[English] 日本語
Yorodumi
- PDB-6kpp: BNC105 in complex with tubulin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kpp
TitleBNC105 in complex with tubulin
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin tyrosine ligase
KeywordsANTITUMOR PROTEIN / BNC105 / tubulin / protein-drug complex
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / microtubule depolymerization / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. ...Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Chem-DO6 / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74524106157 Å
AuthorsWang, T. / Wu, C. / Pu, D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Unraveling the molecular mechanism of BNC105, a phase II clinical trial vascular disrupting agent, provides insights into drug design.
Authors: Wang, T. / Wu, C. / Wang, C. / Zhang, G. / Arnst, K.E. / Yao, Y. / Zhang, Z. / Wang, Y. / Pu, D. / Li, W.
History
DepositionAug 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,73522
Polymers261,3056
Non-polymers3,43016
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22170 Å2
ΔGint-111 kcal/mol
Surface area80880 Å2
Unit cell
Length a, b, c (Å)105.455, 157.664, 183.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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
111METMETLEULEU(chain 'A' and (resid 1 through 119 or resid 121...AA1 - 1191 - 119
121ARGARGTHRTHR(chain 'A' and (resid 1 through 119 or resid 121...AA121 - 150121 - 150
131LEULEUTYRTYR(chain 'A' and (resid 1 through 119 or resid 121...AA152 - 210152 - 210
141ILEILETHRTHR(chain 'A' and (resid 1 through 119 or resid 121...AA212 - 292212 - 292
151ALAALAMETMET(chain 'A' and (resid 1 through 119 or resid 121...AA294 - 313294 - 313
161LEULEUASPASP(chain 'A' and (resid 1 through 119 or resid 121...AA317 - 438317 - 438
271METMETLEULEU(chain 'C' and (resid 1 through 119 or resid 121...CC1 - 1191 - 119
281ARGARGTHRTHR(chain 'C' and (resid 1 through 119 or resid 121...CC121 - 150121 - 150
291LEULEUTYRTYR(chain 'C' and (resid 1 through 119 or resid 121...CC152 - 210152 - 210
2101ILEILETHRTHR(chain 'C' and (resid 1 through 119 or resid 121...CC212 - 292212 - 292
2111ALAALAMETMET(chain 'C' and (resid 1 through 119 or resid 121...CC294 - 313294 - 313
2121LEULEUASPASP(chain 'C' and (resid 1 through 119 or resid 121...CC317 - 438317 - 438
1132METMETGLUGLU(chain 'B' and (resid 1 through 53 or resid 57...BB1 - 531 - 53
1142ASNASNTHRTHR(chain 'B' and (resid 1 through 53 or resid 57...BB57 - 14357 - 143
1152GLYGLYLEULEU(chain 'B' and (resid 1 through 53 or resid 57...BB146 - 273146 - 273
1162LEULEUMETMET(chain 'B' and (resid 1 through 53 or resid 57...BB284 - 406284 - 406
1172PHEPHETHRTHR(chain 'B' and (resid 1 through 53 or resid 57...BB408 - 429408 - 429
2182METMETGLUGLU(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD1 - 531 - 53
2192ASNASNTHRTHR(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD57 - 14357 - 143
2202GLYGLYLEULEU(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD146 - 273146 - 273
2212LEULEUMETMET(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD284 - 406284 - 406
2222PHEPHETHRTHR(chain 'D' and (resid 1 through 144 or resid 146 through 406 or resid 408 through 429))DD408 - 429408 - 429

NCS ensembles :
ID
1
2

-
Components

-
Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50041.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AGU7, UniProt: P02554*PLUS
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63042
#4: Protein Tubulin tyrosine ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

-
Non-polymers , 8 types, 177 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-DO6 / (6-methoxy-2-methyl-7-oxidanyl-1-benzofuran-3-yl)-(3,4,5-trimethoxyphenyl)methanone


