[English] 日本語
Yorodumi
- PDB-8trv: Structure of the EphA2 LBDCRD bound to FabS1C_C1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8trv
TitleStructure of the EphA2 LBDCRD bound to FabS1C_C1
Components
  • (S1C variant of Fab_C1 ...) x 2
  • Ephrin type-A receptor 2
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / Cell signalling / antibody / agonist / high affinity / clustering / activation / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration ...notochord cell development / notochord formation / lens fiber cell morphogenesis / blood vessel endothelial cell proliferation involved in sprouting angiogenesis / negative regulation of lymphangiogenesis / axial mesoderm formation / pericyte cell differentiation / cAMP metabolic process / positive regulation of bicellular tight junction assembly / regulation of blood vessel endothelial cell migration / ephrin receptor activity / leading edge membrane / negative regulation of chemokine production / post-anal tail morphogenesis / bone remodeling / response to growth factor / tight junction / activation of GTPase activity / regulation of lamellipodium assembly / branching involved in mammary gland duct morphogenesis / EPH-Ephrin signaling / neural tube development / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / mammary gland epithelial cell proliferation / RHOV GTPase cycle / EPHA-mediated growth cone collapse / growth factor binding / regulation of cell adhesion mediated by integrin / lamellipodium membrane / RHOU GTPase cycle / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / ephrin receptor signaling pathway / RAC2 GTPase cycle / RAC3 GTPase cycle / vasculogenesis / transmembrane receptor protein tyrosine kinase activity / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / negative regulation of angiogenesis / keratinocyte differentiation / RAC1 GTPase cycle / positive regulation of protein localization to plasma membrane / osteoclast differentiation / cell chemotaxis / skeletal system development / molecular function activator activity / protein localization to plasma membrane / cell motility / receptor protein-tyrosine kinase / ruffle membrane / neuron differentiation / osteoblast differentiation / intrinsic apoptotic signaling pathway in response to DNA damage / virus receptor activity / cell migration / lamellipodium / receptor complex / cell adhesion / positive regulation of cell migration / defense response to Gram-positive bacterium / cadherin binding / inflammatory response / focal adhesion / cell surface / ATP binding / plasma membrane
Similarity search - Function
Ephrin type-A receptor 2, ligand binding domain / : / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. ...Ephrin type-A receptor 2, ligand binding domain / : / Ephrin receptor type-A /type-B / Ephrin receptor ligand binding domain / Tyrosine-protein kinase, receptor class V, conserved site / Ephrin receptor, transmembrane domain / Ephrin receptor ligand binding domain / Ephrin type-A receptor 2 transmembrane domain / Receptor tyrosine kinase class V signature 1. / Receptor tyrosine kinase class V signature 2. / Eph receptor ligand-binding domain profile. / Ephrin receptor ligand binding domain / Putative ephrin-receptor like / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Growth factor receptor cysteine-rich domain superfamily / Sterile alpha motif/pointed domain superfamily / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Immunoglobulin-like fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
IODIDE ION / Ephrin type-A receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsSinger, A.U. / Bruce, H.A. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Celgene CorporationOperating Contract United States
Bristol-Myers Squibb (BMS) ResearchCollaboration and Option Agreement United States
CitationJournal: To be Published
Title: Synthetic Antibodies targeting EPHA2 Induce Diverse Signaling-Competent Clusters with Differential Activation
Authors: Adams, J.J. / Bruce, H.A. / Ploder, L. / Garcia, J. / Khutoreskaya, G. / Jarvik, N. / Costa, L.E. / Gorelik, M. / Pot, I. / Sicheri, F. / Blazer, L.L. / Singer, A.U. / Sidhu, S.S.
History
DepositionAug 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ephrin type-A receptor 2
C: S1C variant of Fab_C1 heavy chain
G: S1C variant of Fab_C1 light chain
D: S1C variant of Fab_C1 heavy chain
E: S1C variant of Fab_C1 light chain
B: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,54326
Polymers162,4006
Non-polymers1,14320
Water00
1
A: Ephrin type-A receptor 2
C: S1C variant of Fab_C1 heavy chain
G: S1C variant of Fab_C1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,66412
Polymers81,2003
Non-polymers4659
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: S1C variant of Fab_C1 heavy chain
E: S1C variant of Fab_C1 light chain
B: Ephrin type-A receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,87814
Polymers81,2003
Non-polymers67811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.933, 110.558, 263.443
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 27 through 28 and (name N...
d_2ens_1(chain "B" and (resid 27 through 43 or (resid 44...
d_1ens_2(chain "C" and (resid 1 through 30 or (resid 31...
d_2ens_2(chain "D" and (resid 1 through 61 or (resid 62...
d_1ens_3(chain "E" and (resid 1 through 162 or (resid 163...
d_2ens_3(chain "G" and (resid 1 through 2 or (resid 3...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LYSLYSMETMETAA27 - 595 - 37
d_12ens_1PROPROSERSERAA63 - 7441 - 52
d_13ens_1ASPASPPHEPHEAA78 - 10856 - 86
d_14ens_1CYSCYSLYSLYSAA115 - 11693 - 94
d_15ens_1THRTHRVALVALAA118 - 15296 - 130
d_16ens_1LEULEUALAALAAA163 - 216141 - 194
d_17ens_1SERSERPROPROAA218 - 329196 - 307
d_21ens_1LYSLYSMETMETBF27 - 595 - 37
d_22ens_1PROPROSERSERBF63 - 6841 - 46
d_23ens_1CYSCYSPHEPHEBF70 - 10848 - 86
d_24ens_1CYSCYSPROPROBF115 - 32993 - 307
d_11ens_2GLUGLUSERSERCB1 - 2391 - 217
d_21ens_2GLUGLUSERSERDD1 - 2391 - 217
d_11ens_3ASPASPCYSCYSEE1 - 2321 - 215
d_21ens_3ASPASPCYSCYSGC1 - 2321 - 215

