[English] 日本語
Yorodumi
- PDB-8sja: Ara H 6 13D9 16A8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sja
TitleAra H 6 13D9 16A8
Components
  • 13D9 heavy chain
  • 13D9 light chain
  • 16A8 heavy chain
  • 16A8 light chain
  • Conglutin
KeywordsIMMUNE SYSTEM / allergy / peanut / antibody
Function / homologyNapin/ 2S seed storage protein/Conglutin / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / nutrient reservoir activity / IgE binding / ACETATE ION / Conglutin
Function and homology information
Biological speciesHomo sapiens (human)
Arachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsSpiller, B.W. / Shrem, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)5R01AI155668 United States
CitationJournal: J.Allergy Clin.Immunol. / Year: 2025
Title: Structural determinants of peanut induced anaphylaxis.
Authors: Smith, S.A. / Shrem, R.A. / Lanca, B.B.C. / Zhang, J. / Wong, J.J.W. / Croote, D. / Peebles Jr., R.S. / Spiller, B.W.
History
DepositionApr 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: 16A8 light chain
H: 16A8 heavy chain
B: 16A8 heavy chain
G: Conglutin
I: Conglutin
C: 13D9 light chain
D: 13D9 heavy chain
E: 13D9 light chain
F: 13D9 heavy chain
A: 16A8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,57512
Polymers216,45710
Non-polymers1182
Water2,684149
1
L: 16A8 light chain
H: 16A8 heavy chain
G: Conglutin
C: 13D9 light chain
D: 13D9 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2886
Polymers108,2295
Non-polymers591
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 16A8 heavy chain
I: Conglutin
E: 13D9 light chain
F: 13D9 heavy chain
A: 16A8 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2886
Polymers108,2295
Non-polymers591
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.466, 112.067, 223.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 214 or (resid 301 and (name C or name O or name CH3 or name OXT))))
d_2ens_1(chain "L" and (resid 2 through 214 or (resid 301 and (name C or name O or name CH3 or name OXT))))
d_1ens_2(chain "B" and resid 1 through 221)
d_2ens_2(chain "H" and (resid 1 through 136 or resid 143 through 199 or resid 202 through 221))
d_1ens_3chain "C"
d_2ens_3(chain "E" and resid 2 through 207)
d_1ens_4chain "D"
d_2ens_4(chain "F" and (resid 1 through 135 or resid 142...
d_1ens_5(chain "G" and (resid 12 through 35 or resid 49 through 118))
d_2ens_5(chain "I" and (resid 12 through 35 or resid 49 through 118))

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_1SERSERGLYGLYAJ2 - 2141 - 213
d_12ens_1ACTACTACTACTAL301
d_21ens_1SERSERGLYGLYLA2 - 2141 - 213
d_22ens_1ACTACTACTACTLK301
d_11ens_2GLNGLNPROPROBC1 - 2211 - 221
d_21ens_2GLNGLNSERSERHB1 - 1361 - 136
d_22ens_2THRTHRTHRTHRHB143 - 199143 - 199
d_23ens_2TYRTYRPROPROHB202 - 221202 - 221
d_11ens_3SERSERVALVALCF2 - 2071 - 206
d_21ens_3SERSERVALVALEH2 - 2071 - 206
d_11ens_4GLNGLNGLUGLUDG1 - 2201 - 220
d_21ens_4GLNGLNSERSERFI1 - 1351 - 135
d_22ens_4GLYGLYGLYGLYFI142142
d_23ens_4ALAALAALAALAFI144 - 166144 - 166
d_24ens_4SERSERSERSERFI169 - 194169 - 194
d_25ens_4GLNGLNGLUGLUFI200 - 220200 - 220
d_11ens_5METMETMETMETGD12 - 351 - 24
d_12ens_5THRTHRASPASPGD49 - 11838 - 107
d_21ens_5METMETMETMETIE12 - 351 - 24
d_22ens_5THRTHRASPASPIE49 - 11838 - 107

