[English] 日本語
Yorodumi
- PDB-6x04: Nup133 (aa55-481) from S. cerevisiae bound by VHH-SAN5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x04
TitleNup133 (aa55-481) from S. cerevisiae bound by VHH-SAN5
Components
  • Nucleoporin NUP133
  • VHH-SAN5
KeywordsSTRUCTURAL PROTEIN / Nucleoporin / Nanobody
Function / homology
Function and homology information


mRNA export from nucleus in response to heat stress / nuclear pore localization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / SUMOylation of SUMOylation proteins ...mRNA export from nucleus in response to heat stress / nuclear pore localization / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / telomere tethering at nuclear periphery / nuclear pore outer ring / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / tRNA export from nucleus / SUMOylation of SUMOylation proteins / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / nucleocytoplasmic transport / poly(A)+ mRNA export from nucleus / nuclear pore / subtelomeric heterochromatin formation / protein import into nucleus / nuclear envelope / double-strand break repair / cellular response to heat / nuclear membrane / chromosome, telomeric region / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Nuclear pore complex protein Nup133-like / Nucleoporin, Nup133/Nup155-like, N-terminal / Nup133 N terminal like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsNordeen, S.A. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077537 United States
CitationJournal: Nat Commun / Year: 2020
Title: Yeast Nup84-Nup133 complex structure details flexibility and reveals conservation of the membrane anchoring ALPS motif.
Authors: Nordeen, S.A. / Turman, D.L. / Schwartz, T.U.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoporin NUP133
B: VHH-SAN5
C: Nucleoporin NUP133
D: VHH-SAN5
E: Nucleoporin NUP133
F: VHH-SAN5
G: Nucleoporin NUP133
H: VHH-SAN5
I: Nucleoporin NUP133
J: VHH-SAN5
K: Nucleoporin NUP133
L: VHH-SAN5


Theoretical massNumber of molelcules
Total (without water)367,48812
Polymers367,48812
Non-polymers00
Water27015
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)85.799, 204.761, 205.833
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

-
Components

#1: Protein
Nucleoporin NUP133 / Nuclear pore protein NUP133


Mass: 48493.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUP133, RAT3, YKR082W, YKR402 / Production host: Escherichia coli (E. coli) / References: UniProt: P36161
#2: Antibody
VHH-SAN5


Mass: 12754.293 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 15% PEG MME 2,000, 0.1M potassium chloride, 0.1M Tris/HCl pH 8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.68→49.68 Å / Num. obs: 100374 / % possible obs: 98.7 % / Redundancy: 8.6 % / Biso Wilson estimate: 72.6 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 29.1
Reflection shellResolution: 2.68→2.8 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.49 / Num. unique obs: 9937 / CC1/2: 0.567 / Rpim(I) all: 0.684 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q9T

4q9t


Resolution: 2.68→49.68 Å / SU ML: 0.4285 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.6567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2614 1999 1.99 %
Rwork0.2435 98267 -
obs0.2439 100266 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.69 Å2
Refinement stepCycle: LAST / Resolution: 2.68→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20000 0 0 15 20015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004720356
X-RAY DIFFRACTIONf_angle_d0.647227693
X-RAY DIFFRACTIONf_chiral_restr0.04973285
X-RAY DIFFRACTIONf_plane_restr0.00353481
X-RAY DIFFRACTIONf_dihedral_angle_d17.43616833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.750.41691350.38076306X-RAY DIFFRACTION89.8
2.75-2.820.32171400.34496799X-RAY DIFFRACTION96.32
2.82-2.910.35321370.31467024X-RAY DIFFRACTION99.13
2.91-30.34081460.30247018X-RAY DIFFRACTION99.11
3-3.110.32531420.2917020X-RAY DIFFRACTION99.16
3.11-3.230.31641430.28647074X-RAY DIFFRACTION99.42
3.23-3.380.29551430.28027080X-RAY DIFFRACTION99.34
3.38-3.560.29221390.25296940X-RAY DIFFRACTION97.52
3.56-3.780.26771450.24397114X-RAY DIFFRACTION99.53
3.78-4.070.27431420.24837114X-RAY DIFFRACTION99.56
4.07-4.480.23431470.20347139X-RAY DIFFRACTION99.43
4.48-5.130.17741430.18887042X-RAY DIFFRACTION97.58
5.13-6.460.27491470.22747258X-RAY DIFFRACTION99.72
