[English] 日本語
Yorodumi
- PDB-3tzv: Crystal structure of an iNKT TCR in complex with CD1d-lysophospha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tzv
TitleCrystal structure of an iNKT TCR in complex with CD1d-lysophosphatidylcholine
Components
  • (Invariant Natural Killer T Cell Receptor chain ...) x 2
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / Immunoglobulin-like / MHC class I-like / Antigen recognition / CD1d / Cell surface
Function / homology
Function and homology information


lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding ...lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding / detection of bacterium / positive regulation of T cell proliferation / cell adhesion molecule 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 / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / basolateral plasma membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / 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 / cell surface / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DODECANE / HEXANE / Chem-LSC / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.056 Å
AuthorsLopez-Sagaseta, J. / Adams, E.J.
CitationJournal: Embo J. / Year: 2012
Title: Lysophospholipid presentation by CD1d and recognition by a human Natural Killer T-cell receptor.
Authors: Lopez-Sagaseta, J. / Sibener, L.V. / Kung, J.E. / Gumperz, J. / Adams, E.J.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Invariant Natural Killer T Cell Receptor chain A
B: Invariant Natural Killer T Cell Receptor chain B
C: Antigen-presenting glycoprotein CD1d
D: Beta-2-microglobulin
G: Invariant Natural Killer T Cell Receptor chain A
H: Invariant Natural Killer T Cell Receptor chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,94311
Polymers148,7056
Non-polymers1,2395
Water905
1
C: Antigen-presenting glycoprotein CD1d
D: Beta-2-microglobulin
G: Invariant Natural Killer T Cell Receptor chain A
H: Invariant Natural Killer T Cell Receptor chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1629
Polymers95,9234
Non-polymers1,2395
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Invariant Natural Killer T Cell Receptor chain A
B: Invariant Natural Killer T Cell Receptor chain B


Theoretical massNumber of molelcules
Total (without water)52,7822
Polymers52,7822
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.591, 117.605, 190.656
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 2:52 OR RESSEQ 54:58 OR RESSEQ 61:95 OR RESSEQ 104:246 ) AND (NOT ELEMENT H)
211CHAIN H AND (RESSEQ 2:52 OR RESSEQ 54:58 OR RESSEQ 61:95 OR RESSEQ 104:246 ) AND (NOT ELEMENT H)
112CHAIN A AND (RESSEQ 1:94 OR RESSEQ 99:130 OR RESSEQ...
212CHAIN G AND (RESSEQ 1:94 OR RESSEQ 99:130 OR RESSEQ...

NCS ensembles :
ID
1
2

-
Components

-
Invariant Natural Killer T Cell Receptor chain ... , 2 types, 4 molecules AGBH

#1: Protein Invariant Natural Killer T Cell Receptor chain A


Mass: 23598.057 Da / Num. of mol.: 2 / Mutation: T164C, C211A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Invariant Natural Killer T Cell Receptor chain B


Mass: 29183.504 Da / Num. of mol.: 2 / Mutation: S174C, C192A, C248S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Protein , 2 types, 2 molecules CD

#3: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 31393.465 Da / Num. of mol.: 1 / Mutation: N42Q, N108Q, N163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813
#4: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769

-
Sugars , 1 types, 1 molecules

#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 9 molecules

#6: Chemical ChemComp-LSC / (4R,7R,18E)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacos-18-en-1-aminium 4-oxide


Mass: 522.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H53NO7P
#7: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14
#8: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 250

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes, 17% PEG 4000, 0.1 MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97918 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.056→20.019 Å / Num. obs: 27183 / % possible obs: 89.18 %
Reflection shellResolution: 3.056→3.1781 Å