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(0.0136726447888, -0.971898927017, 0.235001137118), (0.999775739852, 0.0170890469305, 0.0125073769944), (-0.0161718517416, 0.234777426806, 0.971914621288)-23.1745799774, 32.4363148475, 50.5160710399
2given(0.0156694092829, -0.977534231743, 0.210193471315), (0.999831272995, 0.0133031100107, -0.012666996694), (0.0095861960093, 0.210356490355, 0.977577747195)-23.9330237482, 31.5901637082, 52.018228888
3given(0.0416189255875, 0.999110037507, 0.0068555076964), (-0.979726829813, 0.0394637905524, 0.196412698622), (0.195967354367, -0.0148910103105, 0.980497350243)-29.4604895115, -34.2095114392, -44.1455767851
4given(0.0431872285166, 0.998553921824, 0.0320145045704), (-0.977084252732, 0.0355301665612, 0.209866553618), (0.208425589495, -0.0403444230838, 0.97720576194)-31.479272488, -36.149967031, -44.8436983222
5given(0.0239279361694, 0.998552579627, 0.0481684501537), (-0.990963055982, 0.0173298557446, 0.133010893457), (0.131983618487, -0.0509158307347, 0.989943383549)-32.7478604269, -32.4572952184, -50.6067350743

-
Components

-
Protein , 1 types, 2 molecules GI

#3: Protein Conglutin


Mass: 14509.228 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Cell line (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q647G9

-
Antibody , 4 types, 8 molecules LAHBCEDF

#1: Antibody 16A8 light chain


Mass: 23318.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 16A8 heavy chain


Mass: 23899.611 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody 13D9 light chain


Mass: 22708.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293 / Production host: Homo sapiens (human)
#5: Antibody 13D9 heavy chain


Mass: 23792.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293 / Production host: Homo sapiens (human)

-
Non-polymers , 2 types, 151 molecules

#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 00 mM Bis Tris pH 5.25, 75 mM Ammonium Acetate, 16% PEG 10,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.68→44.96 Å / Num. obs: 76577 / % possible obs: 99.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 75.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Net I/σ(I): 22
Reflection shellResolution: 2.68→2.78 Å / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.37 / Num. unique obs: 7559 / CC1/2: 0.798

