[English] 日本語
Yorodumi
- PDB-7now: Complex of Nucleoporin-98 and nanobody MS98-27 solved at 1.85A re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7now
TitleComplex of Nucleoporin-98 and nanobody MS98-27 solved at 1.85A resolution
Components
  • Anti-Nup98 nanobody MS98-27
  • Nuclear pore complex protein Nup98Nuclear pore
KeywordsNUCLEAR PROTEIN / Nup98 / Nanobody / complex
Function / homology
Function and homology information


structural constituent of nuclear pore / mRNA transport / nuclear pore / protein transport / nuclear membrane
Similarity search - Function
Nucleoporin FG repeat / Nucleoporin FG repeat region / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Xenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSola-Colom, M. / Trakhanov, S. / Goerlich, D.
CitationJournal: To Be Published
Title: Complex of Nucleoporin-98 and nanobody MS98-27 solved at 1.85A resolution
Authors: Sola-Colom, M. / Trakhanov, S. / Goerlich, D.
History
DepositionFeb 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Anti-Nup98 nanobody MS98-27
B: Nuclear pore complex protein Nup98
C: Anti-Nup98 nanobody MS98-27
D: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8389
Polymers62,5034
Non-polymers3345
Water7,170398
1
A: Anti-Nup98 nanobody MS98-27
B: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3714
Polymers31,2522
Non-polymers1192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Anti-Nup98 nanobody MS98-27
D: Nuclear pore complex protein Nup98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4675
Polymers31,2522
Non-polymers2153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.800, 149.810, 85.090
Angle α, β, γ (deg.)90.000, 133.089, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-1075-

HOH

21B-1102-

HOH

31B-1103-

HOH

41C-366-

HOH

-
Components

#1: Antibody Anti-Nup98 nanobody MS98-27


Mass: 13919.286 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pMSC130 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express
#2: Protein Nuclear pore complex protein Nup98 / Nuclear pore