NCS ensembles :
ID
ens_1
ens_2
ens_3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Ephrin type-A receptor 2 / Epithelial cell kinase / Tyrosine-protein kinase receptor ECK


Mass: 33952.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 27-330 / Source: (gene. exp.) Homo sapiens (human) / Gene: EPHA2, ECK / Plasmid: pSCSTa
Details (production host): expressed with a C-terminal thrombin cleavage site and 6-his sequence. The residues LTPR at the C-terminus are derived from the thrombin cleavage site
Cell line (production host): Expi293 / Production host: Homo sapiens (human)
References: UniProt: P29317, receptor protein-tyrosine kinase

-
Antibody , 2 types, 4 molecules CDGE

#2: Antibody S1C variant of Fab_C1 heavy chain


Mass: 23814.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Antibody S1C variant of Fab_C1 light chain


Mass: 23432.895 Da / Num. of mol.: 2 / Mutation: SPHAGLSSP replaced by QGTTS; Q165S, K167Y
Source method: isolated from a genetically manipulated source
Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)

-
Non-polymers , 4 types, 20 molecules

#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 200 mM sodium iodide (PACT Premiere solution E3)
Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2022 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.99→131.72 Å / Num. obs: 44485 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 103.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.05 / Rrim(I) all: 0.132 / Net I/σ(I): 12
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 5.9 % / Rmerge(I) obs: 2.214 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4523 / CC1/2: 0.349 / Rpim(I) all: 0.975 / Rrim(I) all: 2.427 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
X-Areadata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3FL7 & 8TRS