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.05data processing
XDSVERSION Jan 10, 2022 BUILT=20220220data reduction
Aimless0.7.9data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→44.96 Å / SU ML: 0.4171 / Cross valid method: FREE R-VALUE / Phase error: 27.1369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 3911 5.11 %
Rwork0.1941 71984 -
obs0.1964 76577 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.8 Å2
Refinement stepCycle: LAST / Resolution: 2.68→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14367 0 8 149 14524
Refine LS restraintsType: f_bond_d / Dev ideal: 0.0106 / Number: 14679
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2JAX-RAY DIFFRACTIONTorsion NCS1.15572866255
ens_2d_2CBX-RAY DIFFRACTIONTorsion NCS1.12786039035
ens_3d_2FCX-RAY DIFFRACTIONTorsion NCS1.23519447499
ens_4d_2GDX-RAY DIFFRACTIONTorsion NCS1.75238635726
ens_5d_2DGX-RAY DIFFRACTIONTorsion NCS1.11467220309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.710.3681390.3282526X-RAY DIFFRACTION100
2.71-2.750.3471420.3062605X-RAY DIFFRACTION100
2.75-2.780.3421340.2872560X-RAY DIFFRACTION100
2.78-2.820.2671340.2582612X-RAY DIFFRACTION100
2.82-2.860.2941490.2622528X-RAY DIFFRACTION100
2.86-2.90.2941490.2622528X-RAY DIFFRACTION100
2.9-2.950.3171210.242583X-RAY DIFFRACTION100
2.95-30.2811230.2472621X-RAY DIFFRACTION100
3-3.050.3321220.26132581X-RAY DIFFRACTION100
3.05-3.10.291290.2692600X-RAY DIFFRACTION100
3.1-3.160.331170.2822597X-RAY DIFFRACTION100
3.16-3.230.3361750.282520X-RAY DIFFRACTION100
3.23-3.30.311630.2532540X-RAY DIFFRACTION99
3.3-3.380.2741340.242585X-RAY DIFFRACTION99
3.38-3.460.2781480.2262566X-RAY DIFFRACTION99
3.46-3.550.2631240.2252581X-RAY DIFFRACTION99
3.55-3.660.2731350.2252542X-RAY DIFFRACTION98
3.66-3.780.2991390.2272593X-RAY DIFFRACTION99
3.78-3.910.2681360.2252599X-RAY DIFFRACTION100
3.91-4.070.2331540.1882595X-RAY DIFFRACTION100
4.07-4.260.2091530.1642603X-RAY DIFFRACTION100
4.25-4.480.2131330.1492645X-RAY DIFFRACTION100
4.48-4.760.1791380.1422599X-RAY DIFFRACTION100
4.76-5.120.2031580.1432635X-RAY DIFFRACTION100
5.12-5.640.1841360.1572652X-RAY DIFFRACTION100
5.65-6.450.2141400.1792612X-RAY DIFFRACTION98
6.45-8.120.2241390.1832626X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.341138641480.805204660639-0.6884851006733.34330870479-0.7324246657433.353124857860.1833057901240.153621923163-0.0268743994078-1.12081990988-0.339375027776-1.204180343770.6495728240120.6372804342840.2571722843880.8072102015660.1789376162120.322013826940.4701209163550.06971351584650.972544230596-26.1303715017-31.253377357525.6918112258
26.23275284385-0.166945398473-3.522956123854.90759622857-2.009145438886.15599511257-0.255477564860.436151229276-0.620090944044-1.40084566026-0.0141273276419-0.6395650941290.973167903261-0.01337613681270.17734988760.9001207133890.1322950449380.3892271117370.5483471275150.00154816162530.920426490666-29.1461472531-35.063429954224.8751176744
31.568550066221.96684494016-0.23160055986.32166368699-2.975816664722.37335874295-0.4867336974250.302925027144-0.208891761238-0.1070253574540.2848144681580.3152133985390.358368409905-0.2780922329730.1411910229120.7597218158480.02892581910780.309614679960.6162496862690.1752320071680.76939676327-27.6078692341-2.7214812898211.2670180768
47.414352242662.6571356404-3.59998082795.75616015708-1.466623836837.19329297921-0.05597749119950.01757431417080.461026288488-0.7023220059740.178048629234-0.9525124127980.03113550057150.436881239943-0.1339710419490.5394220901370.04030591308250.2266563388920.6124097625170.117007398710.713500362897-22.3404232132.2756009446912.2275283248
