[English] 日本語
Yorodumi
- PDB-8pje: Human Leukocyte Antigen class II allotype DR1 presenting influenz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pje
TitleHuman Leukocyte Antigen class II allotype DR1 presenting influenza A virus haemagglutinin (HA)306-318 PKYVKQNTLKLAT
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / HLA-II / HLA-DR / HLA-DR1 / human leukocyte antigen / major histocompatibility complex / major histocompatibility complex class 2 / influenza A virus / flu / haemagglutinin / HA / infection / vaccine
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of T cell mediated immune response to tumor cell / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of T cell mediated immune response to tumor cell / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of kinase activity / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / intermediate filament / polysaccharide binding / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / macrophage differentiation / negative regulation of type II interferon production / humoral immune response / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / MHC class II antigen presentation / viral budding from plasma membrane / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / negative regulation of inflammatory response to antigenic stimulus / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / lysosome / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / Golgi membrane / external side of plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / positive regulation of DNA-templated transcription / host cell plasma membrane / virion membrane / cell surface / signal transduction / extracellular space / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMacLachlan, B.J. / Wall, A. / Greenshields-Watson, A.L. / Hesketh, S.J. / Cole, D.K. / Rizkallah, P.J. / Godkin, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209213/Z/17/Z United Kingdom
CitationJournal: Cell Rep / Year: 2024
Title: A targeted single mutation in influenza A virus universal epitope transforms immunogenicity and protective immunity via CD4 + T cell activation.
Authors: Hulin-Curtis, S. / Geary, J.K. / MacLachlan, B.J. / Altmann, D.M. / Baillon, L. / Cole, D.K. / Greenshields-Watson, A. / Hesketh, S.J. / Humphreys, I.R. / Jones, I.M. / Lauder, S.N. / Mason, ...Authors: Hulin-Curtis, S. / Geary, J.K. / MacLachlan, B.J. / Altmann, D.M. / Baillon, L. / Cole, D.K. / Greenshields-Watson, A. / Hesketh, S.J. / Humphreys, I.R. / Jones, I.M. / Lauder, S.N. / Mason, G.H. / Smart, K. / Scourfield, D.O. / Scott, J. / Sukhova, K. / Stanton, R.J. / Wall, A. / Rizkallah, P.J. / Barclay, W.S. / Gallimore, A. / Godkin, A.
History
DepositionJun 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Hemagglutinin
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1 beta chain
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,27846
Polymers91,1136
Non-polymers3,16540
Water10,287571
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,33825
Polymers45,5563
Non-polymers1,78222
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1 beta chain
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94021
Polymers45,5563
Non-polymers1,38418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.500, 89.180, 137.440
Angle α, β, γ (deg.)90.000, 90.900, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 18 or resid 20...
d_2ens_1(chain "D" and (resid 4 through 18 or resid 20...
d_1ens_2(chain "B" and (resid -2 through 34 or resid 36...
d_2ens_2(chain "E" and (resid -2 through 34 or resid 36...
d_1ens_3(chain "C" and (resid 1 through 9 or resid 11 through 13))
d_2ens_3(chain "F" and (resid 1 through 9 or resid 11 through 13))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUGLNA2 - 16
d_12ens_1GLYPHEA18 - 20
d_13ens_1PHELEUA22 - 43
d_14ens_1GLULEUA45 - 68
d_15ens_1ILELYSA70 - 73
d_16ens_1SERLEUA75 - 97
d_17ens_1GLULEUA99 - 120
d_18ens_1ASNPHEA122 - 143
d_19ens_1LYSPROA145 - 153
d_110ens_1THRASPA155 - 179
d_21ens_1GLUGLND2 - 16
d_22ens_1GLYPHED18 - 20
d_23ens_1PHELEUD22 - 43
d_24ens_1GLULEUD45 - 68
d_25ens_1ILELYSD70 - 73
d_26ens_1SERLEUD75 - 97
d_27ens_1GLULEUD99 - 120
d_28ens_1ASNPHED122 - 143
d_29ens_1LYSPROD145 - 153
d_210ens_1THRASPD155 - 179
d_11ens_2GLYGLNB1 - 37
d_12ens_2GLUALAB39 - 77
d_13ens_2ASPLEUB79 - 112
d_14ens_2HISGLYB114 - 128
d_15ens_2ILEPROB130 - 168
d_16ens_2SERALAB170 - 193
d_21ens_2GLYGLNE2 - 38
d_22ens_2GLUALAE40 - 78
d_23ens_2ASPLEUE80 - 113
d_24ens_2HISGLYE115 - 129
d_25ens_2ILEPROE131 - 169
d_26ens_2SERALAE171 - 194
d_11ens_3PROLEUC1 - 9
d_12ens_3LEUTHRC11 - 13
d_21ens_3PROLEUF1 - 9
d_22ens_3LEUTHRF11 - 13