3fl7

8trs


Resolution: 3.25→131.72 Å / SU ML: 0.4573 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7391
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.272 1683 4.84 %
Rwork0.217 33088 -
obs0.2197 34771 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.87 Å2
Refinement stepCycle: LAST / Resolution: 3.25→131.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10669 0 23 0 10692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010110933
X-RAY DIFFRACTIONf_angle_d1.161414926
X-RAY DIFFRACTIONf_chiral_restr0.06271678
X-RAY DIFFRACTIONf_plane_restr0.01331934
X-RAY DIFFRACTIONf_dihedral_angle_d16.52833744
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS3.06500889003
ens_2d_2BCX-RAY DIFFRACTIONTorsion NCS0.960819593314
ens_3d_2EEX-RAY DIFFRACTIONTorsion NCS0.745157911437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.350.33021350.30652694X-RAY DIFFRACTION99.51
3.35-3.450.36831430.30112682X-RAY DIFFRACTION99.72
3.45-3.580.30431420.28652726X-RAY DIFFRACTION99.55
3.58-3.720.37451450.27722720X-RAY DIFFRACTION99.72
3.72-3.890.33881510.27042725X-RAY DIFFRACTION99.79
3.89-4.090.33711410.23912744X-RAY DIFFRACTION100
4.09-4.350.24411240.21342755X-RAY DIFFRACTION99.79
4.35-4.690.27471390.20262744X-RAY DIFFRACTION99.9
4.69-5.160.24071390.18942769X-RAY DIFFRACTION99.86
5.16-5.910.24941250.20592771X-RAY DIFFRACTION98.97
5.91-7.440.3011450.22532810X-RAY DIFFRACTION98.83
7.44-131.720.21731540.17322948X-RAY DIFFRACTION99.3
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)
14.47638614222-1.12944522740.2629403140224.055007670780.5125051759023.424837400240.5106051209850.4866482955872.85690946801-0.266636284538-0.071311077072-0.447366955925-0.6594031880980.266114796523-0.2630796149591.22068294384-0.1318885989160.1745577763550.9543888536360.3077757754182.2503341959213.1570507812-23.18074019-6.24560772419
24.37960885195-0.8625692075150.6824563014573.93093855327-1.036860230772.973259074920.337207038360.3996305330280.042029607072-0.2372854335540.1749246149170.05590253240770.5499174590720.121019604064-0.5315963127770.8959694766780.120071823242-0.1771826387240.851290190815-0.1256282628940.75379414528410.8498130544-50.2617497824-2.47305097787
31.30029222479-2.271815197490.01019052222974.72380852346-3.198828005273.700495996690.4396881711510.127607766977-0.609357027817-0.785564083779-0.002045634523840.8587238427541.09069290606-0.224695489643-0.482911841391.509871656330.186851970161-0.5960685943520.94005467321-0.187987846951.1550682754519.746898926-84.484897670316.0673377508
46.13846163721-0.238932580997-5.102269291445.16918747056-0.2285814937856.527784734130.311661263152-0.147207201519-0.329827958984-0.753805654371-0.08335189865051.784432382890.0699060807108-0.796687438698-0.1149585125880.798513407346-0.00634620435228-0.3468426212310.871210562286-0.2569665375281.270300735114.6133277172-75.196370775938.8490458989
54.83611329502-2.63032154156-0.6561140047363.24210664082-1.33114354635.71362284764-0.1266452890590.277915879431-0.249351496707-0.80353057125-0.09408206995931.449455447981.18730684572-0.7272560139110.3751100829881.01056898108-0.14373180485-0.3334476035550.913066181199-0.1153476804721.6694835443911.0379096314-82.211410479540.1336042881
62.57689704373-0.3572455712430.7209869946414.210093791272.320884274114.321138206440.117124314388-0.287427718456-0.617351125057-0.349415422898-0.01956530996510.140530849745-0.4100877199720.0974749337835-0.1281591197230.5897296373140.0538816429712-0.03847043838641.01681202254-0.1853453591920.75857711288922.4609582099-65.37889820350.7936627809
75.369442870780.167777667889-1.184083261946.797403423990.04904833277912.93894328938-0.3179096186190.3925465128480.4446264155670.240100504030.2596565602360.0997377582989-0.105007790434-0.399055801063-0.04400883271350.578858560542-0.0969765987243-0.0161745238891.34130251952-0.2695330716970.67969295637225.6305918059-53.497239942860.8458067654