55.256598480483.942555694633.82976146655.180832605190.3812897359655.11306605382-0.098694276957-0.4643373796360.694775256677-0.111962870272-0.2352496837620.642060987732-0.463999698727-0.8172524193230.2330647450440.4773517488390.1169970257260.1495024622460.4182116930030.03210774700840.512410974661-47.0689819064-15.743479469631.9673348242
64.314397588540.5516299189050.4540175868965.84419834502-0.7770355596122.87242499788-0.1523834886420.305062250416-0.336717142457-0.8117743266310.176149912510.6439299541850.5138990196690.02732046234760.02558867366960.5373445334040.02173127790410.08614614974310.37510632542-0.02168941368240.444251892509-51.7194935726-29.460547793330.4330217973
73.620808889351.18777102108-0.05505044126219.131992552-0.551789582373.415836062270.04414214443370.227793235430.0338591143948-0.212779254789-0.128096139455-1.548363084970.1317373661650.5437934614770.143114579030.4356135054940.04539346835950.1811930063250.4366899041890.03030907116350.615700232145-36.7400420646-21.637949124832.498452483
85.58238084282.661059756880.04989488520045.951338493740.3932938117642.339719632370.223862759868-0.735807217323-0.2481330056990.747771281189-0.2228423517980.03919962229030.3017684168-0.0694765213229-0.01983520524590.5415695485320.04313591032120.1001945372410.4712170673540.05585826582340.387014868525-46.5129420207-26.546129010539.9600647649
91.758931755063.547731710180.4060237969427.814837533251.386919637673.2205420553-0.0232271608498-0.0380394831813-0.310219501232-0.1174985266410.0594266731548-0.4820518009690.0389285823109-0.032783961865-0.05617966845560.4007799681370.1139428193360.1292871365680.422380188474-0.009840596855180.517997347144-40.1250073115-19.862213605634.8334097978
102.269310276891.56771579917-1.075518709764.40546282671-2.497290518542.88767265113-0.2761702570620.02282524457350.00980011019841-0.4339234428380.280176914024-0.2117755990180.297972695224-0.0510184903916-0.02810271724620.3972532425330.0933520036560.06301994014680.448448265703-0.03391914520740.339616171869-41.1345413082-20.636360108430.0950927224
116.60676015734-2.8559228593-0.8289826548313.542232425226.253176789882.073849081821.312400579740.998878236830.843976143601-1.865251525710.638672140064-0.335928904517-1.518653948170.652848700525-2.016570603461.14717451530.03818993474890.1991709847560.8670138012130.1306079278580.804509947785-33.65012065373.855526354112.8008695717
124.711085390532.091559536670.468284908434.073677328480.1684695931954.44286623597-0.3007971382810.449522866827-0.00763934979924-0.5549622734890.4394173565110.1901253159660.0574559083864-0.102897350083-0.1130703433350.5591356950420.02789648773950.1489252540050.4727515803890.1127370557280.613947317781-36.9577916912-3.5355897241516.4281352634
135.877735795672.42664226234-5.168609126855.06456913198-0.1798051402135.78370308146-0.3360588623421.3595101840.578131142586-1.433538118570.5742199648881.1227396171-0.712104361216-0.724752116795-0.2344822957440.932900525977-0.0737464767449-0.1304923886720.9390208589320.3440504996650.834307621411-44.4324939978-1.047943558229.41152888649
144.2503034538-0.4945820105211.477531574354.72846738338-0.3603586964923.97536504286-0.1370753298940.039994717318-0.00615647728945-0.07535292738080.0597161849181-0.581627391263-0.04840131136740.2045897949050.09240870859670.383442864063-0.09322788917410.03668184581250.419233095306-0.01389970836380.447126826795-55.774627601116.6083629216-19.9428047588
154.53287110405-0.777229235547-1.911550997492.682605409070.3854085175213.711049214760.1359899931860.166464602317-0.0419530680874-0.241422059848-0.0407421104392-0.6179516939780.3846522038170.5021522386890.01400287656310.527543462512-0.006931036070180.04164618490640.451332244983-0.01368227766260.547000427097-46.82870318539.28262712209-29.6790807536