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.056→20.019 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.5 / σ(F): 1.34 / Phase error: 32.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2885 1359 5 %
Rwork0.2363 --
obs0.239 27183 93.61 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 18.363 Å2 / ksol: 0.259 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5279 Å2-0 Å20 Å2
2---15.2245 Å2-0 Å2
3---12.6966 Å2
Refinement stepCycle: LAST / Resolution: 3.056→20.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9421 0 83 5 9509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039754
X-RAY DIFFRACTIONf_angle_d0.66813285
X-RAY DIFFRACTIONf_dihedral_angle_d13.6023367
X-RAY DIFFRACTIONf_chiral_restr0.0471489
X-RAY DIFFRACTIONf_plane_restr0.0021698
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1776X-RAY DIFFRACTIONPOSITIONAL
12H1776X-RAY DIFFRACTIONPOSITIONAL0.03
21A1304X-RAY DIFFRACTIONPOSITIONAL
22G1304X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.056-3.16490.40881300.33612417X-RAY DIFFRACTION89
3.1649-3.29110.34431360.30732459X-RAY DIFFRACTION91
3.2911-3.44010.3651130.27872460X-RAY DIFFRACTION91
3.4401-3.62050.32111380.27362464X-RAY DIFFRACTION91
3.6205-3.84580.31011250.26062491X-RAY DIFFRACTION91
3.8458-4.14030.30491240.23862564X-RAY DIFFRACTION93
4.1403-4.55260.25771440.20382587X-RAY DIFFRACTION95
4.5526-5.20120.24051510.19392709X-RAY DIFFRACTION97
5.2012-6.51520.29281530.24082764X-RAY DIFFRACTION99
6.5152-20.01920.24861450.20782909X-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)
10.90120.1765-0.60651.67980.75480.8796-0.06190.4402-0.2955-0.7120.1625-0.2818-0.3452-0.03140.36690.34520.01630.0950.5078-0.05390.1522-21.421431.331245.1887
21.5002-0.0717-1.19574.80442.3742.09160.45570.05650.0191-0.11470.2762-0.6617-0.27010.4488-0.31560.5323-0.11170.13770.7259-0.09850.5347-10.546135.790246.2331
30.4635-0.02680.14480.9364-0.15710.07040.12510.3465-0.2894-0.2873-0.09940.0016-0.04040.13871.2770.48960.1270.32490.6693-0.17970.553-10.031525.323241.3801
41.39310.11310.79861.7967-0.66452.75970.0230.4053-0.3268-0.57550.1565-0.39510.33950.26150.50170.3583-0.26990.1610.6557-0.15310.4636-15.574230.518743.2122
50.2074-0.00110.81040.21570.10323.24770.2504-0.1920.35470.1193-0.04550.05610.4489-0.0063-0.0030.1603-0.05340.02550.4339-0.15630.4972-14.864639.224974.3338
60.9103-0.1171-0.43081.0835-0.49590.5567-0.16890.3024-0.0065-0.3960.03150.64840.0604-0.5019-0.43910.1586-0.0801-0.10430.6421-0.03640.6104-19.482840.439974.4752
71.6745-0.56620.03661.80210.16290.8113-0.03-0.1665-0.2139-0.0441-0.2318-0.02740.0818-0.0885-1.43520.2094-0.23990.1630.6424-0.05730.4372-14.309742.566272.0527
82.20431.2285-0.1512.0782-0.80862.06350.3082-0.43020.30870.71490.11190.5411-0.3994-0.2220.90570.2277-0.15790.12420.37740.02170.2482-16.937747.157978.1223
91.13150.7803-1.00320.5458-0.66860.951-0.1481-0.3299-0.28210.08990.05890.25560.215-0.4032-0.39990.5641-0.02710.46350.58530.02721.229-24.10440.655682.5107
100.58220.4207-0.41221.12790.08230.7527-0.31480.5581-0.3034-0.82520.3658-0.6680.0281-0.1047-0.48380.7167-0.32640.63740.8829-0.10130.7101-3.539350.045139.6792
111.62090.0876-0.40251.3137-0.14381.09230.116-0.070.12930.0413-0.0257-0.13-0.0735-0.2883-0.0734-0.2936-0.20260.17390.19520.26140.3536-4.283451.969369.3266
121.4065-1.01360.08583.37750.14491.0272-0.19970.11690.09920.4001-0.0349-0.02190.01030.2987-0.0660.35380.13670.06720.36370.1590.4722-31.3139-7.036886.5005
130.3284-0.3811-0.19530.44810.26551.46260.11890.24810.0787-0.3315-0.3161-0.3284-0.10390.397-0.04350.39010.17370.20990.58990.270.7013-20.4276-12.005280.4695