6.46-49.680.23741500.24537339X-RAY DIFFRACTION97.12
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)
12.35648278661-0.0843070487864-0.9498161606847.51014701225-3.765412326776.92005657668-0.1908411678880.9060229368380.420107608835-1.47204522537-0.4464308453720.124984907364-0.727227264851-0.1271208775870.3541504920981.532185499480.197185326864-0.3335192977040.9839177961640.2204384338430.8297316701329.9998922039340.7157587730.0136382696
24.126142126631.56009138047-0.9104911047073.63266825212-1.817126951076.21227154121-0.05522109538890.82681360195-0.216526656638-1.036628613050.132566289262-0.04177253387880.302089126826-0.276218995501-0.05881289364180.7414009498570.2711239597410.03304725346110.64621475366-0.03878658783290.32197910868513.896438950122.08622551739.3293762927
34.762949570620.2794279448880.5353914089748.083292652082.183002451041.708776706610.02974381613130.421955780651-0.10662916717-0.715078945213-0.254258572691-0.473727296041-0.07241997486590.2539370455330.2088424928830.587857136790.158840199995-0.05631000985760.5532027276130.1362232470710.40821727072217.055575224122.083462858648.2346459187
42.024261204673.094344280160.1434157706168.20793491732-1.800941912689.22026420303-0.0299919441748-0.0929217880190.38262844586-0.269399954022-0.201213361932-0.0964945547726-0.1250445704810.2711375752560.1809574690780.4853207320430.154680087004-0.06756490887950.466179027610.06894168754370.45388745367317.952409450537.619497924255.3181326749
54.81422092421.509252477130.9847935718957.915192826082.799141462266.11376280015-0.2091782423280.135390067096-0.262751721598-0.525062550410.02664771963690.380536651548-0.2309554933270.1119475953410.1634961575830.5007665609630.150764814991-0.01239976480050.4960119643530.003610244203860.45265265650413.7916874838-2.0154862486655.8260076611
63.810068181744.43992108795-4.923708266199.24716394672-2.612225072898.776665423460.910037280841-1.96268748977-0.6669796203320.999012512463-0.879268253252-0.758333539478-0.4671985514221.44307480822-0.1733160881750.4551498380610.142990636557-0.0571446861810.971377657234-0.07880345112990.5404202279514.2660426084-1.2996033332964.9193238051
72.168567948320.462401389178-0.1784004454683.80145682419-0.4451099703691.64677827287-0.06797885300480.0484632588097-0.107772920122-0.456245648787-0.216850084949-0.2615071761690.180455049570.1407555652710.2737953397990.5897968510510.163300459598-0.06842935096320.541239171243-0.05470357375390.60139792930116.5393594092-1.8939971731354.1623789658
82.965221154561.494265901612.880083905824.779438726290.4315547687156.420022226330.948158582584-0.478373669003-0.7218069590031.39624440747-0.390844298289-0.5834125891451.393981368270.615465021179-0.3989486092381.11517916010.0327551527865-0.2481089010151.076357369180.1666676338990.67465304465842.94950779614.49648889063119.590786024
90.2679756257730.218089100847-1.156910958426.15888110264-4.345389724596.797428116791.48701264435-0.940615365516-1.154208546210.501606426591-0.704311956087-0.7850109717691.19095116275-0.881611943331-0.3291237902571.14993256389-0.31722602661-0.5745683032131.34778731910.2081847426630.6830600571648.992593004114.1538687371128.027012115
102.55458611461-1.93563658971-1.394395881523.59537441538-0.555381324254.071046516090.126161401266-1.258663537170.4016624238672.136003203660.102410302272-0.857715953258-0.3148308217570.636952551486-0.206791911090.83164669237-0.237099196254-0.2616193514951.130629219520.08499347448120.49637998063648.610532910524.4135394619131.267042535
111.260923118060.4457415776580.1040844564827.294715399871.378041486586.283616508780.255494052151-0.8813442807380.4593310089050.539574225909-0.121106871071-0.07422392647960.0289617180511-0.105261401552-0.1047255936940.416224864416-0.0531075686541-0.08305251387550.893871543538-0.04171438481710.45270896845844.255420352628.5519092307118.522631753
124.044226148151.83043625781.618358405411.885585611881.808961981382.11657012219-0.0479104017662-0.388508709013-0.0265504872343-0.1613361860190.0317925608443-0.122657167027-0.265384516325-0.04215195085420.0323413854550.22308241202-0.0275040359722-0.0488186387960.4963700985850.04576302012670.38708915163437.411961682126.6354056476101.799652094
134.73131735959-0.417489405021.189098309855.914178592610.07243566820157.32032445602-0.064681316228-0.5068141297490.4704184171570.209456504074-0.0186128034495-0.5614181338850.1650206264330.2123557958360.08158288093130.2070531440.0208378610238-0.07410038726980.3226252921290.04571689143380.42436038823834.574316721417.0219132141101.102597948
