-97.537335.7026-33.6782
281.52591.66490.6522.49752.19253.4007-0.01430.578-0.3731-0.6236-0.17240.7662-0.0596-0.19150.11360.2176-0.0476-0.07450.2782-0.0950.3472-85.970618.5504-40.6541
297.49752.07022.14874.66134.73468.16010.0861-0.75690.5570.4658-0.09930.6852-0.1394-0.54590.13270.2425-0.0020.01030.2796-0.06160.3417-90.127727.8365-30.4828
304.7362-2.6874-0.55315.2214-0.85843.1613-0.0305-0.09690.06130.0040.06930.0061-0.16480.2753-0.04590.1708-0.1069-0.02850.42320.0980.1579-19.436627.9287-50.9539
313.41-0.2686-1.5340.48890.14032.157-0.08610.08510.24550.03720.0377-0.0782-0.01770.03580.05260.171-0.0484-0.0310.27970.08190.1504-29.766326.1484-47.8371
324.6059-0.6211-2.93692.4913-1.02516.3118-0.18780.1292-0.1684-0.1384-0.0074-0.0490.12880.16690.12410.1548-0.0991-0.0350.27820.06010.154-29.545518.3137-51.4492
336.8474-5.5042-6.186.85595.93777.238-0.2383-0.3863-0.38380.3980.05450.00380.37070.2630.15650.2168-0.0415-0.03410.33030.0890.1643-24.819717.0907-42.0449
347.3685-1.8869-4.2243.06540.71514.9090.1917-0.23530.55870.32690.1245-0.3797-0.22930.6413-0.26550.2146-0.09720.01980.25550.07030.1333-26.80925.9768-40.7799
353.1731-0.9958-2.61751.26061.47494.0186-0.3178-0.1635-0.03840.10480.2593-0.17590.29830.35980.07610.2094-0.0649-0.00980.37920.07860.1671-20.676219.041-52.3192
364.4207-1.1603-3.81770.40421.51186.03430.27140.69680.3337-0.1211-0.14020.0793-0.1-0.6218-0.08220.2325-0.0489-0.02990.40090.13780.2093-38.687128.5414-51.881
376.67050.0026-2.66520.95091.16732.5336-0.1399-0.5547-0.48370.02630.3419-0.25910.49110.8799-0.15410.26410.049-0.01370.70980.05830.282-4.241420.1448-56.6606
387.9059-0.0562-1.22826.51441.22239.53970.0306-0.0403-0.2769-0.1531-0.0802-0.3802-0.21681.04670.00810.2353-00.00350.527-0.02660.38352.629721.1088-70.4605
395.47151.06994.04819.6115-1.25859.4142-0.22130.01541.02420.3290.66230.1433-1.202-0.3018-0.39810.35570.03980.08910.5681-0.00860.5205-4.442630.4429-70.1461
407.1322-0.48490.11055.3622-0.07427.91290.0144-0.3854-0.22780.10020.254-0.65180.23440.6328-0.1240.249-0.0587-0.04680.43590.00680.3382-1.116119.6779-68.195
416.24812.9613.61044.8908-1.6558.5003-0.1655-0.20891.02880.528-0.372-0.6221-0.43020.98630.5110.3924-0.13120.080.6511-0.09850.76428.619127.1147-65.6655
421.3133-0.2979-0.3441.6056-0.58523.44180.01350.3665-0.0276-0.2056-0.11930.0112-0.0511-0.19890.08720.2625-0.052-0.03160.44560.05320.1697-41.032722.3954-67.9649
432.37-1.12380.92514.1213-0.81622.6679-0.150.2310.1345-0.19710.07790.16780.0266-0.53450.01210.2237-0.0778-0.04140.41540.04120.1634-38.868422.0311-65.1243
447.5090.3018-4.49321.18671.61265.4480.57580.26550.614-0.36820.0760.1573-0.53510.0416-0.52680.40330.02350.06670.52020.12280.262-26.32928.0862-83.5683
454.47440.12452.03771.9359-0.22023.56250.48190.4596-0.8392-0.20460.0703-0.06940.44130.2626-0.50950.40620.0217-0.02380.4533-0.04730.2887-11.008616.3987-79.3815
467.02961.6849-1.16593.73470.15082.865-0.04640.0097-0.39010.07150.0622-0.26770.13510.2072-0.02560.1986-0.06-0.03660.10160.03520.1783-35.106311.693712.1192
472.82061.9620.84612.74720.87251.95980.0706-0.016-0.10160.04690.0856-0.06180.1293-0.0388-0.12930.1287-0.0361-0.00550.09870.02550.1711-29.558521.486114.0962