Mass: 17332.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: nup98 / Plasmid: pTP290 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: A0A6I8SCP2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 84 % / Description: Chunky prisms
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 34% (v/v) PO/OH, 0.1 M Tris-HCl pH9, 0.16 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 20, 2018 / Details: Dynamically bendable mirrow
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.85→47.83 Å / Num. obs: 88309 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 45.5 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Net I/σ(I): 16.9
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 6453 / CC1/2: 0.395 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E0Q
Resolution: 1.85→47.83 Å / SU ML: 0.2808 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 4411 5 %
Rwork0.1838 83773 -
obs0.1851 88184 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.54 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4393 0 17 398 4808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724520
X-RAY DIFFRACTIONf_angle_d0.8966127
X-RAY DIFFRACTIONf_chiral_restr0.0565645
X-RAY DIFFRACTIONf_plane_restr0.0054797
X-RAY DIFFRACTIONf_dihedral_angle_d3.42182844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.4781430.46642697X-RAY DIFFRACTION97.29
1.87-1.890.39121460.43512762X-RAY DIFFRACTION99.01
1.89-1.920.3781470.37862797X-RAY DIFFRACTION99.43
1.92-1.940.35331450.36412774X-RAY DIFFRACTION99.42
1.94-1.970.36681450.34512767X-RAY DIFFRACTION99.83
1.97-1.990.36041480.33852797X-RAY DIFFRACTION99.83
1.99-2.020.35521460.32342779X-RAY DIFFRACTION99.39
2.02-2.050.31831450.29232763X-RAY DIFFRACTION99.66
2.05-2.080.27991480.28512809X-RAY DIFFRACTION99.7
2.08-2.120.28771480.25512809X-RAY DIFFRACTION99.8
2.12-2.150.28021450.25322752X-RAY DIFFRACTION99.83
2.15-2.190.2511470.23552799X-RAY DIFFRACTION99.73
2.19-2.240.26211480.2282795X-RAY DIFFRACTION99.9
2.24-2.280.24111470.22442795X-RAY DIFFRACTION99.83
2.28-2.330.21661460.21432768X-RAY DIFFRACTION99.93
2.33-2.380.2881480.21222826X-RAY DIFFRACTION99.93
2.38-2.440.24441460.21652772X-RAY DIFFRACTION99.93
2.44-2.510.24611480.20622812X-RAY DIFFRACTION99.87
2.51-2.580.25121470.21072787X-RAY DIFFRACTION99.97
2.58-2.670.23981470.19892792X-RAY DIFFRACTION99.97
2.67-2.760.22451490.19562823X-RAY DIFFRACTION99.97
2.76-2.870.22941460.2012788X-RAY DIFFRACTION100
2.87-30.24831480.20212797X-RAY DIFFRACTION100
3-3.160.21881470.20282806X-RAY DIFFRACTION100
3.16-3.360.22881480.19142813X-RAY DIFFRACTION99.97
3.36-3.620.17731480.16862801X-RAY DIFFRACTION100
3.62-3.980.17531470.15322800X-RAY DIFFRACTION100
3.98-4.560.14641490.12642821X-RAY DIFFRACTION100
4.56-5.750.14881480.12352828X-RAY DIFFRACTION99.97
5.75-47.80.17791510.15142844X-RAY DIFFRACTION99.73
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)
14.468162419110.7471495478212.749939610631.26576621299-1.42350733045.534655800530.151497559527-0.00370601206089-0.879021269714-0.3985787129050.03842219063161.118788846590.133719291698-0.588323516572-0.190388851480.332448657863-0.08784759716460.02626034380740.484108626592-0.03085718798240.463643680512-29.163487441654.758882758153.8254547519
27.99441645589-3.796884222972.911954719482.72842806764-3.54716495127.332376741850.156257330664-0.75124534352-0.755526290096-0.2648935428340.3789023525710.8537730871730.101062901267-0.730761327755-0.4208361922740.329857278179-0.0298569160714-0.003435963443610.4223230244030.00857998358020.534844683913-25.776837030453.853332850358.3948688254
38.90871803774-2.444322123374.348339130822.87217932183-4.457910518158.847136396290.540011336958-0.0881033035746-0.857133831953-0.173590540509-0.2749744671330.3726503814710.6381076005120.08710988349020.1033628644310.434115738180.0170757753472-0.06936417974930.308836416529-0.04177407300310.481560207532-16.182229141453.187996834553.8139866549