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.999999071285, 0.00134061954109, 0.000245293668599), (0.00134493038461, -0.999827762082, -0.0185104654768), (0.000220435927996, 0.0185107781887, -0.999828636567)-1.01540150521, -1.31613479791, -68.714335242
2given(0.999991811189, 0.00210878331496, 0.00345406830302), (0.00215376792429, -0.999912236435, -0.0130721349174), (0.00342619886166, 0.0130794671336, -0.999908590173)-0.821113379329, -1.10405958026, -68.6602497384
3given(0.999933147196, 0.00849877621049, -0.00784040448567), (0.00834704167884, -0.99978107363, -0.0191867586466), (-0.00800175198232, 0.019120031775, -0.9997851751)-1.55795844237, -1.40377260236, -68.6871232628

-
Components

-
HLA class II histocompatibility antigen, ... , 2 types, 4 molecules ADBE

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21562.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1 beta chain / Human leukocyte antigen DRB1 / HLA-DRB1


Mass: 22487.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01911

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Hemagglutinin


Mass: 1506.807 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: P03435

-
Non-polymers , 4 types, 611 molecules

#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0, 25 % PEG8000, 15 % Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.7→32.81 Å / Num. obs: 109380 / % possible obs: 99.45 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.46 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.0833 / Rpim(I) all: 0.049 / Rrim(I) all: 0.097 / Net I/σ(I): 9.48
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 10898 / CC1/2: 0.545 / CC star: 0.84 / Rpim(I) all: 0.539 / Rrim(I) all: 1.039 / % possible all: 99.55