140.570082629851-1.44657396236-0.3661721527094.064691122820.1944892783815.85821241351-0.03838083894340.137753603184-0.0747083381244-0.1368794653890.191056877042-0.452964487744-0.1128923522140.292447242917-0.153266545340.2024111345140.014307451346-0.1034458147680.520050782692-0.01925539968430.41214587117637.118070764419.622265690694.8786517962
150.9118220548230.6314921975251.690152756812.358871783361.66505824225.905403112560.141455961516-0.314871080147-0.672760723722-0.08457904344720.00965527885981-0.6923346276040.447577025773-0.524618920956-0.07869331964950.509533278438-0.0679327849428-0.1727433396170.5887384983750.1167090919690.82546608314535.81819740959.18185571364105.831238226
169.491837386173.025399417964.193577034899.01270372673-0.4572902154794.15629460798-0.6943557178111.96887269139-1.3285736761-1.89777385820.261416875745-1.241464587020.2469771383921.619346792020.2396502318970.677513526122-0.08077948670560.006009001839620.902854844154-0.09044170101690.80119993780341.76297325926.6313383298394.9821605406
174.933157056663.117442595415.48152275886.600214872543.902056927696.978821837810.595915532179-0.173965892782-0.8552743785431.49332289145-0.375740233356-0.689202291781.090482114560.365346083614-0.2157144117930.904161189135-0.0290333469736-0.4435906505130.8733583295970.1480576925570.9109539139.94078623412.56527213453113.378435499
183.83226382056-1.70880876140.7257489638159.71358680716-0.3784482435195.85811450978-0.2401456231080.703473142947-0.124035054963-0.4050356494340.1536522576980.1871513595230.4405154967320.03919684655960.07496084737520.373308162342-0.0781411128701-0.03043902653830.6251652410920.03249758146190.29878339385921.146266524527.129499424970.3905424336
196.389793761333.581745392693.137987097727.72010865776-4.099034050067.55057551879-0.396641891888-0.610374958128-1.25612628732-2.38711499308-0.47185965502-1.250855101242.353851342982.268140679560.7001990956440.715047425430.06626245648330.1145764180820.597760103452-0.02543791892190.77002557255227.4820429249.5887089222277.5840707124
200.989419742124-1.771077933450.7174104648574.96239297842-2.10408339043.74006513995-0.107758390271-0.2250363218850.09069113988840.8643584630990.03586924072920.337461129449-0.335659488947-0.001352265195070.04944170651540.145763289655-0.0403287259646-0.0920593134670.446368946143-0.01940940365430.48988517465420.021360184426.97424798584.2291351113
212.74452739277-1.66648328043-2.611900599862.05518258345-0.4120760235156.548688916150.1411341961530.114118510012-1.12448525566-0.277007774673-0.8188651231110.9087386175670.469473592197-0.1274496914470.7682995769280.366398090575-0.049444429508-0.1018277843910.4585507322950.04694680890650.75102650822816.735140905717.485104277176.7171968514
220.3611405388211.166496317170.04533859052553.876477120730.1925447303781.96148556727-0.1975165056680.2237792881910.0575615162301-0.3175779439870.2038779324850.118676005076-0.145396164899-0.214949739629-0.01664398931010.201634296097-0.00884051477228-0.0545529506770.549457556322-0.0009286858774440.5104814977920.732307493726.215697060777.7080538845
233.82337534864-5.304039809042.761330017657.26484268166-4.265981695965.344932489330.2843348954060.7318435181540.6397791900930.067405111102-0.875727548511-1.086467430550.1079915583961.158070828750.5512423326370.2679652346150.00760218944303-0.03754786218670.5392169433330.01592097119580.66964576508128.523112990724.594814539678.491500703
242.255606138410.74682603492-0.07028784025333.36561325261-0.6439053531744.253998626690.3967882637340.685602048944-1.20013333776-0.165982243745-0.0907951348453-0.5421054963630.8282424292150.0319023936188-0.2749354730741.010548874490.0897852926939-0.1932877713230.660458419821-0.2925445099671.1328250161323.0988599322-39.429537125147.7964796949
253.084384542-1.000183128860.8250198045026.321130674241.429118539354.232875521910.2273998434480.149003685068-0.915907121296-0.193103938353-0.261959597949-0.7804352675030.7616395079230.3054007228180.04857667007061.065225506890.181219280496-0.2068420302330.591249046810.02120352221351.5142968187234.098653085-47.004542621364.732625363