42.383948101573.611393552563.398779061867.409786525022.867506500728.30700101353-0.1069194748150.912724917881-0.239127002316-0.9268890466820.3397924481860.363951715533-0.105767746854-0.465292024769-0.4861668792830.4622966074810.0677524448957-0.09010578362740.746798562142-0.1068051962330.443913037722-22.122380747459.402223498144.4395147413
52.15120041410.314582922758-0.4488969112320.217668669640.05389192822453.549360110150.06977905105570.1382564925520.0369816570236-0.001910282641260.08087346952070.218211647861-0.1326235712360.0930689160207-0.1304627835440.4795015288030.0700749091021-0.09814394416860.365851098161-0.04213801416480.527141224109-17.929989522563.922745667455.7550956737
65.693769191-6.002025462844.518303283697.38862500782-6.335173096626.393269462350.17577263266-0.0720736540203-0.0259104392881-0.318511175598-0.2465172544580.1442242757080.14400323259-0.0882115677550.04056964774010.398981008011-0.00391079004586-0.006895636757510.393062993824-0.02649115569870.540155218891-23.147732376656.712553822661.2681265974
79.84579869144-3.159888117050.1959420780357.768627429735.148073509875.399916679390.1993391822021.416591178690.25799031709-1.1433704466-0.3915810760320.420671723992-1.35339867856-0.6689586566490.2320093315430.5822996284550.0957999369159-0.07365871424810.6925656586480.01155177701730.484977023352-32.446611524667.531421534447.8071150899
82.58432472493-2.01836419719-1.231600650133.36891080247-0.5940370336342.244540512630.008936306274020.455967989538-0.576441017158-0.279687821345-0.2220180993260.241061759457-0.154992217598-0.1579797712220.1795628981280.3737287023230.0250499263303-0.05409053554110.341203038779-0.01982289389720.365906198912-16.205671292255.471294059849.4283626546
95.805229928812.914663938612.25499117296.24997667538-1.343151034858.31243986140.1989355761440.1507239790980.388944897465-0.123478547373-0.327265215162-0.3262029722730.00584297226567-0.2187589405190.2925261341220.370735385050.0325452848230.003026912463560.4101451754990.01040652583450.449275020576-11.203665164759.341002220446.2869225158
103.34235477037-2.64846081093-0.8533759911887.443866107410.2519250277572.707500920350.1554686145980.0281775860618-0.718808624005-0.590084749409-0.1589989294151.18646352360.156958843336-0.697903023932-0.0003182031492850.3923444034950.020567131492-0.1101801163290.462300509104-0.1092048546620.478056028242-26.702941805154.535340765848.4306593681
110.6651190670040.9569190083691.084208439024.405836189693.374876539453.639243948980.146820762195-1.110936468430.6634344462181.22239263036-0.605440911058-1.10874422677-0.344803336974-0.244623428840.4457388757180.512829088296-0.210183270186-0.06138286594030.70271216983-0.04109645176160.6312859941914.7961163324481.774984736857.4459587919
127.81209096107-2.693540446083.2701899782.22202306973-1.648260171485.25973769811-0.0752164442588-0.1432217317740.9635714182920.18801645627-0.279926277121-1.29693285359-0.374121234240.3799132026410.5673167910280.493093344623-0.0766315234652-0.007403093508210.5258739990270.0782439957240.6141920886049.9672261451780.484361626450.4484898012
137.50221745810.01197686034822.245871648893.6859718131-0.7660997208163.157887767180.135054345251-0.2461396918820.341114339868-0.0686151613214-0.40425689476-0.312468075320.01942518882870.09742366379220.3183640348310.336133293387-0.02664676282350.01231153132580.4012007481420.03104013319310.3237663999672.4381152747377.636419291948.509183543
143.72146449252-3.576671708191.962252433948.6663526755-0.561313519092.66874218451-0.0286856131973-0.365589714687-0.04246557160050.134318382186-0.2434462515610.199533328136-0.153399051286-0.1948096994150.1389017427550.401392112989-0.01833408703420.02416591638010.4274184148010.07088625179590.30478296758-6.6247573385570.763651309349.5205467228
152.69155132997-3.796218804183.150313996986.89503538768-4.038127031163.488361352360.02111651245960.310392744707-0.05242951075770.457479969277-0.130349489360.0605064591105-0.1512460342260.08611838815030.04391910985360.3854641681370.04580626319070.05251860296760.378240488752-0.004965696468960.4319772838117.6491293011351.306212409452.9552186306