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→32.81 Å / SU ML: 0.2137 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.4456
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2026 5555 5.08 %
Rwork0.1708 103810 -
obs0.1724 109365 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 204 571 7091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01876712
X-RAY DIFFRACTIONf_angle_d1.63879060
X-RAY DIFFRACTIONf_chiral_restr0.1129956
X-RAY DIFFRACTIONf_plane_restr0.01391166
X-RAY DIFFRACTIONf_dihedral_angle_d9.3188937
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.457217567336
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.593800169687
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.247503677638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.31841860.28033510X-RAY DIFFRACTION99.57
1.72-1.740.31441820.27213440X-RAY DIFFRACTION99.51
1.74-1.760.32321850.26173394X-RAY DIFFRACTION99.58
1.76-1.780.32241900.25313468X-RAY DIFFRACTION99.67
1.78-1.810.25611960.24363468X-RAY DIFFRACTION99.59
1.81-1.830.26651650.24173426X-RAY DIFFRACTION99.58
1.83-1.860.35061690.29843472X-RAY DIFFRACTION99.56
1.86-1.890.33121880.28913497X-RAY DIFFRACTION99.54
1.89-1.910.29441660.2623387X-RAY DIFFRACTION99.64
1.91-1.950.25421700.2213496X-RAY DIFFRACTION99.59
1.95-1.980.26551950.20273471X-RAY DIFFRACTION99.46
1.98-2.020.21191850.18113394X-RAY DIFFRACTION99.61
2.02-2.050.21971730.18633493X-RAY DIFFRACTION99.59
2.05-2.10.2251810.1873494X-RAY DIFFRACTION99.78
2.1-2.140.22821780.19063425X-RAY DIFFRACTION99.7
2.14-2.190.21971840.18793505X-RAY DIFFRACTION99.7
2.19-2.250.21931770.1783440X-RAY DIFFRACTION99.83
2.25-2.310.22291630.17553524X-RAY DIFFRACTION99.76
2.31-2.370.22411970.17783409X-RAY DIFFRACTION99.75
2.38-2.450.23651820.17333502X-RAY DIFFRACTION99.89
2.45-2.540.19972130.16893413X-RAY DIFFRACTION99.64
2.54-2.640.19712090.16533469X-RAY DIFFRACTION99.81
2.64-2.760.20481960.16733487X-RAY DIFFRACTION99.78
2.76-2.910.16982080.16183415X-RAY DIFFRACTION99.64
2.91-3.090.20011940.16743449X-RAY DIFFRACTION99.24
3.09-3.330.17381530.16313505X-RAY DIFFRACTION99.46
3.33-3.660.17731830.14663461X-RAY DIFFRACTION98.91
3.66-4.190.17882030.14023449X-RAY DIFFRACTION98.41
4.19-5.270.1441820.11823478X-RAY DIFFRACTION98.71
5.28-32.810.17362020.15323469X-RAY DIFFRACTION97.61
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)
15.15179149271-3.026789359695.018926371693.61627691126-3.824539381385.305438252210.3253066293750.54507600128-0.0127877146876-0.405843314837-0.402300245963-0.2204385644990.4061473001941.012295284210.1908626915740.2289211407450.0596815010510.05169323692490.2277408925780.01954308078990.2433996125516.25814314209-17.3390220828-20.7869721019
22.76990171412.54561290972-1.101917021374.62752673511-0.9937291925833.352385187940.0764409117955-0.02417042906520.137100009597-0.0519826659653-0.05029691209390.0760339456038-0.213909820501-0.05280444796350.0003683271949980.08626840673190.00410598109996-0.004083569422370.132328212494-0.002469206789170.137371276653-2.9234838401714.1773327251-53.8806853992
35.90839665402-0.5404248698831.174143026486.05760578645-2.430857007495.915195941310.008795753813540.249002662697-0.133434166997-0.3936688638620.0267228707848-0.1150634836850.1252193158760.215782177862-0.001125660835060.13322744502-0.00206303126260.03533632097870.118677201571-0.01801659755330.1260899963763.5219359154212.9574018028-64.3659645656
41.218020092790.2206781416910.584159061691.24050649493-0.1319097492031.276291494230.0511711676360.0281405996709-0.00407201483414-0.137523873855-0.05757803468050.04800153434130.101029156079-0.0186431698795-0.01707432217740.1355394896310.00545870148170.006336516494190.120353663538-0.01905187224960.153850626358-11.93770870326.19623668708-58.8680729835
52.657244845931.020937727091.905572411653.379013714763.029063676183.13150641584-0.05229706950310.04177777836430.127917285264-0.2347269103420.05494919138160.0338988196984-0.2648753878040.237297944076-0.005171619222040.1748946539530.012128260189-0.002524175551820.1398036552640.01106609301430.176209153462-12.058167978310.8686013147-61.7500491536
62.134658213360.1868157252031.710433634152.05394763335-0.5242518664926.8946610861-0.005414193486290.2211070661930.0153043496974-0.4916902982580.03910791674920.4354771817110.407307041279-0.515164005093-0.03778851529960.225849489892-0.0257995092447-0.09651117170120.224718855057-0.01079550870090.254495694789-23.85707561462.08806899708-68.1636295514