261.62339066636-1.91276382175-1.637737622565.63202457311.487369509798.080806215360.217473408652-0.4376379259610.0578618053260.05025944539590.0362722705241-0.3224413210120.5680629523570.383051719404-0.2770265490570.605919453025-0.0733116281915-0.1893315237420.5240941055860.03179090905920.8331661531824.8187631669-24.221220560373.6920698818
273.014595793530.4642336928062.25422921534.257072262520.58882777797.243851486410.2587051837060.110058787825-0.352572509048-0.0800739964825-0.213943759768-0.3544099516110.322002526087-0.00342776281556-0.09501348471150.4823448492730.1396260700090.02348448266570.41916882643-0.01659491020140.67036227834124.9938795531-25.074748899460.0160490291
284.09328469710.0422662247865-0.9471956348225.13146066690.4034090369828.719118606770.391029067308-0.343731268087-0.08144491515541.13201996018-0.0472457376870.00496006935992-0.2790485074611.11508799913-0.2201900246410.53035079576-0.107145419187-0.1917245950310.619079058262-0.1135550697990.8505011868331.6457293087-4.6105639282997.2832845535
295.47797629294-1.221848905553.1878299077.14673202448-1.41986356517.12131642454-0.03098293854480.320311681688-0.8078720780510.429875348054-0.17706146548-0.990550862144-0.2907903784530.5669073456940.1584897524180.461439125781-0.0040011062032-0.08818370302420.4825484751270.02705616421850.75113053456129.986726376-10.127697443986.6927271457
303.478570745990.707074434487-3.455986513377.61739552619-2.24851012837.39795499362-0.1749505316880.696292757365-0.157098405667-0.15438691139-0.01974644879280.5482432810790.527238907696-0.715152271240.1989697413390.657331187758-0.247445787889-0.08813451797560.818741888502-0.07241856365980.7644135089620.6614084961-10.947317593190.4695849564
311.08120770334-0.353775074281-1.062510249613.548402712620.9738231906477.497842758440.0297508479808-0.309879863543-0.172876326082-0.2328235094030.0338577326615-0.5352661890120.6896589983340.0469315137875-0.06762166515870.464949797106-0.0504633179174-0.08649704691710.60185216343-0.06676514648680.77597446335130.0895381175-10.425155383190.8037607938
322.66259859202-0.2098853640541.151886294354.900195853680.739305199786.4516431840.061931617399-0.00431225921920.5094534557940.574705626795-0.450497879085-0.0488014408835-1.31919986385-0.3601042135230.4189174507190.7294183542580.0196669466825-0.02211168518280.468660591485-0.02066507554450.481855220288-4.3513715709153.023819667106.323477922
334.57071954571-3.702643567612.628941063537.75016441785-5.05567720693.33430022895-0.8141108280970.2578988121181.010114951521.716753181180.136332897106-0.0667307864313-1.1506240249-0.02904321533040.5641406535571.039951550130.0630209785834-0.144471597030.732312744034-0.1448020510630.487915239445-0.24234942711459.2319940981122.148275492
345.029352021050.2573001688892.261582380248.636625001581.718266514947.70932788478-0.10290717458-0.04006281452030.3543238141730.6131378110440.136044744046-0.50682545409-0.473967417518-0.188075089159-0.02997659484220.687004145653-0.00347713424888-0.05821540068430.5445321013740.04178355174450.4744456254153.280373090943.5935859611124.992942324
351.77736218605-1.57772846392-0.558976451225.770935012162.080142799894.04878079917-0.31248158378-0.1431649420840.01053385989270.828552862980.3475821321240.11015950370.2319854906210.073272751416-0.03485364362320.350501521205-0.03303106599030.06912469381290.451201829940.03443772455510.345921269488-1.3636099662927.0716348078116.957147206
362.340401255-1.37645344117-0.1171305066275.07802814419-0.3657914914754.13834240731-0.08374136032490.0792712100403-0.2622777005420.200513852770.08068492972320.353278581154-0.186858862099-0.278169452384-0.009546784880380.237454598811-0.0508962471883-0.003701527619870.487116914051-0.05141573844390.363867941766-5.3676299288431.6852967752102.245510412
370.00484725202707-0.1694532246930.2096062018493.24802913028-3.926654391854.761390062780.233244882185-0.359999475353-1.129874884990.295743739840.5493852747671.844834257510.814555177075-1.12010662431-0.7464985164180.932170937428-0.3325659900920.2110763130960.598368015014-0.1662872919541.09230151304-5.51936074241-4.20885332061102.159776542
387.87833918692-0.7201231056853.326932738671.537538549482.51393717436.934879365470.1246994299640.427551761098-0.574294988103-0.4415626304110.0213271260431-0.3301958258141.916680128630.43746781963-0.1628866705540.983095673328-0.1176952845290.2684976767730.6026874769320.06353984934180.8278791707167.65628670177-11.9472819996106.019470256