162.07692343949-3.646474529842.70435186897.57513565383-4.186524441777.248401277820.599201874911.03658218818-0.398093104854-1.10390164621-0.515459313118-0.2212052857250.5008942318120.748978104812-0.0102906573470.5019257197210.1279918721080.06803901574780.526099069681-0.0358999838840.55217620065112.741661324343.727675011344.9331875293
175.18076872721-5.14758525621.57852173735.12406254301-1.864413312696.05854132890.4308162633990.950997645721-1.29631947575-0.873292026878-0.1446422322550.5440735581530.4926695254450.243327174327-0.3232971751520.548779172510.0272424434271-0.04525912340590.452848203316-0.04860879795850.5463832533210.02734269476451.405266783342.1710980468
186.13862688944-2.63241636003-0.8822836354288.03072071558-2.199306211512.458661493120.07562064138660.4186239678330.112202692719-0.495090063871-0.505584173525-1.091102376960.4676214250250.785566055370.2791742351350.3956561120610.04926360762130.1303854243780.4405409817440.04743679632090.4403038053337.9680039711756.620400614342.3869819165
194.9196827554-4.757166237054.550861635334.80168532659-4.585593769737.662158814860.6058714764440.700712156897-0.238036004121-0.553896337808-0.5236553974410.03727099884220.2649001505240.0990322835354-0.1537671110560.458372693832-0.0100279673050.007084816920650.3995911080.07268093789360.435091455527-0.50486742819163.037400898943.0834576263
206.36175339994-3.942647816911.802317019847.26565536167-1.914949352658.09843878883-0.01217639306720.4098056313711.397044950240.0571409950886-0.185123476986-1.06610798467-0.7763353765590.6151025488890.2880214430640.317384469618-0.1460004638340.02554755708510.4998037700670.1188552290940.580207499662-10.54814356599.012264087134.0462842571
216.467784199090.938738161654-4.355334694695.31048052715-1.934068344297.623066099150.458510509696-0.2141921367832.384367836270.6055596541260.186327592345-0.863145919416-1.40929343805-0.160968120712-0.6372882080560.738457045705-0.0209804671529-0.1503008557810.511747618777-0.03829865187640.943399380332-17.2781416452106.92041478441.9050881913
224.33259138867-0.867002564204-0.8330679229920.918845239986-0.01103243322833.61918629861-0.0617538134935-0.08651230857780.2712508476650.2133638137650.0714684779926-0.203740331496-0.2044813760930.220960300911-0.01118614388880.4587300602910.00975797880592-0.08420579951280.3159010458830.01606349166360.456155835443-19.484294766894.707725230840.9109422306
234.24414050692-3.0345307442-5.233749712423.081708699413.840842346287.24237581522-0.2999990828230.3142723539240.3874277717910.08939114991930.291613650905-0.191783741843-0.2728552172940.201641820057-0.1367034463420.474518595739-0.0389366263012-0.08147878194410.4490083463290.04731849781610.449435181791-17.119758573197.784459467132.3089144622
242.26730973480.3151962197061.930354640850.266202838002-0.6299042520425.23371779006-0.265242380996-0.872825376693-0.1474682908642.671983226410.230518957551-0.0833458720125-0.007978588147070.05336414039150.09347505630860.8470505696960.112642379241-0.009486224429450.6635666222710.07875536906160.314903264084-31.289615140583.957113037369.9242171731
252.0950858874-2.443698799741.484802022462.83540059725-1.862135329642.65136064435-0.382780696692-1.08172951938-0.4022062155390.9798656992450.3552056520921.0988950594-0.0278124543473-0.51418733972-0.1765230508850.7346620837410.1738686625390.2099241973220.6668240587160.1000876609660.552511261376-39.720436771982.326121937768.0041736612
262.10550895579-2.528214250980.6566817284087.54035519025-1.69246032692.78790407708-0.236341231209-0.349233633669-0.4597857823440.6553205870250.3405326730680.7463963505260.19528207894-0.00600938612845-0.1158212486150.5050993490490.0899654212040.1016417467890.4861143290880.05318400416360.487038693313-36.944725717476.27830463162.5965729603
273.19933805961-0.6264677429270.5603433152536.82781906311-0.0316550123893.950342242870.122684370771-0.136728686559-0.162889884242-0.110613343459-0.2980442432210.721966892616-0.1256187984240.05095590192260.1994550990210.4057558524020.05500685783960.05592320794430.4216971072180.02301631267560.411560114999-36.899979616684.193916036758.9735882678
