[English] 日本語
Yorodumi
- PDB-7uvq: Pfs230 domain 1 bound by RUPA-97 and 15C5 Fabs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uvq
TitlePfs230 domain 1 bound by RUPA-97 and 15C5 Fabs
Components
  • (Fab Heavy Chain) x 2
  • (Fab Kappa Light Chain) x 2
  • Gametocyte surface protein P230
KeywordsCELL INVASION/IMMUNE SYSTEM / Antibody-fragment / malaria transmission / CELL INVASION / CELL INVASION-IMMUNE SYSTEM complex
Function / homology6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / cell surface / plasma membrane / Gametocyte surface protein P230
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsIvanochko, D. / Julien, J.P.
Funding support Canada, United States, 4items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)428410 Canada
Ontario Early Researcher Awards Canada
Bill & Melinda Gates FoundationOPP1170236 United States
Canada Research Chairs Canada
CitationJournal: Immunity / Year: 2023
Title: Potent transmission-blocking monoclonal antibodies from naturally exposed individuals target a conserved epitope on Plasmodium falciparum Pfs230.
Authors: Ivanochko, D. / Fabra-Garcia, A. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Newton, J. / Semesi, A. / de Bruijni, M. / Bolscher, J. / Ramjith, J. / Szabat, M. / Vogt, S. / ...Authors: Ivanochko, D. / Fabra-Garcia, A. / Teelen, K. / van de Vegte-Bolmer, M. / van Gemert, G.J. / Newton, J. / Semesi, A. / de Bruijni, M. / Bolscher, J. / Ramjith, J. / Szabat, M. / Vogt, S. / Kraft, L. / Duncan, S. / Lee, S.M. / Kamya, M.R. / Feeney, M.E. / Jagannathan, P. / Greenhouse, B. / Sauerwein, R.W. / Richter King, C. / MacGill, R.S. / Bousema, T. / Jore, M.M. / Julien, J.P.
History
DepositionMay 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gametocyte surface protein P230
B: Fab Kappa Light Chain
C: Fab Heavy Chain
D: Fab Heavy Chain
E: Fab Kappa Light Chain


Theoretical massNumber of molelcules
Total (without water)117,6325
Polymers117,6325
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.000, 155.000, 92.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAGLNGLN(chain 'B' and (resid 111 through 125 or resid 127...BB111 - 124110 - 123
121SERSERTYRTYR(chain 'B' and (resid 111 through 125 or resid 127...BB127 - 140126 - 139
131ALAALATHRTHR(chain 'B' and (resid 111 through 125 or resid 127...BB144 - 164143 - 163
141ASPASPASPASP(chain 'B' and (resid 111 through 125 or resid 127...BB167166
151ASPASPTYRTYR(chain 'B' and (resid 111 through 125 or resid 127...BB170 - 186169 - 185
161VALVALARGARG(chain 'B' and (resid 111 through 125 or resid 127...BB191 - 211190 - 210
211ALAALAGLNGLN(chain 'E' and (resid 111 through 125 or resid 127...EE111 - 124112 - 125
221SERSERTYRTYR(chain 'E' and (resid 111 through 125 or resid 127...EE127 - 140128 - 141
231ALAALATHRTHR(chain 'E' and (resid 111 through 125 or resid 127...EE144 - 164145 - 165
241ASPASPASPASP(chain 'E' and (resid 111 through 125 or resid 127...EE167168
251ASPASPTYRTYR(chain 'E' and (resid 111 through 125 or resid 127...EE170 - 186171 - 187
261VALVALARGARG(chain 'E' and (resid 111 through 125 or resid 127...EE191 - 211192 - 212
112VALVALPROPRO(chain 'C' and (resid 109 through 127 or resid 134...CC109 - 126114 - 131
122GLYGLYSERSER(chain 'C' and (resid 109 through 127 or resid 134...CC134 - 161139 - 166
132HISHISSERSER(chain 'C' and (resid 109 through 127 or resid 134...CC164 - 188169 - 193
142TYRTYRASNASN(chain 'C' and (resid 109 through 127 or resid 134...CC194 - 199199 - 204
152PROPROASNASN(chain 'C' and (resid 109 through 127 or resid 134...CC202 - 204207 - 209
162VALVALLYSLYS(chain 'C' and (resid 109 through 127 or resid 134...CC207 - 214212 - 219
212VALVALPROPRO(chain 'D' and (resid 109 through 127 or resid 134...DD109 - 126120 - 137
222GLYGLYSERSER(chain 'D' and (resid 109 through 127 or resid 134...DD134 - 161145 - 172
232HISHISSERSER(chain 'D' and (resid 109 through 127 or resid 134...DD164 - 188175 - 199
242TYRTYRASNASN(chain 'D' and (resid 109 through 127 or resid 134...DD194 - 199205 - 210
252PROPROASNASN(chain 'D' and (resid 109 through 127 or resid 134...DD202 - 204213 - 215
262VALVALLYSLYS(chain 'D' and (resid 109 through 127 or resid 134...DD207 - 214218 - 225