167.228056670622.653257021890.6160849115287.15467247002-0.5977205673347.80029801828-0.1296537392910.6740988427891.23058075039-1.130651584080.0820922173265-0.542743272952-0.1673854705340.5696044876180.0448576639870.6466550866680.1560791768590.1634145854840.7177369024260.1580931665980.955906672027-34.45664697986.79394083478-40.268553257
174.955871342582.454134379641.668869093073.87040372259-0.3295173472387.0498001869-0.2299869925830.0349843981104-0.0440130359981-0.177719120236-0.1804996546360.9082357169730.149197433495-0.1748359997740.1877768587480.5449194580530.02669627456050.2044968851490.4413796435790.1004818359990.611371216314-48.4468908053-56.124532110445.7997272499
181.99454864371-4.42336899998-0.1857633446976.2259717488-4.372611154664.1501210629-0.6662559802581.36211852942-1.36450861027-2.547518854740.308717553209-1.645722697442.237157960980.7151768002490.1316479107031.681218000420.1170765334120.1795141037310.86641213856-0.2213729970322.02375118-45.7414736425-70.577473570435.3328901413
194.6941141516-0.2964419744731.594627314762.076874116513.355652532062.25906183350.09575972089330.371016230637-0.320727200132-0.544712384711-0.5160424537770.3856842517130.571703284993-0.5992903632040.5527148885560.914900755218-0.01757556377890.2028263055990.5663943619710.1020102945280.729769236894-55.1721265355-54.878641073341.4815277003
206.63346816238-2.31891938717-0.9476655569617.140661905940.1252846944138.83572397264-0.134081607730.0531423852421-0.294920399278-1.32066801074-0.121713616294-0.7750485206910.9770421333110.9427291645660.007625732985120.979625617071-0.003770115160280.3618691772870.517545256090.1228190347790.773836093809-39.8918214214-56.665944705639.4355598779
212.1188109258.788041903144.372885707136.176673358731.863947423142.225441813910.5155217066860.804190594362-1.75818142463-0.398612083008-0.0689882062218-0.9196022371220.4913781534920.393643943569-0.3419028486840.7740276718650.06605940567660.2290908798680.591048297886-0.0418536479890.849822939486-44.4010965187-45.682510207436.2479636111
225.05627234113-0.5558778826875.682527538458.20798391453.528111107119.66378543573-0.1201344704071.496001343440.379021391198-0.04549764618440.0995751917975-0.102413980409-0.3630010585780.760461997641-0.009634178494150.475418399526-0.1258509369850.1313377320920.7178624740430.1239938641690.501837141419-87.343924107421.0934923253-8.50226736482
238.341400359492.42077641756-2.82326977741.993139332459.040318045332.00518444672-0.5946610787150.5357137386151.41550474002-0.878165201957-1.383367288823.76408037155-0.267233713501-3.483850935081.844803670711.115926994260.111023514164-0.1650949009791.58811836375-0.4107764557231.62520114759-102.12381865117.9061603301-17.8035295821
242.07048478803-1.08482269875-4.997794758412.338371796931.814044663097.53957363294-0.1088943178910.3097590666921.43776664153-0.605912752790.265009976453-0.226971158179-1.097382302150.494975808231-0.327915808730.602545885086-0.1806571623120.01583612381430.6650247512560.1590029230770.86079365222-86.792770623426.7138491323-14.0680523001
255.00091426833-1.82187434575-4.693189856767.09798335247-0.3652712235756.3657652474-0.6013350329291.30511958983-0.854087468022-0.2325228188650.3942758004440.412148501141.02209444842-0.670758296350.2484082058290.471488098438-0.1255824422120.007550821052630.829924515843-0.09311394951050.701658033734-88.386282706911.0654894999-13.7708464165
262.1621709844-1.94616956871-0.1387737286489.75146293789-1.512938240415.58839280063-0.5046610708410.968043594313-0.5661303615220.4029326558221.004508039091.06877926871-0.11807649731-1.10206382809-0.2884080495640.376646288891-0.118261526860.01619822739160.7828249091750.07918530853510.626641860297-78.435273561916.3127589048-18.3365426743