285.26558005337-5.68121759285.690427249436.15231741409-6.096920286076.18087833788-0.221090987665-0.3954069190530.7357472232530.839204313846-0.125496911375-0.487756540534-0.8138737576070.3296138272370.4604836548840.593473436654-0.014417581405-0.04338208130580.486932874033-0.01024412260540.354726114474-29.997730597891.447992366961.04748394
295.22760308527-0.742807507519-2.447687611847.400374963363.320451688855.601863850060.0498702368353-0.28426001635-0.2843024759360.0118261869622-0.20803565211-0.2769862959390.03638816029650.4020508816550.12635857980.4171596948790.0220183754015-0.07445431656650.3857017319880.06125345396680.350449704541-29.069404257287.427703904252.6723492844
300.729894309623-1.41701665828-0.1989762989345.985175693562.486652522461.155228988390.02712781555710.03364668868720.1220154957550.370500397202-0.119288841004-0.1081091955360.108191670597-0.01889432578310.0991548293060.4092733252250.06177188454490.01255527144570.380769446648-0.0190861207080.495449339112-42.2171591086108.19900562655.4103200576
315.86758880005-0.2684307111081.686485440291.99524600572-1.63493496391.698429100720.02213541966030.4366653629050.490195605696-1.00138467916-0.09457405785421.06719982869-0.0866372138065-0.8630552244460.1810322236320.4109740821910.118646497553-0.07058954190830.457689831631-0.04155696370660.622248336392-51.4054790218112.15044175748.3874517639
327.14188390805-6.12405620017-2.883162104428.439355808562.598923817426.468431553280.4420773653440.57400166058-0.167389985168-0.238777417927-0.382645661820.369460286628-0.338022096226-0.3758080439390.004542050341420.4505962660320.0657088508834-0.02501811897330.375600022147-0.06518899540320.389341946558-43.532894702199.68483290444.86400263
335.05360206819-4.92319764858-4.210234012684.789639766024.026578664487.783788198770.1702966221710.394473660061-0.311176402480.100098842989-0.3315814586420.4246347474810.0980848444373-0.3787553092170.2678885971810.4735383929220.03407019811570.005733917527390.329503763033-0.01879562364620.427707586912-41.906556218294.768499412750.5377169221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 40 )
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 53 )
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 74 )
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 84 )
7X-RAY DIFFRACTION7chain 'A' and (resid 85 through 92 )
8X-RAY DIFFRACTION8chain 'A' and (resid 93 through 106 )
9X-RAY DIFFRACTION9chain 'A' and (resid 107 through 115 )
10X-RAY DIFFRACTION10chain 'A' and (resid 116 through 129 )
11X-RAY DIFFRACTION11chain 'B' and (resid 714 through 726 )
12X-RAY DIFFRACTION12chain 'B' and (resid 727 through 738 )
13X-RAY DIFFRACTION13chain 'B' and (resid 739 through 781 )
14X-RAY DIFFRACTION14chain 'B' and (resid 782 through 804 )
15X-RAY DIFFRACTION15chain 'B' and (resid 805 through 825 )
16X-RAY DIFFRACTION16chain 'B' and (resid 826 through 833 )
17X-RAY DIFFRACTION17chain 'B' and (resid 834 through 845 )
18X-RAY DIFFRACTION18chain 'B' and (resid 846 through 857 )
19X-RAY DIFFRACTION19chain 'B' and (resid 858 through 866 )
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 18 )
21X-RAY DIFFRACTION21chain 'C' and (resid 19 through 33 )
22X-RAY DIFFRACTION22chain 'C' and (resid 34 through 115 )
23X-RAY DIFFRACTION23chain 'C' and (resid 116 through 129 )
24X-RAY DIFFRACTION24chain 'D' and (resid 714 through 726 )
25X-RAY DIFFRACTION25chain 'D' and (resid 727 through 738 )
26X-RAY DIFFRACTION26chain 'D' and (resid 739 through 755 )
27X-RAY DIFFRACTION27chain 'D' and (resid 756 through 773 )
28X-RAY DIFFRACTION28chain 'D' and (resid 774 through 781 )
29X-RAY DIFFRACTION29chain 'D' and (resid 782 through 804 )
30X-RAY DIFFRACTION30chain 'D' and (resid 805 through 825 )
31X-RAY DIFFRACTION31chain 'D' and (resid 826 through 833 )
32X-RAY DIFFRACTION32chain 'D' and (resid 834 through 853 )
33X-RAY DIFFRACTION33chain 'D' and (resid 854 through 866 )

+
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