82.028991831040.226213950320.772306157475.35786964185-0.05934700064483.533776526160.285333223651-0.305118411187-0.3292907473320.1102159347340.06413965615180.2918209338460.695581965931.04269547725-0.3837245946650.9286508189470.341757330724-0.1678585323021.09031280489-0.179572840130.72881484745738.162437662-78.812243384235.811226542
92.57952772806-1.058175964720.2003869442685.556289640450.6637814722944.957456187260.655004339045-0.0417667001227-0.372443881161-1.22481476825-0.5989898760270.8724995549810.07647693421280.4835722530260.0129180361250.9400284711370.187864948498-0.2026227030090.962340621652-0.05967906184170.71795649400534.9763274297-73.321138136529.0963324754
103.138750596891.883044181010.3013234683149.303397814412.237662747084.305279757930.1252189205780.09434285018730.306678868816-1.74873629773-0.01584328482131.112159987520.3037844578720.536955698559-0.06156778153330.9860460232990.263050403605-0.2567331731850.848273094434-0.1763708110130.86245962049934.0888586446-73.680674241933.7418962786
117.875342484187.290517622854.489965933549.132614907354.476026586253.9089475840.879092548483-0.1798184788450.04043265951520.0658030791055-0.518380407476-0.2638137285140.5601102022190.0993990871057-0.4232710090870.902319803141-0.002712699791130.02116313943921.36991120259-0.3326134417970.80525412932338.1741725741-72.335117388943.5362718462
125.050289186430.9804610678962.465002781596.80526947903-0.3864132642627.901129303840.235866795444-0.635732920338-0.113333976737-0.009027963143290.389696831626-0.197092605534-0.0921862194165-0.53177036552-0.8370678737350.644279308689-0.0263397728816-0.04440979126081.32642525259-0.1682613425920.63173353975335.554210436-58.760826058966.5210045629
139.825251551034.130372478880.9211198165898.95440629493-5.127734616554.3957226905-0.0919274653764-1.28665185705-1.91087184770.500605648933-0.0940628035226-1.38751690179-1.79535044013-1.741514106850.5677831571160.7859067290550.0874632796862-0.00254880754741.15472558903-0.137268015880.71797180813342.2230217068-67.429120099774.4396219706
144.914206094831.84231899578-1.620474391224.98503487648-3.075132972398.51383623435-0.8389179696021.23016948174-0.465930173473-0.726343623661.08766729685-0.1284622123810.810929720024-1.26238292810.1469916203940.687093601601-0.1683015380820.04336644605531.38388234271-0.2134142315410.95240511347737.7269203479-62.790203948355.9662861122
158.26582920305-0.565977682831-0.6304519006982.71789930399-0.5718277935596.469475457920.0846726022135-1.81924286833-0.6529084167140.7533194843560.0103453539140.340464139907-0.2602599912240.638969792225-0.1889148058060.789928815607-0.01039387463560.08700967967521.65941050744-0.1522001774620.77492275300739.4289339316-61.382098199774.0892589896
165.594880780660.920025864951-0.4170182670514.739985077411.178145154172.392629445050.3918515433910.203244768881-0.481046977018-1.259354562-0.3594051221280.7142210479470.0737584053915-0.271754154415-0.02771821494491.028313225980.203905639499-0.2162936319590.804654801896-0.02859548180890.7492801896447.8896428522-107.73769472333.0574928469
177.770484666463.0775584522-1.022631188737.169950606543.91830310047.551346329990.0747510162779-0.684794400497-0.01504440175930.282827377060.0681418208284-0.1261101605180.0748831992026-0.342533184715-0.1956667527720.648378367942-0.0475036175281-0.04266783364131.0227345160.289681627350.73978367967860.5100189396-106.18518281664.5682539727
184.708940398051.37249944601-0.9372088147258.868175459131.443760154054.459609688960.434118950836-0.125413966960.0211634189042-0.945855004302-1.06935967307-0.00671681404228-0.03642131061650.7394396800210.4056461416991.056054792650.1233451980470.1197397661871.110398004090.2256323045940.87929066706474.9324848997-104.81966449932.1385308112