140.15460.30150.55581.85360.17732.66410.0480.06680.2126-0.17320.25660.0041-0.21560.35141.47980.33010.01090.18580.33350.28620.2352-31.45560.080176.976
151.58670.28770.07790.66750.11222.0389-0.0729-0.0496-0.3788-0.01240.35090.54670.2885-0.1596-0.04730.3798-0.0422-0.01120.23970.28010.4466-42.5892-10.798480.4016
161.8558-1.54290.65712.1932-0.40671.0060.25630.57990.2659-0.4562-0.0990.068-0.2137-0.07790.14580.3771-0.0658-0.20150.27210.26040.2725-41.9025-4.604370.1743
175.1233-3.72974.26526.2812-3.39423.57440.00850.3385-0.2054-0.2606-0.17270.15550.22110.2342-0.00980.95560.16970.00050.80340.11880.3964-24.2951-19.68670.6687
180.4496-0.0164-0.3620.6387-0.17221.5492-0.0998-0.0953-0.0727-0.0350.12560.07010.1779-0.053-0.22340.66890.1547-0.12390.03830.24980.5301-25.1024-35.101596.7798
191.0268-0.1489-0.18470.64-0.04040.04180.0363-0.2163-0.41480.02160.03170.2251-0.0953-0.1350.13730.61930.1806-0.01780.16210.31910.663-30.3168-37.1425100.9349
201.7572-1.0906-0.43733.3559-1.81752.22730.0232-0.0611-0.1062-0.08880.1220.0630.241-0.01760.59120.71690.0336-0.22480.29960.22670.5795-22.3958-44.33896.0718
211.9966-2.2774-0.88373.2040.88660.41790.09880.1218-0.43380.0281-0.2845-0.09280.0791-0.09560.07840.6916-0.0986-0.03380.4880.15280.4874-33.2277-17.9673103.0551
222.0791.28231.47071.09661.25231.4302-0.0974-0.0769-0.08370.4141-0.1876-0.0583-0.2150.05270.00550.9380.0695-0.39340.8270.24170.76-13.5767-27.783106.6216
230.88831.12530.0791.5103-0.26271.5687-0.09240.11920.14590.0003-0.0972-0.08070.11890.2251-0.29020.54790.11870.00060.27140.20420.3693-26.6915-18.2625101.2693
243.4189-2.66473.09412.1323-2.30823.4869-0.2465-0.50270.19270.15490.284-0.1194-0.5060.00110.23180.9229-0.0371-0.15890.5527-0.0330.2822-28.4432-9.2123104.1634
252.58960.16211.05951.25080.15192.48630.0782-0.3998-0.19450.720.1707-0.10330.0341-0.2765-0.05890.53240.0489-0.07240.38620.22160.4073-26.3079-12.617899.0308
261.5616-0.94651.33860.8131-0.78961.3371-0.1468-0.14030.02950.14730.26290.0833-0.17770.00420.55670.7542-0.0233-0.23370.53670.13920.3321-24.3916-15.335698.4495
270.13910.1509-0.07820.3414-0.06440.04610.1156-0.52750.05820.77760.09560.4252-0.3849-0.1707-0.07510.8312-0.0544-0.23871.11510.26230.6455-14.4268-22.1282115.3571
281.4454-0.83180.83340.70980.0171.5417-0.0128-0.3577-0.20640.3129-0.1325-0.14290.06260.0615-0.59510.79090.07930.0020.46790.31240.3579-29.3585-14.4808110.6623
291.58640.7978-0.71482.3867-0.48052.27650.14480.0142-0.02390.24960.0253-0.1542-0.07780.4430.49810.24820.0691-0.04270.1107-0.06250.0714-28.259626.870260.5145
301.3926-0.2070.21854.1433-3.04773.72750.10580.0249-0.0629-0.17320.03250.0115-0.10970.3660.04850.2678-0.02870.02750.1402-0.05190.206-31.481119.125758.4131
312.43381.7426-0.27855.03062.57982.07250.14030.20460.4420.1147-0.10750.7733-0.4632-0.2024-0.10260.35140.10480.09870.15010.00530.1532-40.803525.33263.114
320.2646-0.0095-0.22341.21110.33431.2079-0.08730.4416-0.0431-0.16510.23850.40070.06430.04430.02570.1859-0.065-0.0530.3518-0.03190.3816-41.471815.842256.4082
333.4578-1.87441.27863.9334-2.20512.7336-0.0530.4082-0.4859-0.3675-0.01380.07060.27770.5847-0.00950.17290.02390.02570.2197-0.09570.1759-32.738715.695855.2426
340.23620.34490.14130.94680.09560.6878-0.1050.0920.0572-0.33150.13710.1455-0.10380.0035-0.10760.0992-0.00410.055-0.00930.0670.0511-37.957227.426457.1301
350.83130.27230.05151.9879-1.01311.2644-0.0541-0.05480.05320.1984-0.1386-0.1465-0.08180.0744-0.1410.16740.10990.04310.20380.13590.2291-36.287520.751566.6845
361.66560.22490.52661.2496-1.85353.208-0.0212-0.0394-0.0157-0.2864-0.1148-0.00690.62620.22010.30050.258-0.10320.08920.48890.08550.4698-35.60453.656446.2019