394.658246010082.187839955363.517825972044.50023965356-0.02077679147393.48400178755-1.22715085487-0.3911711950840.360902426661-1.35211726013-0.3673761972514.141230373740.75806844828-1.480656853251.316244904430.948945405859-0.2013982164270.06608024514260.669439698629-0.2741981286311.42069446087-6.544942711734.0580554270593.1054949057
406.52484395714-3.32646567156-2.448719567865.443708841030.9750614416666.95583621594-0.465051683005-0.8344435585640.05175390502661.31291198592-0.7553549237370.5905391645090.391854588952-0.3784421317411.034826779170.464258161905-0.1767286268920.05652567550440.4754292929190.004618963139210.5684303572423.467948938131.8618788165106.902020004
419.31743918091-2.631417458823.300001976719.24395790380.3230990847383.56567131582-0.214396777433-0.08315972293080.3096116415010.665235174862-0.0651831142429-0.463580422728-0.2528536911820.1315624450440.2790999274490.357162613171-0.1648503464780.004988767332280.462574055221-0.0536917356430.4319250564717.750628713376.04391193499103.823456072
428.45926809184-1.89357438586-1.776649691524.27352984277-0.7226553086289.779559263740.284141492296-0.6303604065580.2397107402530.386827705256-0.486767929237-0.864114476716-0.7082463785930.5587044285310.2123800660750.480161431866-0.0920501971326-0.06718181771250.7217041377440.1339872861080.61769571069416.50818328210.472705479215106.490177067
435.29821868505-3.02464065984-5.539257684792.982226038332.060564913626.890779193790.6934032424042.27384204187-0.247986245673-0.771897335463-0.5735126913090.593871602625-0.09072969895530.004110556027410.0003655516323840.515662805419-0.02139826129230.03679496668090.596961453976-0.02565793237980.5316126438444.50056470093-1.0057462913994.3064797643
441.29291907687-1.080199464420.4617499492722.48760145095-0.5051326140222.16202614091-0.06736631318960.06149227967980.1922806271860.0755664713585-0.289472110433-0.1942348530440.3772033714530.08694223234750.3537704175390.520783411728-0.1385642043670.05899127997330.4889689085570.01708910687760.5089713452275.23194588992-1.65927181209104.717690464
457.61972640612-5.460044866944.502554873494.98490518007-5.761641822558.68873914337-0.419613114387-0.75064038512-0.9459054840110.8912651658680.5146991832171.047347518390.028419005822-0.817503186219-0.1644415758360.47622893207-0.1160735857580.02579563211330.511189651044-0.04506712631040.621740786931-2.147757378762.08930659708106.053538516
464.547183338631.902827438481.586621868774.46160292495-1.556784461097.378487617880.8696719914710.542342805488-1.15653520014-0.986828919155-0.293326013245-0.2740227595891.7291167412-0.5515238865-0.3133987664361.331447696680.284792371461-0.3158775159211.10940648546-0.3701128963131.04069777872-24.2527743993-11.697368578146.5789310371
473.253089930512.1002855721-1.352738997772.59857089402-1.685123970933.52568418044-0.3201665271430.5563823900130.357170238646-1.72715028504-0.06923543252240.01452713397730.104996657655-1.14634942258-0.06998942663361.959859686760.649393746108-1.440051393561.6252502735-1.052626096590.169630608526-31.4447024125-0.54794133648334.3533504023
482.690235609192.817892387371.833862211694.088007290180.1477159636144.43176119205-1.95467721780.178774069682.60080450283-1.825759889731.082538696152.10516722213-1.233413757440.1623981209230.8155129611082.158554110390.271432521503-0.9752449944641.31919750084-0.2121947470651.4297495655-35.935285886211.336449103830.4741540279
498.638865121262.217587417052.029438948057.809391019521.141649631970.542960475486-0.3169936449330.7603608682710.0336510150853-2.61758294097-0.1659628822770.4198255087570.118889997208-1.298130850090.1120186229691.527437795450.324012052226-0.5104634709551.20764346019-0.1335422174090.792561256371-27.960309319215.436414251138.10298006
503.30623621756-2.035449609490.1008660511553.57345948640.5482880027072.50857651798-0.3400569918860.470687232995-0.178461804229-0.4672922962181.238239306140.36521370102-0.86157898966-0.874437434257-0.2434191373671.735649227220.377021327945-0.9566055023741.27047846120.2597529176791.11656527527-34.128561220220.57578842938.5330486588
512.59708523323-0.3214238303371.119060345611.11072754744-1.218882342871.640912475710.0251667868735-0.22943912206-0.0105940403174-1.05861391512-0.3927877269272.17322196541-0.3308304325-0.7934440228860.2657975876920.9730037312170.412971428794-0.6143922510631.25191875696-0.3181800002951.29059625532-32.016427259116.989676914950.510963678