197.93126550676-3.70854195264-2.011607338482.459436356721.777432217681.851077207020.4667294632721.01299989513-1.27842881116-0.713136522161-0.618903221369-0.153473280058-0.2004553098710.6716850771220.5194026990811.318245658860.2713080511450.09461202796411.200957656840.1741898781591.0113496000569.0599520584-103.98345192724.5082457149
205.998224459840.540468198122.710966863435.0563914543-2.357139721354.928690804410.001203617849420.1285863144360.514589525381-0.830087580299-0.735264484547-1.14570877852-1.037402192110.3865473931041.200913829441.31768235410.1529636351280.1201527142310.7648439264360.1892776394970.80199257641964.6005715463-93.856695161730.6093406466
219.170712188141.938728400484.87284739144.48930638551-3.675617401598.340617494710.02665480755621.727205763780.203528967005-0.322041886756-0.855973668776-1.136815091570.1581783795292.388720407090.3811670805571.391293646180.4028879251230.2611058417541.316110498990.2671145374411.3261940123273.8026639752-99.50585643723.016465976
226.922511932143.085335171071.777638804015.18717734879-2.392575368515.680044160310.09050972961470.244635525816-0.396388547888-1.21303997153-0.206027673265-0.191441803417-0.5657976590951.041548310070.3375581720931.100160698030.2650346878730.08656457713950.9156353112880.01425431432190.62812834671467.4482897643-99.654515756330.3988132836
236.912857287632.176485283645.776146016412.757596155831.95734572295.34500172498-0.5615652037971.00338707916-0.241990619317-0.8471475355680.0746160266049-0.377518204507-0.6995856016811.82205056760.7205570723131.179493192410.06047715909170.07732369895461.203999450670.172145960040.82849593354371.7917842902-106.11927863137.8349538025
247.217759586924.7691102674-1.828692246157.90289931609-1.749573945257.983628923180.155409122035-1.136175859270.3902755300020.237458802997-0.1762372724950.6942803186531.272590746270.632633500695-0.2180142498040.8881624587010.09130196904660.08970620954611.537773924430.6798657930051.1346739125564.735660646-115.70806609870.4626602973
257.61044490264-2.07096946417-5.937222593072.385909288393.284828487878.858519438890.9536347016150.2777380223420.202943447274-0.6027938290920.429542708412-0.0650756972501-0.2511715205230.408211140612-1.726338518040.806306999925-0.0341078093848-0.01311152649311.110896104880.3998545080350.88160556741673.6839743537-111.66475689458.0991468568
262.19294954688-0.9307337695211.246165994325.164940777142.16630703435.33410749510.0259305596694-0.663931565625-2.616793567692.105921209390.856451114989-1.001513350881.393085612641.04282291547-0.8151228740011.288542521070.2581796607550.05378654390171.134853349560.2154994625751.209792269176.3431132515-125.06859236263.2091271845
275.352497129715.98684320189-2.228509501549.79019372625-2.881784131175.01990241617-0.6981037395120.7841063743011.32914533672-1.343035811271.669571251522.306387246920.190086169417-0.333202789267-1.208639850620.688531487689-0.0628961178848-0.1176808450141.252601369770.2953628536911.0741366968271.5968443657-109.02961401453.4763078971
289.91339094303-5.67623431206-1.96796652065.447320768025.122586326087.60975931294-0.442303455218-0.438777427967-3.004512320390.742173539828-0.967773848930.7567456647650.7349342652590.4585783614691.709441921120.657883363777-0.188538081373-0.00331943606651.315317608590.342196862741.274615048665.7086679077-123.70491385266.7954481096
292.15512000624-5.37309403568-3.155851108195.166064137874.979212395135.829060558310.200508501033-1.23922576757-0.28128689390.03014178759580.8436181001620.16917352511.58089816385-0.100263348776-1.360000792740.765369622909-0.192746309534-0.1080885029881.216211772040.4091950534551.1886491951377.0217642246-120.89568409865.6207285702