NCS ensembles :
ID
1
2

-
Components

#1: Protein Gametocyte surface protein P230


Mass: 22694.705 Da / Num. of mol.: 1 / Fragment: domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PFS230, PF230, S230, PF3D7_0209000 / Production host: Homo sapiens (human) / References: UniProt: P68874
#2: Antibody Fab Kappa Light Chain


Mass: 23192.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Fab Heavy Chain


Mass: 24158.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Fab Heavy Chain


Mass: 24074.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody Fab Kappa Light Chain


Mass: 23511.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M di-ammonium hydrogen citrate, 17.5 %(w/v) polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 3.29→29.76 Å / Num. obs: 19432 / % possible obs: 99.9 % / Redundancy: 16.7 % / Biso Wilson estimate: 128.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.037 / Rrim(I) all: 0.152 / Net I/σ(I): 14.5
Reflection shellResolution: 3.29→3.55 Å / Rmerge(I) obs: 1.565 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3974 / CC1/2: 0.778 / Rpim(I) all: 0.39 / Rrim(I) all: 1.613

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OHG

6ohg


Resolution: 3.29→29.76 Å / SU ML: 0.5063 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.9346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 987 5.09 %
Rwork0.2154 18420 -
obs0.2178 19407 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 150.73 Å2
Refinement stepCycle: LAST / Resolution: 3.29→29.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8062 0 0 0 8062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01358255
X-RAY DIFFRACTIONf_angle_d1.63111236
X-RAY DIFFRACTIONf_chiral_restr0.08291263
X-RAY DIFFRACTIONf_plane_restr0.01221433
X-RAY DIFFRACTIONf_dihedral_angle_d12.04841127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.460.37661420.33032608X-RAY DIFFRACTION100
3.46-3.680.28641370.29752612X-RAY DIFFRACTION100
3.68-3.960.33931390.28642616X-RAY DIFFRACTION100
3.96-4.360.27751450.21642615X-RAY DIFFRACTION100
4.36-4.990.23871380.18842637X-RAY DIFFRACTION100
4.99-6.270.26461430.21342642X-RAY DIFFRACTION100
6.28-29.760.23591430.18642690X-RAY DIFFRACTION99.79
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)
16.595515205230.274623851799-0.7571142497291.627544348251.442144407332.954040158260.621161361106-0.0439948721606-1.747187807670.180719224744-0.4887330741780.1007952837910.9668650617160.2182319015520.06737480341181.246738611550.05659101119870.1515879776880.996610266856-0.01112258914521.3028455822270.205295773-72.17611876536.947579363
27.446703249622.178005429982.691949163511.95299486307-1.56027534376.73370711237-0.7146505813410.6464102954692.736494356780.136881284979-0.131784272433-0.957210041362-2.031100627780.9518423217880.7287121856561.0097243439-0.191917387375-0.2081019097630.706501976443-0.00184800743281.2048076665869.7532826869-50.350573360937.219665151
36.782129382211.23208460761-3.431893476046.156811941621.329445391727.59763975779-0.7578737774990.705817000223-0.7286180898480.2931281966580.1287211134570.283818370816-0.01105976773531.330069310790.5019773817210.97045261304-0.278654927620.05448713022611.27033321018-0.03681885885181.1379940339483.7181203583-64.797654449732.1846605816
49.71083584151-3.51717283463-3.234732002316.072369676321.760734336294.140194250950.2673319854070.347877430939-0.404089302139-0.473468177819-0.1573074643120.340303760705-0.4055839649880.616383094026-0.1718229680010.854081592196-0.1538202286710.01504921526040.874156162666-0.08801937836640.70467733774871.5420011146-58.261240895232.5707413186