271.765562685491.211926151881.227576729424.40194569912-1.735357390583.510131678960.103953619405-0.154646913709-0.1878330165440.0768494347703-0.1057658204080.009052096831730.196930181-0.132381936289-0.003925754662260.466531350985-0.0145421668460.1756911580340.403109935380.008941693653790.500147769193-48.1938488447-71.695198199762.5227256819
289.24387559185-7.243682613123.159724955138.90832187172-7.233813001838.316211988650.1765201409470.6607859371280.32615561206-1.55864101846-1.02356969803-1.785994796641.294195531670.4368882102040.7388126389260.7600123006730.1647452514170.378198533940.5873134081890.1526455756321.07483569635-38.1827260921-70.914666956455.125125375
291.816895547470.827931163072-0.1345364364885.9658287155-3.519912892076.08909466450.0276097833775-0.0768999999607-0.292091720709-0.285314451125-0.229413531014-0.3367637879190.4530517717670.1665935402630.233392435220.474312399332-0.03773418469740.1714551177730.366090206630.003278904751420.57997818091-46.9920897322-71.814005753962.4910690508
303.604332197271.192823539230.7132793213274.056775319470.1310876140024.784473788570.129724715112-1.16851371285-0.08529576905341.30979984040.235491131218-0.7851564078170.6776395085180.777116552716-0.3704567500530.8999530041070.036032426275-0.2824250810620.8138820770230.0363861528730.68531709935-44.2043727736-79.526592863696.4454451177
313.923347473750.121691111767-1.448944455313.912820625232.413971913456.295688254230.0133007130765-1.49324362573-0.07756530871052.437890626420.443862572249-0.1669367149721.786959634140.333587754-0.5386472311891.4762795538-0.00900575527566-0.24898471190.9925271016110.08836809719710.755157972041-47.4794329216-81.1210755186103.32989827
320.7591620901290.287983570643-2.330039821190.7214416718370.1128236631758.467096684620.0815881240223-0.7241781234920.382082639318-0.048269705566-0.104204878103-0.835361569183-1.194241449961.30104474335-0.08827693819330.766629536273-0.2997849120280.1100720531290.700159516595-0.07809117798370.977590399408-39.8287516256-51.259975447178.4590966583
334.71307424021-0.6986532053020.1994228538994.34356845656-0.3745839838286.586020381240.4774832755430.1070706532721.125855601040.182255952957-0.314109848639-0.588715251619-0.9424251512560.291733895282-0.08741439800850.556882919124-0.06151227870990.1273779685820.3702417996980.02904871029550.776301629536-44.112259043-49.814539021167.6127230556
341.28273738165-0.5970820201550.1351137438141.73285380209-1.137876997665.510133962770.209559168135-0.250661098250.5228387221340.221326278381-0.255809434751-0.29868730749-0.6730076832690.197305727806-0.03042369248860.513733618936-0.1299915115480.1186082042130.419450943024-0.05205691812210.746963482152-43.9950338888-54.057447041174.2796953959
350.472496683099-0.514725202148-0.3751926444981.96775895086-1.459940653271.48392478295-0.137084406568-0.4120701509470.05878342420150.7339781800050.292625348262-0.2424992348990.4360640102570.433148937181-0.1409596583950.971863878628-0.111130650444-0.3293300348581.07506169152-0.2074352831070.934288817612-35.5728948114-71.2886450558101.753973344
361.97579717247-6.767390752270.4104231865014.4288438413-0.7702232088780.623305636043-0.0568744160842-0.08016801882850.9755324941220.06589333645880.314740871904-0.9634486821930.9038248831920.0113959089512-0.01670615623550.949798735293-0.194957229396-0.1855705815810.93221169626-0.1939312287971.09345863665-32.4098446674-68.039738410191.3220201023