306.0695712442.8289313408-4.890912033688.96400476809-4.327343911254.193343851080.18400173702-0.555687804748-2.354245010911.31670672019-0.4862765739210.03774381716630.071004248269-0.505423210941-0.03082444105660.927625576103-0.0941109099871-0.1320704418791.763497805680.4729805658960.92280344988978.1274264851-117.49363845369.9997862089
311.259091240081.52456774053-0.7331382229483.11849477103-1.136017639681.536012763890.57770849904-0.9416696917521.58485027085-0.159097566483-0.1398639175311.0087201804-0.686817227560.468526389835-0.4973618840491.678395704140.1471636001080.2466071198931.57715022088-0.6373741243052.1604598883542.9572471993-30.340942589428.7306559423
324.49550705525-2.32960218707-0.6940366300496.6864163650.7320980098431.669908698581.554540892-1.171002190920.474435850714-2.06390030795-0.0962588640557-0.631985732627-1.828980269940.623763458623-1.423309357921.877420875620.04305833219270.3595366276491.26037955779-0.4715397707211.7064613532234.6869209714-26.243647921225.5404004078
334.61789548247-0.3392783580192.494078279249.613757165620.9809204057963.303474468511.76556053817-0.4865753760250.2938446623290.3788993079380.9192584728210.809962579587-0.5607344103410.24820475737-1.616521939851.68760548489-0.05199216161810.4209982166861.4971082943-0.3185364558731.7864151803231.5457209611-32.918912631530.8412237842
342.46614552069-1.79033118832-0.7718377967586.059388085360.2217804828380.5497716749890.086489841345-0.2829390504080.0552812552157-0.8816143554020.1653359892890.3754930087290.0600031409250.153934466082-0.2955659019641.548059028430.210775995664-0.1784205660061.10011123492-0.1091966898520.66885607258545.7957164707-71.77473302114.9376951129
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 178 )AA27 - 1781 - 143
22chain 'A' and (resid 179 through 259 )AA179 - 259144 - 224
33chain 'A' and (resid 260 through 329 )AA260 - 329225 - 294
44chain 'C' and (resid 1 through 57 )CB1 - 571 - 52
55chain 'C' and (resid 58 through 99 )CB58 - 9953 - 91
66chain 'C' and (resid 100 through 158 )CB100 - 15892 - 136
77chain 'C' and (resid 159 through 239 )CB159 - 239137 - 217
88chain 'G' and (resid 1 through 44 )GC1 - 441 - 38
99chain 'G' and (resid 45 through 91 )GC45 - 9139 - 75
1010chain 'G' and (resid 92 through 111 )GC92 - 11176 - 95
1111chain 'G' and (resid 112 through 131 )GC112 - 13196 - 116
1212chain 'G' and (resid 132 through 162 )GC132 - 162117 - 147
1313chain 'G' and (resid 163 through 173 )GC163 - 173148 - 158
1414chain 'G' and (resid 174 through 192 )GC174 - 192159 - 177
1515chain 'G' and (resid 193 through 232 )GC193 - 232178 - 215
1616chain 'D' and (resid 1 through 143 )DD1 - 1431 - 121
1717chain 'D' and (resid 144 through 239 )DD144 - 239122 - 217
1818chain 'E' and (resid 1 through 18 )EF1 - 181 - 18
1919chain 'E' and (resid 19 through 44 )EF19 - 4419 - 38
2020chain 'E' and (resid 45 through 75 )EF45 - 7539 - 61
2121chain 'E' and (resid 76 through 91 )EF76 - 9162 - 75
2222chain 'E' and (resid 92 through 111 )EF92 - 11176 - 95
2323chain 'E' and (resid 112 through 131 )EF112 - 13196 - 116
2424chain 'E' and (resid 132 through 146 )EF132 - 146117 - 131
2525chain 'E' and (resid 147 through 162 )EF147 - 162132 - 147
2626chain 'E' and (resid 163 through 173 )EF163 - 173148 - 158
2727chain 'E' and (resid 174 through 192 )EF174 - 192159 - 177
2828chain 'E' and (resid 193 through 206 )EF193 - 206178 - 191
2929chain 'E' and (resid 207 through 216 )EF207 - 216192 - 201
3030chain 'E' and (resid 217 through 232 )EF217 - 232202 - 215
3131chain 'B' and (resid 27 through 102 )BG27 - 1021 - 72
3232chain 'B' and (resid 103 through 134 )BG103 - 13473 - 100
3333chain 'B' and (resid 135 through 169 )BG135 - 169101 - 125
3434chain 'B' and (resid 170 through 329 )BG170 - 329126 - 284

+
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://pdbjlvh1.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