528.18105344632-0.6855700270163.322211493540.857756455376-1.338934350653.69495035771-0.5128776994870.1865969502341.02645812372-0.715388138826-0.05485079412250.34791622665-1.123754858980.1662031420190.5242556959310.8857871612750.200392506902-0.2930665371920.572144830715-0.1239747159920.672963596179-17.480547189219.433524306659.424831078
535.847274618411.033545489060.2214023363726.90077645706-0.2170659453286.0188336883-0.02987922937460.09685835233581.35220856842-0.558825776658-0.257721546130.339210349892-0.446124282041-0.7478929251220.271716800630.7321895906320.185493269484-0.2390825489910.614822180958-0.1320691972410.55291266813-18.893981162610.638820848757.4724989523
543.927883892381.4106325574-0.01942876829236.338939975140.720123734325.2598880122-0.25346794816-0.921003694760.6975225733860.0626955821589-0.01751691113450.669670879185-0.742357625426-0.726419994830.2450226902840.6144069951840.105567880758-0.204019093970.842904820164-0.2645696286670.604155659662-21.313361510913.849436231463.3895976057
558.570573976320.637261059651-1.475143560787.714630887720.7127308878135.797574746180.2095760562850.0909077471143-0.548876005884-0.453697981945-0.1202209685310.239429455606-0.304154332773-0.091375762381-0.2295983847580.8816956274760.271342505838-0.2685067415690.797736293995-0.2732860853010.712384475392-21.047036291.9274802906755.3230642362
564.8633921650.24787085320.7516341081276.790072458530.1605636121785.891565732620.260371085776-0.430693199492-0.4494920359840.121023483491-0.6727723907640.416650057495-0.583062011759-1.208225631320.5165840756730.4928681303560.0448630740482-0.2348105789870.85607869503-0.1386574068180.619599862539-21.2051114585-1.7929638054860.3108062045
572.91236699461.122681091012.381486754254.95497748016-1.636209669363.40867067079-0.0317852886613-0.101470977693-0.168425016445-0.289451414067-0.08239271072020.7498433765640.104801081823-1.745620419520.1321274690760.9553331437560.117408325313-0.4730411935791.22435270876-0.2814265365320.93955816863-27.1636599198-6.0675588989948.1065796534
581.649431495630.614805886930.08366995693036.2667097267-0.4707697380476.276779207130.255663946209-0.1335586041460.08403997222860.852535870342-0.0563040776015-0.864938272072-0.315630414387-0.381691353773-0.1486878103990.2590997071390.0890167332442-0.05873505700540.791730509559-0.1583877401510.492572979994-6.1770218886229.406281879984.920861018
595.28845796801-0.1456791728012.74740283876.842620663552.598531518286.647229358240.01771712160240.425710867693-0.102882637305-0.5004261704890.04487175477020.7542275258280.547498668639-0.684101089-0.1302056768670.250560929334-0.0731436899538-0.0003323230525310.779485915492-0.01992104146420.443251330828-9.4079999353721.986179881875.5338160232
604.355123134182.885390318692.356737785032.916747293763.074235303563.62804461742-0.03968360812450.660491732262-0.446865225439-0.4982981790010.1953897367070.007027515158650.3070608485450.135118812743-0.1132443342320.4388917852810.004918534610470.05588377305980.612847460941-0.04235300912390.5392143333550.12753743567421.925993820374.475030266
612.917186239623.052566975822.029845853623.171593703652.413688835633.153503716750.01936626227590.2215330541320.0330636625737-0.414383898641-0.0507475111521-0.496471696192-0.0960454492994-0.1595742695720.1006952583440.317754582740.0400739371659-0.0006549567787210.639301715339-0.08075708236880.465151604494-6.1743962647626.657221258177.4830575096
624.493665202653.897257043522.884876114253.957462084124.090164492825.32878984132-0.109460414529-0.6398226164250.804572840122-0.208525488175-0.4874718872821.801557316010.0478752958134-1.194463081370.5051683981630.409036073157-0.0215413283945-0.06264724823670.787045726173-0.06382299745660.449148105045-13.386228920622.670893917678.0185846961
632.813756686980.535162701871-0.1898154606545.61901221978-1.601232786733.42753639960.13853267144-0.474158465182-0.917403082476-0.369150498683-0.53415359517-0.33474367891.08206828198-0.2974176493750.3501920779091.54530874998-0.1605386336730.07171394530330.820068655530.2569117487630.802545488368-0.355077412932-45.2522031033112.204928288
648.754249861434.4085820784-2.601534435255.98622272188-4.097652823142.94834232111-0.456990616224-0.100029214449-1.83608210989-0.7862048235920.3638216100611.243087342991.65197797042-0.09191898645480.0670018868962.04986355176-0.3793171643670.1825260559990.7120849153380.05646656321821.43049611086-6.22071473847-52.423103415999.2538326