53.82924753174-3.023342359260.4665696600214.722281318560.8007839409261.628733579160.0402357798921.24448489911-3.05281198343-1.07065777049-0.211664788839-0.4278629672620.0402878352138-0.622569374856-0.007755855310711.03879815721-0.2186615368080.01777626054651.17359923351-0.2959171812581.0922426437671.8139203712-68.180881526724.2749701822
68.60773030614-5.9092328028-1.347105162489.46804272678-0.7377260575854.035352473810.240536427710.47281092603-0.8422126623230.625560159744-1.035955204931.22583301875-0.2832645003860.471859893380.7910415584650.834896138335-0.356377999231-0.1379272810130.971644778561-0.05509444068960.99996212833657.932040252-65.304038915833.3772867883
77.3991975334-4.40408704071-0.7192119135597.489206937723.268890210277.16829000162-0.4241203948850.739514452155-0.28644426329-0.2238665159850.022753772741-0.1392688821170.4766187661940.1670095655720.2195932826630.682930444111-0.17258373240.05524426286170.684370976506-0.07756917519120.73863435970966.8143056048-61.661609010233.5029325112
84.579387672180.2170616576793.256650564471.385263504542.250256816177.65238474214-0.2496472190270.08665780367590.624028507868-0.4749614944171.07728775995-0.617632078969-1.613131915370.158167886643-1.183882576091.67982775941-0.187640721273-0.2519996022071.038026620980.2115416904182.2076565241942.2597613784-27.328905728430.0666000359
92.06134774451-0.998444425844-0.134573644436.33911462693-0.296212580774.672477612790.08157177738680.6767803348560.646876970301-0.2666518348680.175972685379-0.124091455271-0.460563747275-0.570780865416-0.5000712981520.948971529097-0.0818738482381-0.07322429125151.192411157230.4407435807891.5592368006243.7077944292-39.020385143328.1400652062
102.132590674440.540577822292-2.357786146893.74226431255-0.004254460778077.23934876071-0.1911277667040.7538479131341.91349269315-1.05305022249-0.102961939991.906112758610.0660900841318-0.9419101608360.3259336583471.27257400198-0.293882890676-0.4539808453561.114665761920.2233543593272.3017099932443.908276834-33.901207856426.0846912061
114.39600875159-2.18907071561-1.072427461183.42133560051-1.047061752063.089275468820.419250740483-0.2904508196790.20732364077-0.9508465288770.5756169846210.409455904988-0.641104042751-0.993743536876-0.5861167378121.48163767192-0.15215134646-0.2834721944480.849358367463-0.03767726827841.8193841730737.4673365821-31.007887998630.7135759445
123.993560467521.855919880171.132674585014.81109159968-0.303669240790.134674451871.4933250596-3.872453188731.1762168052-0.664180164708-0.1006998472611.581727452890.2764425162471.363047708390.1647876615391.31975723450.2475702309360.3435317104672.496643874220.7622233142082.748444551162.02105821656-20.444245811733.4129250792
132.273084014863.115608272841.151254916830.8506591326011.693443727175.620214696410.703942277422-0.9841613097340.5368026612740.4396206873161.282145586941.490118307240.862810375806-0.621504378547-1.390619911241.375294812760.5917921300610.2554116536371.841682750620.6540041921033.1051827552610.2038116564-19.786879142332.7707602051
145.37549555922-0.7844425726452.905967705093.275831804491.752430159726.67157380814-0.614421398511-0.5629116366580.6022561217270.4698733670441.062929979921.09610453128-1.41852668059-0.991455280463-0.7997911337781.388903647950.1385818152160.5178201494711.548551805190.11460131193.0399750452916.304255807-12.865364893337.1533340715
154.74958795317-2.482984076651.873862360912.536643838771.615821103262.294058473220.67243715065-0.354655701630.278842297635-1.431818348381.342217817251.207797890150.158736148809-0.854590307405-0.007246286959471.91022077342-0.05293904166160.1850507093671.409754902850.4353099401062.6640574851620.5365701467-24.081660028926.747208762
163.32732248506-2.99652827047-1.845969979212.382643489561.573361479230.7971737044490.232350622226-1.348139884660.7585862164220.7012664842270.7277067328883.69556557464-1.315374322430.534213256690.1001529926291.498057101730.2889883758260.5605968379343.202740154670.2045670948294.4702738593-0.0172857471858-13.443713209344.3707945195