71.240975167390.804936016146-0.3590747284361.7958425822-0.149376404161.378646287720.280107088653-0.2873654916450.2957861536930.273067979108-0.2599053743690.0500833551123-0.3484124955040.141937685985-0.00765191814320.222996374792-0.05107493453970.01909066765220.183081343382-0.04079209869210.23155644097-1.2356661480721.6323401654-45.3529821958
84.93606259116-1.272983145981.483103862312.20134127143-1.056176086192.04476519314-0.005769432785340.117430235934-0.0318845816541-0.06109127313090.04545361094110.1837061858410.0428058325763-0.162181825817-0.02639080646880.1908290824720.0138342525855-0.004843619872690.1535190621610.004098080812440.155340498512-23.164806908427.4768933838-78.4810236029
95.884062913944.36100384587-5.155464404656.25205092532-5.119436515315.074842055220.268462133198-0.645439893456-0.1146650424410.40180571764-0.571563452568-0.339135243068-0.2404037921771.149246642840.394223879480.160059409086-0.033343982043-0.02160208262090.208865305177-0.01701117216560.2468130197347.2994224326416.9084867486-47.6222620661
102.3330061542-2.519302709990.9538512989754.81132218235-2.139467366013.913734197660.101938777435-0.03248503558-0.156757775151-0.115599692158-0.08237451009980.07175249244770.229672669238-0.03482398662620.01605049924560.113458649295-0.009660688013890.01085059818510.1283002031980.007770995531860.143295014262-3.86002382943-14.4706272519-14.6095238853
116.354909045580.898727436574-1.138274105746.25357680795-1.292053931045.634472610430.0343413588362-0.2912240273930.1623981787870.308763087511-0.0278786026036-0.205037034083-0.1051228460550.211281628397-0.009087440098930.148146121425-0.00432520278526-0.02386816131780.121169932146-0.005630141830580.1299784715182.53129488177-13.0900922728-4.12283246015
124.67074599527-1.524344992786.028897288441.96729069464-1.527718099237.913533972760.07600016535230.3063357208110.18045494438-0.362534086456-0.304072779056-0.252302752510.2174850186060.2474537615630.2137751876770.2067018101950.04977442915630.07838835133450.2398918337890.04017683661080.2054211556641.13714940182-8.2183380505-25.675940482
131.30420347697-0.30411459892-0.9872699084871.617427656520.1061782419664.188402026810.0454419036274-0.1274816555840.005546178965860.261569131093-0.008737182970420.166872964031-0.104773199960.0376736866201-0.01464129335410.155599601718-0.01036875900840.02139282701150.12804195434-0.01842089419310.168640256752-16.9074575228-7.22456891428-5.74015466068
141.29727265372-0.443542449811-0.7402825717941.668456715770.1703875379066.46065486613-0.0170344371694-0.1513080585270.05614372682060.5102128947750.02633935553510.462307280633-0.357632488982-0.515682196859-0.02394478606670.267472314004-0.01187816087010.1098104785220.18686062756-0.0181867912010.253057547028-21.8187817169-3.8493126863-0.667209035503
150.84175670241-0.359967460210.3631849190342.29695478823-0.2396645982971.65868575020.2666115094620.178338749652-0.199630695499-0.427102209737-0.217593489545-0.03706320702140.3660294533370.161465847666-0.0439098781370.2758884771770.06145927802880.01213938378230.186203952669-0.004960406572840.200761835268-2.47057387246-21.8104741295-22.9572449437
164.175309663881.34032597747-1.431007494211.52047451872-0.8054796192682.10677816119-0.00121502439612-0.08180792137970.095655058428-0.01909225378760.01712324414380.1456308958810.0325831456665-0.165635570505-0.008427103726710.224977078231-0.01971828309710.02307971302420.1914549249880.009035234075910.189925282994-24.2443022154-27.591625556510.1303291064
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'F' and (resid 1 through 13 )FF1 - 131 - 13
22chain 'A' and (resid 3 through 26 )AA3 - 261 - 24
33chain 'A' and (resid 27 through 55 )AA27 - 5525 - 53
44chain 'A' and (resid 56 through 133 )AA56 - 13354 - 131
55chain 'A' and (resid 134 through 154 )AA134 - 154132 - 152
66chain 'A' and (resid 155 through 181 )AA155 - 181153 - 179
77chain 'B' and (resid -2 through 89 )BB-2 - 891 - 92
88chain 'B' and (resid 90 through 190 )BB90 - 19093 - 193
99chain 'C' and (resid 1 through 13 )CC1 - 131 - 13
1010chain 'D' and (resid 3 through 26 )DD3 - 261 - 24
1111chain 'D' and (resid 27 through 55 )DD27 - 5525 - 53
1212chain 'D' and (resid 56 through 76 )DD56 - 7654 - 74
1313chain 'D' and (resid 77 through 144 )DD77 - 14475 - 142
1414chain 'D' and (resid 145 through 181 )DD145 - 181143 - 179
1515chain 'E' and (resid -3 through 89 )EE-3 - 891 - 93
1616chain 'E' and (resid 90 through 190 )EE90 - 19094 - 194

+
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