652.822510369961.6350011742-0.5324210457436.62862914174-2.050062737153.2862271433-0.0189142549399-0.0716731012680.183368894907-0.3091369275990.1600196723150.9722492072311.17121635491-0.49444780361-0.06284035674461.09285736582-0.287361006113-0.3571783527580.553653270520.0836572584750.996208598285-6.15892176985-32.73679585891.3818467078
666.9003918170.0820979708693-1.809184690835.72099819227-0.2593661137275.31623578265-0.1339447207170.393255762907-0.134325670401-0.231202247675-0.118098497175-0.1316929711040.568300461328-0.2314577978340.2075462850050.836917310321-0.158931931105-0.2371405387910.5433670993210.06560697307030.663041122205-3.09589066352-25.337025997196.7567185682
678.061137104770.529126557457-3.31090965262.84135389392-4.016989814046.700202110560.0500654426663-0.9999350556840.04424818564091.22845874601-0.0510455242168-0.00419555241121-0.07908937841520.210605024868-0.04162751229081.165274387980.0217128663582-0.08962622687080.6218399197190.06349047262620.8259812355011.32311527373-26.1800436056112.00570083
684.586865618990.7168483014610.4962579758432.90367190671-0.7957704556950.354709767451-0.147895893220.7069669643980.448393726773-0.5950270311750.2311582249710.240782647917-0.0972446685293-0.2171008172420.0342484181250.7297944451290.16995778756-0.2732413223210.8334916668190.106552644170.979011198351-13.2574749231-10.373273298463.5291803203
693.19086463087-1.93260222123-0.3996518475642.4346602567-1.570522105895.866230117670.15504740378-0.1303834559780.2865023544630.187193472650.1462327216920.05319406955770.390770856479-0.90591469128-0.251558395730.784670644147-0.0695768004059-0.3872662116890.6962631020180.09263569584610.853336476811-7.71023356038-13.567830548572.7534861263
709.035668449710.6851532793584.778442941024.41341112622-2.920031396747.045048502650.573051242371-0.460358013575-0.7044211441990.586667722443-0.356890065948-0.9521303992761.130007488270.7173874803620.09321017227780.7202473966910.114757532458-0.3285338829860.678418478291-0.02098593355221.16278854334.01872652312-14.074558177275.8093658817
712.926673005110.227978556663-2.651478622310.9793544425930.1213509524455.452728445450.344334641834-0.195387225540.511591953491-0.2646202359990.252601424526-0.3815433888130.5551064266410.521975919161-0.6661726254930.6831707036650.103287668093-0.3642329908550.7556244546540.08390903939250.967552766696-1.70360468142-10.987026578867.6292895872
725.58636426641-2.70058761396-1.661185470132.36509603034-1.071875697544.007858974740.1195851645140.576325345752-0.0614162348232-0.1694918746770.163527377824-0.4651395444540.5472501534030.248614771505-0.1350893880720.9608293622310.00577403450341-0.1472466752740.926776744083-0.04497477682190.938191492431-6.44301642974-19.374865226757.1828818453
732.91793107216-2.016543884-2.646165425064.52190572481-1.2955073615.83753640286-0.217206604368-0.3549857671330.1083435050820.777783237210.384804088436-0.1303462432680.3860268242240.947344997272-0.2039196515160.8995529742110.074490184416-0.4379229745120.843553882228-0.05721762590860.954093950439-9.41595893271-13.834514819277.2181979572
743.43928443448-1.880194815422.560950320541.12015606906-1.988779955227.89553613192-0.639491911528-0.559672899891-0.173095089360.7534894587020.2914834296680.6721630873220.00999570273228-1.892851367510.3590802112261.049051278170.0981098902399-0.3750607542760.733838860338-0.09286409028590.793584857868-9.81786228899-13.95782193585.7792291539
756.99982570127-4.66238319377-6.19500886585.679316088865.056593171715.81066388404-0.2264190617321.585553256620.231324963875-0.0119470723293-0.549183822580.06307548116861.11971660375-3.443751928940.793548300360.985033501364-0.213422853466-0.4870556894361.338358963320.1044275562591.01729905912-15.839431869-15.82827508763.1330354905
763.137328741962.04275976455-0.1962805429241.382875035630.634358082196.213187508310.1721730275020.2625249762021.20983909677-0.937254044206-0.2489052933710.354216230344-0.755063256577-0.6973117292180.1433285249851.387319808920.23948985747-0.2350968433410.6677517651070.209560385821.0252117069814.105701793750.429809475345.9993954307
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'G' and (resid 169 through 279 )GG169 - 27965 - 152
22chain 'G' and (resid 280 through 331 )GG280 - 331153 - 204
33chain 'G' and (resid 332 through 382 )GG332 - 382205 - 255
44chain 'G' and (resid 383 through 481 )GG383 - 481256 - 334