372.636336922961.3862027062-0.1091569152431.87401065570.2743608751948.593706765110.297789274692-0.273662376375-0.2530710889850.197320683780.667570943629-0.4997642339591.19427059310.300080125944-1.129016903120.876293050446-0.202740339406-0.2047375980510.666081327921-0.1574937441960.952879998287-41.6814343893-69.425794928995.3467336712
388.97875081221-7.985023755916.477586586157.24550910107-6.986797855056.34757991531-0.879202519398-0.2946622598490.7931671775150.6412226222440.682589839668-2.16043379931-0.4757399364230.8816531359980.1569390416550.825894765112-0.013967081407-0.1189162774630.95441938968-0.3716074202191.10028342264-28.3521428021-66.251882836598.3532609372
398.31139993024-1.38555181908-1.402099510683.922856494960.7249280306496.55307157456-0.2523749886550.0867190339817-0.0169802641180.117145237336-0.05976156259250.5034976337120.252347945115-0.2827765298830.2543181404320.321104667969-0.002088416504070.03330789750890.2925961000740.005325985720840.443633606626-103.11985274219.68482215567.45313044245
402.465361617012.7367196448-8.343822085864.872719160560.01444064679298.20870637029-0.1083467624261.316745743392.085220618620.2050314589510.8436171510650.70745979042-0.144226870611-0.849679471089-0.8394928015610.3371080012650.104033283234-0.07089514147330.6551109977820.2507417812260.661767918194-98.441786717625.467255289610.9286140782
413.26992062421.143619288090.2904170970333.365518203360.1554474780588.453014972490.0445145132188-0.69601507105-0.6296989296391.038377480120.109047161327-0.7364360812280.5355123030140.253185757854-0.1981602505220.7157821430070.150510753278-0.09170852429950.5547564320570.1498214400310.572152244807-110.37274457623.963448248444.8559446932
423.981240552671.896022868351.355264141464.994007677940.5259109085659.063596090750.0572866683964-0.320508102957-0.6658620701940.510711222639-0.053294719415-0.429103235909-0.05060839636980.379209501015-0.152202743710.5062562736020.151143098074-0.1070760603990.5546663477720.1381147316210.670795448032-109.25393563527.088588423739.734533855
431.707147824170.778998603288-0.5785944250791.9512902042-0.1331510659156.765575639310.0605827517793-0.654410930913-0.2228893271850.856029888707-0.263901706339-0.39096955423-0.4222672352330.1227241464750.2191464695250.9135611280330.127564315317-0.09639536954870.6853477532290.1751824718160.648592778025-111.74174655628.688692137151.5556938284
445.56882205952-0.5686903150460.6496137669632.786999909240.7778155752647.37827350795-0.360361244232-0.781246887121-0.322125407140.2698492909810.123318028868-0.5780015732730.2953390518680.7472678891040.2045135484430.3649539658260.09844839680220.05378435686770.5753916120650.133967523680.624506408113-82.264329754319.275537454516.057139932
452.828207750982.26477297391-1.475123639313.462471976450.5606699757084.066100807270.0883930288401-0.639564527659-1.883024039290.920813927198-0.316912522977-1.271422379770.8584257630271.117114056260.2732198629621.024412892090.290748191143-0.3199158036271.000233311240.199764304091.31400952235-99.02482703514.93898443247.2045574818
464.17207003657-1.02327735628-1.104308769735.967790112421.081761694933.61479022935-0.02712163336610.192961941481-0.339727949769-0.1175142685620.1366356879180.1775250643181.00473781437-0.264127215274-0.08049428859840.622682023976-0.153543325237-0.05049527930960.417446754125-0.02570135863940.451472926204-63.2857598978-4.07978568704-25.8068394722
473.80085047167-0.433502076637-1.687510104752.6608679278-0.04958192139782.84815060113-0.0851970187680.560392541364-0.228338220677-0.610817023375-0.00223061811731-0.1091926705170.595259913397-0.07122352432140.1427358867840.800338082314-0.05850348789090.03350517748230.419780244588-0.03775854977670.551874773206-56.1305228677-2.83711562597-31.4076841813