484.1492-1.17414.62924.4816-1.225.6848-0.0831-0.68510.06480.30.04140.0784-0.1415-0.45790.06630.222-0.06880.02170.12590.05150.2383-34.106820.294621.8695
495.21181.58830.86931.9599-0.08622.3415-0.13760.12680.0601-0.09770.0870.2269-0.1406-0.01440.05680.1688-0.0356-0.00490.07210.03310.1594-39.19819.714911.0988
504.9312.28172.27461.39330.81491.25370.0076-0.66390.0571-0.022-0.11580.07830.0467-0.0905-0.01910.1839-0.0312-0.00880.06790.00240.154-41.315313.83625.9686
511.7283-0.0404-1.52842.2358-0.50944.34560.09920.4205-0.242-0.443-0.08040.0911-0.0625-0.0774-0.09590.3711-0.0777-0.02840.0429-0.01940.2199-56.35987.069-17.9465
521.9414-0.569-0.97424.47611.00557.1444-0.1402-0.1432-0.2209-0.0484-0.0214-0.41040.93520.93580.15760.32010.0446-0.01880.16980.06390.3379-49.67360.6463-3.6275
533.9124-0.3927-1.64954.03872.33536.59380.0251-0.41640.1949-0.1743-0.03720.0496-0.2034-0.04270.0120.1985-0.03990.01730.06490.0360.1703-53.5911.5014-4.3427
541.80590.5178-0.70570.4212-0.94442.276-0.17680.4579-1.0322-0.67690.158-0.24180.80180.06560.00660.6513-0.06280.07020.148-0.09160.4592-53.9127-3.6963-17.3377
557.5388-2.29772.63987.1516-0.94316.43360.1241-0.3339-0.6101-0.4258-0.02550.25780.8654-0.2496-0.07490.3507-0.0486-0.0180.11950.07330.3304-59.0612-2.935-4.6841
561.81210.6940.56662.60061.22792.1689-0.1150.4320.1361-0.17450.00190.0524-0.22470.2820.07940.1763-0.0646-0.01650.23460.05120.1366-21.170628.0713-5.2125
573.53030.228-3.51968.37310.16483.6006-0.0944-0.35920.38790.5926-0.19350.1059-0.18710.27960.24240.1621-0.0315-0.02440.09960.05520.2045-25.073533.00047.8089
587.11912.57034.24452.8133-0.14564.27650.29560.0371-0.51860.0854-0.1705-0.19970.31210.5627-0.09080.17130.0050.01060.2168-0.00640.1547-29.087614.9524-19.7594
592.0650.7237-0.81381.1492-0.75952.2260.0943-0.19690-0.0038-0.06930.0278-0.09280.2310.0460.2295-0.0355-0.01380.06190.00080.1769-49.278814.3159-13.0724
602.80220.2138-1.40760.4145-0.46041.80730.19720.07690.21170.0665-0.01980.0878-0.24430.1052-0.15140.2609-0.0381-0.01670.07560.01080.1674-49.003220.2682-17.7361
617.495-1.5893-4.44130.47250.5654.35670.18240.3311-0.21360.052-0.13490.0847-0.0219-0.1205-0.02330.2113-0.0503-0.03430.12690.0590.1575-45.194819.034-25.4554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 84 )A0 - 84
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 158 )A85 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 182 )A159 - 182
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 269 )A183 - 269
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 30 )B20 - 30
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 41 )B31 - 41
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 46 )B42 - 46
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 51 )B47 - 51
11X-RAY DIFFRACTION11chain 'B' and (resid 52 through 61 )B52 - 61
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 71 )B62 - 71
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 77 )B72 - 77
14X-RAY DIFFRACTION14chain 'B' and (resid 78 through 90 )B78 - 90
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 96 )B91 - 96
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 84 )C1 - 84