378.41071.8989-0.1560.8994-1.45884.31140.0159-0.38151.01050.0537-0.0458-0.0034-0.7674-0.089-0.93730.3675-0.00320.08350.34750.13190.469-41.907563.622258.1069
380.6157-0.4394-0.0840.40050.1880.2087-0.13-0.09610.20790.27560.1042-0.36870.2670.06630.0380.53440.0785-0.05260.50970.29410.6453-29.330150.998656.7126
392.38620.88371.10353.10562.71383.1886-0.2430.3377-0.2269-0.3183-0.08220.07060.03380.0863-0.15910.4477-0.1320.1630.43330.15430.509-39.715949.050753.5985
400.6315-0.2587-0.64371.03181.45383.78270.0697-0.17280.1287-0.2735-0.0029-0.3369-0.90190.738-0.31750.3673-0.09280.01690.48950.32010.603-34.255558.493856.6775
412.8388-3.6957-0.53367.4679-0.33880.6222-0.10080.04980.1863-0.18940.0024-0.26090.28520.62010.0190.33570.1096-0.01550.5783-0.05240.7966-27.578159.080348.5253
420.70880.4405-0.03451.5518-0.23960.96590.0283-0.1072-0.05370.1686-0.1302-0.111-0.00210.075-0.08910.1980.02590.15870.20870.24580.0903-48.074125.474478.7432
430.88630.092-0.1231.2273-0.35190.5534-0.0221-0.09160.28850.1134-0.0192-0.05720.04-0.0811-0.0464-0.0413-0.1440.1060.01350.20950.3071-47.705952.179365.838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:30)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 31:42)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 43:60)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 61:106)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 107:134)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 135:149)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 150:169)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 170:189)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 190:200)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 2:111)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 112:246)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 8:32)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 33:59)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 60:88)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 89:140)
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 141:164)
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 165:176)
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 177:222)
19X-RAY DIFFRACTION19CHAIN C AND (RESSEQ 223:265)
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 266:278)
21X-RAY DIFFRACTION21CHAIN D AND (RESSEQ 2:11)
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 12:21)
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 22:30)
24X-RAY DIFFRACTION24CHAIN D AND (RESSEQ 31:41)
25X-RAY DIFFRACTION25CHAIN D AND (RESSEQ 42:61)
26X-RAY DIFFRACTION26CHAIN D AND (RESSEQ 62:69)
27X-RAY DIFFRACTION27CHAIN D AND (RESSEQ 70:77)
28X-RAY DIFFRACTION28CHAIN D AND (RESSEQ 78:97)
29X-RAY DIFFRACTION29CHAIN G AND (RESSEQ 1:13)
30X-RAY DIFFRACTION30CHAIN G AND (RESSEQ 14:30)
31X-RAY DIFFRACTION31CHAIN G AND (RESSEQ 31:42)
32X-RAY DIFFRACTION32CHAIN G AND (RESSEQ 43:60)
33X-RAY DIFFRACTION33CHAIN G AND (RESSEQ 61:76)
34X-RAY DIFFRACTION34CHAIN G AND (RESSEQ 77:92)
35X-RAY DIFFRACTION35CHAIN G AND (RESSEQ 93:112)
36X-RAY DIFFRACTION36CHAIN G AND (RESSEQ 113:125)
37X-RAY DIFFRACTION37CHAIN G AND (RESSEQ 126:139)
38X-RAY DIFFRACTION38CHAIN G AND (RESSEQ 140:154)
39X-RAY DIFFRACTION39CHAIN G AND (RESSEQ 155:169)
40X-RAY DIFFRACTION40CHAIN G AND (RESSEQ 170:190)
41X-RAY DIFFRACTION41CHAIN G AND (RESSEQ 191:203)
42X-RAY DIFFRACTION42CHAIN H AND (RESSEQ 2:105)
43X-RAY DIFFRACTION43CHAIN H AND (RESSEQ 106:246)

+
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