170.1157073247740.588953254660.6139671253171.275583087092.689464625034.322392443081.22963652934-1.77898914550.117517825705-0.675396535382-1.734349880151.33180475008-0.0992302323555-1.4155239406-0.198363705791.640319057330.1399870117080.1964097284642.357469158420.4579078727513.711456214389.46463731477-9.0306605831630.3726817975
186.94834484940.2449006255650.6117049861927.845543971690.9552253283727.703793984150.16071677022-0.7084571768140.913433782634-0.0261865917843-0.1267317544610.690040905564-0.231151928872-0.2772795474330.06217657891460.687811156895-0.1326184939110.01407275264520.719253045961-0.1164253992751.2569135955733.0716628969-50.590491106741.6819192406
194.49868367053-5.703489568012.113008923541.13087376835-1.274527174994.952811973490.234610634694-0.620808487530.544955970917-0.6431466168761.249461048060.666028864758-0.184611805045-1.64898481151-1.46568555791.50625323713-0.34092707673-0.1656763361221.847324894250.2065382929482.645807669637.74122441087-30.603994360131.5677391201
209.95741267029-0.1361688187650.3843610959546.88685731720.4269411753057.91619428535-0.0702817515086-0.8976152760710.2610627976421.141361604570.211432671761-0.672478967090.5350539100650.0913056399306-0.1379778023730.8844289533640.0172156635093-0.09239720205070.711837541690.006138055901190.55602013432690.0463962913-50.664447903653.6306585407
213.58141007072.41519957426-0.2718565964458.975239175622.499803282386.160375057050.308754794856-0.515591883132-0.8544209374291.331656324950.01695284034770.06301167125940.9068341833840.424293705601-0.392383876610.964440660006-0.034515015799-0.06050111769860.8308823843140.08321633087890.58966676313791.2406435154-55.478825626255.1589858477
229.3347101562.056996125573.158150485744.794110699792.490615504544.25437104414-0.0273463182927-0.4281468245940.06454094947590.5177671282140.348307039853-1.359979739760.206758410940.691036190329-0.3882166096191.101787635110.15150921908-0.0222840987311.019735318360.005092762287460.913826518345106.392025437-44.94585920952.124866946
237.46675217385-0.176288222591.880497160186.01206673421-1.396979635833.9411210546-0.0977142139052-0.545504017575-0.1977617134690.8737799988820.925562995631-2.109298742320.003767118745180.540387156032-0.7881747895771.112109098470.157343048718-0.2789986987711.49728540644-0.5669877674391.82374707716122.125955666-38.680806482159.8016389581
244.925565282970.4457509454931.343224092383.052847223794.289055036175.709160064850.2270884614270.2678445279240.972947206223-0.1735734587820.724525658816-0.727318286927-1.067084714711.80653000365-0.8884571277790.967945539743-0.1570695618390.271007571181.79706228088-0.2336873877281.18604266517103.46369641-44.404211031930.4136624801
256.66185601601-0.357088483194-2.338443927935.390714013071.544736401128.70657195562-0.204273222290.9288679499680.483177281739-1.562020245030.302857776256-0.661981255491-1.278369212520.514598925852-0.08312832358461.26581770344-0.4231300819570.1698385157181.237420522230.1062790245530.81735454123793.41993322-42.365621055633.358209191
268.078054652962.69846320627-1.164353879373.35848382669-2.173702568842.024673822740.174340680832-0.3626941671860.3814902455190.0343202699559-0.0717759518642-0.496747792574-0.8835534283230.646631956219-0.2172620739871.30784443346-0.2295194109750.2178312690941.35274336272-0.1697983492640.688903472305102.088304288-42.577150012836.1854526037
276.61805375516-2.322557639022.265256241915.20687411109-1.405246665610.726344663880.565158085411-0.719815683480.9101006207242.101181170860.799670606189-0.502042361181-0.335246438131-1.41959824908-0.1841862978781.454526157890.0641040804772-0.597431758991.9861417221-0.2361737073931.97913077694133.534134046-44.329172273357.5853440269