17X-RAY DIFFRACTION17chain 'C' and (resid 85 through 171 )C85 - 171
18X-RAY DIFFRACTION18chain 'C' and (resid 172 through 216 )C172 - 216
19X-RAY DIFFRACTION19chain 'C' and (resid 217 through 269 )C217 - 269
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 11 )D1 - 11
21X-RAY DIFFRACTION21chain 'D' and (resid 12 through 19 )D12 - 19
22X-RAY DIFFRACTION22chain 'D' and (resid 20 through 41 )D20 - 41
23X-RAY DIFFRACTION23chain 'D' and (resid 42 through 46 )D42 - 46
24X-RAY DIFFRACTION24chain 'D' and (resid 47 through 51 )D47 - 51
25X-RAY DIFFRACTION25chain 'D' and (resid 52 through 61 )D52 - 61
26X-RAY DIFFRACTION26chain 'D' and (resid 62 through 71 )D62 - 71
27X-RAY DIFFRACTION27chain 'D' and (resid 72 through 77 )D72 - 77
28X-RAY DIFFRACTION28chain 'D' and (resid 78 through 90 )D78 - 90
29X-RAY DIFFRACTION29chain 'D' and (resid 91 through 99 )D91 - 99
30X-RAY DIFFRACTION30chain 'E' and (resid 1 through 17 )E1 - 17
31X-RAY DIFFRACTION31chain 'E' and (resid 18 through 37 )E18 - 37
32X-RAY DIFFRACTION32chain 'E' and (resid 38 through 52 )E38 - 52
33X-RAY DIFFRACTION33chain 'E' and (resid 53 through 65 )E53 - 65
34X-RAY DIFFRACTION34chain 'E' and (resid 66 through 75 )E66 - 75
35X-RAY DIFFRACTION35chain 'E' and (resid 76 through 91 )E76 - 91
36X-RAY DIFFRACTION36chain 'E' and (resid 92 through 102 )E92 - 102
37X-RAY DIFFRACTION37chain 'E' and (resid 103 through 116 )E103 - 116
38X-RAY DIFFRACTION38chain 'E' and (resid 117 through 140 )E117 - 140
39X-RAY DIFFRACTION39chain 'E' and (resid 141 through 156 )E141 - 156
40X-RAY DIFFRACTION40chain 'E' and (resid 157 through 187 )E157 - 187
41X-RAY DIFFRACTION41chain 'E' and (resid 188 through 198 )E188 - 198
42X-RAY DIFFRACTION42chain 'F' and (resid 3 through 73 )F3 - 73
43X-RAY DIFFRACTION43chain 'F' and (resid 74 through 109 )F74 - 109
44X-RAY DIFFRACTION44chain 'F' and (resid 110 through 124 )F110 - 124
45X-RAY DIFFRACTION45chain 'F' and (resid 125 through 242 )F125 - 242
46X-RAY DIFFRACTION46chain 'G' and (resid 1 through 17 )G1 - 17
47X-RAY DIFFRACTION47chain 'G' and (resid 18 through 52 )G18 - 52
48X-RAY DIFFRACTION48chain 'G' and (resid 53 through 75 )G53 - 75
49X-RAY DIFFRACTION49chain 'G' and (resid 76 through 91 )G76 - 91
50X-RAY DIFFRACTION50chain 'G' and (resid 92 through 120 )G92 - 120
51X-RAY DIFFRACTION51chain 'G' and (resid 121 through 135 )G121 - 135
52X-RAY DIFFRACTION52chain 'G' and (resid 136 through 150 )G136 - 150
53X-RAY DIFFRACTION53chain 'G' and (resid 151 through 175 )G151 - 175
54X-RAY DIFFRACTION54chain 'G' and (resid 176 through 185 )G176 - 185
55X-RAY DIFFRACTION55chain 'G' and (resid 186 through 200 )G186 - 200
56X-RAY DIFFRACTION56chain 'H' and (resid 1 through 94 )H1 - 94
57X-RAY DIFFRACTION57chain 'H' and (resid 95 through 109 )H95 - 109
58X-RAY DIFFRACTION58chain 'H' and (resid 110 through 124 )H110 - 124
59X-RAY DIFFRACTION59chain 'H' and (resid 125 through 188 )H125 - 188
60X-RAY DIFFRACTION60chain 'H' and (resid 189 through 225 )H189 - 225
61X-RAY DIFFRACTION61chain 'H' and (resid 226 through 243 )H226 - 243

+
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://pdbjlc1.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