483.904485695963.89553530257-0.2513244553374.661639753292.196900007065.382000057320.299815508853-0.603278627941-1.10416765349-0.369893511951-0.488202324451-1.775658805761.002902958620.4298205956580.1478520988990.9831504188140.2005595409060.1842797390560.6300788392040.2346467090661.12666271862-34.6165038914-9.84375469292-36.1203734224
493.04130951593-0.5913244647270.4513636805450.2395512827580.1667882101021.192813564330.2125210021890.302735914027-2.832362989910.05320765152830.230986900127-3.028058049340.5030509686450.691360062566-0.3254142988770.8540612169750.1173340949830.2546475901531.0125696308-0.08768946949542.30420581263-23.4857830265-10.7405814324-38.6249617707
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 2 through 48 )LA2 - 481 - 47
22chain 'L' and (resid 49 through 103 )LA49 - 10348 - 99
33chain 'L' and (resid 104 through 130 )LA104 - 130100 - 126
44chain 'L' and (resid 131 through 214 )LA131 - 214127 - 210
55chain 'H' and (resid 1 through 17 )HC1 - 171 - 17
66chain 'H' and (resid 18 through 33 )HC18 - 3318 - 33
77chain 'H' and (resid 34 through 45 )HC34 - 4534 - 45
88chain 'H' and (resid 46 through 83 )HC46 - 8346 - 83
99chain 'H' and (resid 84 through 100 )HC84 - 10084 - 100
1010chain 'H' and (resid 101 through 128 )HC101 - 128101 - 128
1111chain 'H' and (resid 129 through 143 )HC129 - 143129 - 141
1212chain 'H' and (resid 144 through 192 )HC144 - 192142 - 190
1313chain 'H' and (resid 193 through 221 )HC193 - 221191 - 219
1414chain 'B' and (resid 1 through 100 )BD1 - 1001 - 100
1515chain 'B' and (resid 101 through 143 )BD101 - 143101 - 137
1616chain 'B' and (resid 144 through 222 )BD144 - 222138 - 214
1717chain 'G' and (resid 12 through 34 )GE12 - 341 - 23
1818chain 'G' and (resid 35 through 50 )GE35 - 5024 - 28
1919chain 'G' and (resid 51 through 71 )GE51 - 7129 - 49
2020chain 'G' and (resid 72 through 107 )GE72 - 10750 - 85
2121chain 'G' and (resid 108 through 118 )GE108 - 11886 - 96
2222chain 'I' and (resid 12 through 33 )IF12 - 331 - 22
2323chain 'I' and (resid 34 through 50 )IF34 - 5023 - 27
2424chain 'I' and (resid 51 through 71 )IF51 - 7128 - 48
2525chain 'I' and (resid 72 through 106 )IF72 - 10649 - 83
2626chain 'I' and (resid 107 through 118 )IF107 - 11884 - 95
2727chain 'C' and (resid 2 through 48 )CG2 - 481 - 47
2828chain 'C' and (resid 49 through 61 )CG49 - 6148 - 60
2929chain 'C' and (resid 62 through 106 )CG62 - 10661 - 105
3030chain 'C' and (resid 107 through 172 )CG107 - 172106 - 171
3131chain 'C' and (resid 173 through 207 )CG173 - 207172 - 206
3232chain 'D' and (resid 1 through 17 )DH1 - 171 - 17
3333chain 'D' and (resid 18 through 76 )DH18 - 7618 - 76
3434chain 'D' and (resid 77 through 127 )DH77 - 12777 - 127
3535chain 'D' and (resid 128 through 153 )DH128 - 153128 - 146
3636chain 'D' and (resid 154 through 173 )DH154 - 173147 - 164
3737chain 'D' and (resid 174 through 192 )DH174 - 192165 - 183
3838chain 'D' and (resid 193 through 220 )DH193 - 220184 - 206
3939chain 'E' and (resid 2 through 92 )EI2 - 921 - 91
4040chain 'E' and (resid 93 through 106 )EI93 - 10692 - 105
4141chain 'E' and (resid 107 through 151 )EI107 - 151106 - 150
4242chain 'E' and (resid 152 through 172 )EI152 - 172151 - 171
4343chain 'E' and (resid 173 through 213 )EI173 - 213172 - 212
4444chain 'F' and (resid 1 through 119 )FJ1 - 1191 - 119
4545chain 'F' and (resid 120 through 222 )FJ120 - 222120 - 217
4646chain 'A' and (resid 2 through 48 )AK2 - 481 - 47
4747chain 'A' and (resid 49 through 130 )AK49 - 13048 - 126
4848chain 'A' and (resid 131 through 176 )AK131 - 176127 - 172
4949chain 'A' and (resid 177 through 214 )AK177 - 214173 - 210

+
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