287.60254649672-0.962971930799-0.398204146446.32071548166-1.118890664140.424058802224-0.610984131725-1.442728254041.300313724720.5031295535030.66166664715-2.19216794861-0.286316927946-1.32506146823-0.2688323023941.32760422806-0.1993715923420.2236858576911.92211120343-0.5261259536821.86663665708127.927002987-42.46250565348.4428823969
293.624092994333.13701444221-1.414374502063.10367928290.109678918464.53292300619-1.31848375951.08613330551-3.56191178414-1.843402377692.40682863651-0.8855095614910.9829923345191.41788152263-1.117062699291.79277151545-0.1436291044590.3128693996332.47284174977-0.9493155443131.68333208804127.177976133-45.966618116839.3775366807
303.388395751231.85243397256-1.85644918251.09318544194-0.8332043690582.39391884493-0.7776913644540.2545702512190.0364363547271.302191616651.63266370353-2.184507816380.6388582780690.556948802395-0.4963849877351.34209125230.0721608978985-0.3418777721281.94157737067-0.7879334909382.20256003123123.99072865-44.38337486544.0298425739
314.31495435808-2.97965697111-2.513920739252.51462059650.647302356390.8585300435651.948869274872.12135897242-1.25170066366-0.727062037341-0.856984478522-0.5070009462731.621971111.95845017456-0.8203914684051.317507518380.19612946346-0.3542134350571.82381356942-0.5177799636482.45696679629134.194832464-49.87748814350.0822247104
322.30930395765-4.503726413662.693729227199.49550078942-3.733669874247.05103261613-1.14877274443-0.178224630293-0.369813999720.0903861316276-0.144382688078-1.872391460040.7368533062791.451316858671.29899090221.400372063470.1350622462680.557058278482.37580604515-0.4010858319642.29290197008137.555523022-42.011344080543.3987394257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 561 through 583 )
2X-RAY DIFFRACTION2chain 'A' and (resid 584 through 594 )
3X-RAY DIFFRACTION3chain 'A' and (resid 595 through 607 )
4X-RAY DIFFRACTION4chain 'A' and (resid 608 through 635 )
5X-RAY DIFFRACTION5chain 'A' and (resid 636 through 645 )
6X-RAY DIFFRACTION6chain 'A' and (resid 646 through 676 )
7X-RAY DIFFRACTION7chain 'A' and (resid 677 through 734 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 18 )
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 61 )
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 90 )
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 113 )
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 126 )
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 139 )
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 163 )
15X-RAY DIFFRACTION15chain 'B' and (resid 164 through 179 )
16X-RAY DIFFRACTION16chain 'B' and (resid 180 through 190 )
17X-RAY DIFFRACTION17chain 'B' and (resid 191 through 214 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 109 )
19X-RAY DIFFRACTION19chain 'C' and (resid 110 through 216 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 59 )
21X-RAY DIFFRACTION21chain 'D' and (resid 60 through 95 )
22X-RAY DIFFRACTION22chain 'D' and (resid 96 through 135 )
23X-RAY DIFFRACTION23chain 'D' and (resid 136 through 216 )
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 18 )
25X-RAY DIFFRACTION25chain 'E' and (resid 19 through 75 )
26X-RAY DIFFRACTION26chain 'E' and (resid 76 through 113 )
27X-RAY DIFFRACTION27chain 'E' and (resid 114 through 128 )
28X-RAY DIFFRACTION28chain 'E' and (resid 129 through 139 )
29X-RAY DIFFRACTION29chain 'E' and (resid 140 through 150 )
30X-RAY DIFFRACTION30chain 'E' and (resid 151 through 172 )
31X-RAY DIFFRACTION31chain 'E' and (resid 173 through 197 )
32X-RAY DIFFRACTION32chain 'E' and (resid 198 through 214 )

+
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