55chain 'H' and (resid 2 through 65 )HH2 - 651 - 64
66chain 'H' and (resid 66 through 75 )HH66 - 7565 - 74
77chain 'H' and (resid 76 through 117 )HH76 - 11775 - 116
88chain 'I' and (resid 61 through 103 )II61 - 1031 - 36
99chain 'I' and (resid 104 through 163 )II104 - 16337 - 62
1010chain 'I' and (resid 164 through 197 )II164 - 19763 - 84
1111chain 'I' and (resid 198 through 279 )II198 - 27985 - 153
1212chain 'I' and (resid 280 through 331 )II280 - 331154 - 204
1313chain 'I' and (resid 332 through 357 )II332 - 357205 - 230
1414chain 'I' and (resid 358 through 382 )II358 - 382231 - 255
1515chain 'I' and (resid 383 through 420 )II383 - 420256 - 285
1616chain 'I' and (resid 421 through 443 )II421 - 443286 - 308
1717chain 'I' and (resid 444 through 481 )II444 - 481309 - 346
1818chain 'J' and (resid 2 through 25 )JJ2 - 251 - 24
1919chain 'J' and (resid 26 through 32 )JJ26 - 3225 - 31
2020chain 'J' and (resid 33 through 65 )JJ33 - 6532 - 64
2121chain 'J' and (resid 66 through 75 )JJ66 - 7565 - 74
2222chain 'J' and (resid 76 through 100 )JJ76 - 10075 - 99
2323chain 'J' and (resid 101 through 117 )JJ101 - 117100 - 116
2424chain 'K' and (resid 61 through 140 )KK61 - 1401 - 54
2525chain 'K' and (resid 141 through 312 )KK141 - 31255 - 177
2626chain 'K' and (resid 313 through 357 )KK313 - 357178 - 222
2727chain 'K' and (resid 358 through 481 )KK358 - 481223 - 328
2828chain 'L' and (resid 2 through 22 )LL2 - 221 - 21
2929chain 'L' and (resid 23 through 45 )LL23 - 4522 - 44
3030chain 'L' and (resid 46 through 76 )LL46 - 7645 - 75
3131chain 'L' and (resid 77 through 117 )LL77 - 11776 - 116
3232chain 'A' and (resid 61 through 163 )AA61 - 1631 - 66
3333chain 'A' and (resid 164 through 192 )AA164 - 19267 - 91
3434chain 'A' and (resid 193 through 266 )AA193 - 26692 - 152
3535chain 'A' and (resid 267 through 331 )AA267 - 331153 - 217
3636chain 'A' and (resid 332 through 481 )AA332 - 481218 - 367
3737chain 'B' and (resid 2 through 9 )BB2 - 91 - 8
3838chain 'B' and (resid 10 through 22 )BB10 - 229 - 21
3939chain 'B' and (resid 23 through 32 )BB23 - 3222 - 31
4040chain 'B' and (resid 33 through 40 )BB33 - 4032 - 39
4141chain 'B' and (resid 41 through 58 )BB41 - 5840 - 57
4242chain 'B' and (resid 59 through 65 )BB59 - 6558 - 64
4343chain 'B' and (resid 66 through 76 )BB66 - 7665 - 75
4444chain 'B' and (resid 77 through 100 )BB77 - 10076 - 99
4545chain 'B' and (resid 101 through 117 )BB101 - 117100 - 116
4646chain 'C' and (resid 61 through 86 )CC61 - 861 - 21
4747chain 'C' and (resid 87 through 140 )CC87 - 14022 - 55
4848chain 'C' and (resid 141 through 200 )CC141 - 20056 - 83
4949chain 'C' and (resid 201 through 227 )CC201 - 22784 - 110
5050chain 'C' and (resid 228 through 266 )CC228 - 266111 - 130
5151chain 'C' and (resid 267 through 298 )CC267 - 298131 - 160
5252chain 'C' and (resid 299 through 331 )CC299 - 331161 - 190
5353chain 'C' and (resid 332 through 357 )CC332 - 357191 - 216
5454chain 'C' and (resid 358 through 382 )CC358 - 382217 - 241
5555chain 'C' and (resid 383 through 412 )CC383 - 412242 - 268
5656chain 'C' and (resid 413 through 454 )CC413 - 454269 - 310
5757chain 'C' and (resid 455 through 481 )CC455 - 481311 - 337
5858chain 'D' and (resid 2 through 22 )DD2 - 221 - 21
5959chain 'D' and (resid 23 through 52 )DD23 - 5222 - 51
6060chain 'D' and (resid 53 through 76 )DD53 - 7652 - 75
6161chain 'D' and (resid 77 through 100 )DD77 - 10076 - 99
6262chain 'D' and (resid 101 through 117 )DD101 - 117100 - 116
6363chain 'E' and (resid 60 through 218 )EE60 - 2181 - 98
6464chain 'E' and (resid 219 through 266 )EE219 - 26699 - 132
6565chain 'E' and (resid 267 through 357 )EE267 - 357133 - 215
6666chain 'E' and (resid 358 through 427 )EE358 - 427216 - 274
6767chain 'E' and (resid 428 through 481 )EE428 - 481275 - 315
6868chain 'F' and (resid 2 through 17 )FF2 - 171 - 16
6969chain 'F' and (resid 18 through 52 )FF18 - 5217 - 51
7070chain 'F' and (resid 53 through 58 )FF53 - 5852 - 57
7171chain 'F' and (resid 59 through 81 )FF59 - 8158 - 80
7272chain 'F' and (resid 82 through 89 )FF82 - 8981 - 88
7373chain 'F' and (resid 90 through 100 )FF90 - 10089 - 99
7474chain 'F' and (resid 101 through 108 )FF101 - 108100 - 107
7575chain 'F' and (resid 109 through 117 )FF109 - 117108 - 116
7676chain 'G' and (resid 59 through 168 )GG59 - 1681 - 64

+
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