Mass: 372.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H20O7 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6% PEG, 5% glycerol, 0.1M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 79756 / % possible obs: 98.72 % / Redundancy: 6.6 % / Biso Wilson estimate: 45.3494782657 Å2 / CC1/2: 0.989 / Net I/σ(I): 20.3
Reflection shellResolution: 2.75→2.8 Å / Num. unique obs: 7408 / CC1/2: 0.715 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I55
Resolution: 2.74524106157→48.2656461817 Å / SU ML: 0.30000744212 / Cross valid method: FREE R-VALUE / σ(F): 1.35039005021 / Phase error: 23.6704504182
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234792706359 4015 5.060116452 %
Rwork0.194280154566 75331 -
obs0.196346564371 79346 98.7443220708 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.6130080251 Å2
Refinement stepCycle: LAST / Resolution: 2.74524106157→48.2656461817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17168 0 216 161 17545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034006438355417805
X-RAY DIFFRACTIONf_angle_d0.73810838906724138
X-RAY DIFFRACTIONf_chiral_restr0.04644354585122618
X-RAY DIFFRACTIONf_plane_restr0.004842626059523177
X-RAY DIFFRACTIONf_dihedral_angle_d18.48668552810699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.77750.321255527871190.2712591231242266X-RAY DIFFRACTION86.9803063457
2.7775-2.81140.2851350152831260.2739278890682468X-RAY DIFFRACTION95.8610495196
2.8114-2.8470.3164719656251280.2597782775972567X-RAY DIFFRACTION98.2142857143
2.847-2.88440.3240739935761250.2705235483072566X-RAY DIFFRACTION99.2622648469
2.8844-2.9240.2828106959641580.2591110152642599X-RAY DIFFRACTION99.7106690778
2.924-2.96570.3454367362811460.2554683414782596X-RAY DIFFRACTION99.7453619498
2.9657-3.010.2842236239551420.2379444392472592X-RAY DIFFRACTION99.9269005848
3.01-3.0570.2752395242741370.2410831536962590X-RAY DIFFRACTION99.9267130817
3.057-3.10710.263540396341290.2335355898892650X-RAY DIFFRACTION99.9280834232
3.1071-3.16070.3014394426441240.2237205544952570X-RAY DIFFRACTION99.9258160237
3.1607-3.21810.3110716258121150.2381069111112670X-RAY DIFFRACTION99.9641062455
3.2181-3.280.2756918848951340.2370005270852575X-RAY DIFFRACTION99.8157700811
3.28-3.3470.2783524007531600.2286728352692578X-RAY DIFFRACTION99.9270072993
3.347-3.41970.2807868087711270.2192446919752641X-RAY DIFFRACTION99.8917358354
3.4197-3.49930.2559613169881600.2005161242652587X-RAY DIFFRACTION99.8545983279
3.4993-3.58670.2338973112781310.1933504173042624X-RAY DIFFRACTION99.7826874321
3.5867-3.68370.2025090999261480.1905585554072596X-RAY DIFFRACTION99.8544395924
3.6837-3.7920.2262935487321280.1843602635912620X-RAY DIFFRACTION99.6374184191
3.792-3.91440.2251731773831610.1741015706082612X-RAY DIFFRACTION99.6764917326
3.9144-4.05420.2158701293421380.1628908203022642X-RAY DIFFRACTION99.6773036931
4.0542-4.21640.1807610503911380.1637191317322598X-RAY DIFFRACTION99.6358339403
4.2164-4.40820.1907531215991610.1575199567722602X-RAY DIFFRACTION99.5317002882
4.4082-4.64050.1909889996661400.146652516232626X-RAY DIFFRACTION99.2821249103
4.6405-4.93090.1736198524661490.1498566745172613X-RAY DIFFRACTION99.0319110792
4.9309-5.31120.1941985879071250.1661216612572632X-RAY DIFFRACTION98.9946140036
5.3112-5.84490.2502298138731360.1906615413912667X-RAY DIFFRACTION98.6971830986
5.8449-6.68870.2455971315131360.1988142112312612X-RAY DIFFRACTION97.793594306
6.6887-8.41980.2327120065471570.1776773868672642X-RAY DIFFRACTION97.6963350785
8.4198-48.2650.2077282336751370.1846323549292730X-RAY DIFFRACTION95.6304202802
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)
11.68427138817-0.1236598725930.1103622454153.371717362871.025748324651.99633583722-0.1361735820760.2158336127520.286340348714-0.3826093269940.358718913224-0.352934391153-0.8291548494860.415890719066-0.3184924062230.629634430954-0.1730761542440.1336832103490.469561298456-0.1392700829570.34732370565229.413123020297.837788201354.5322089142
21.57591194237-0.248696015897-0.4808962622523.743218557871.103298180142.550668343530.05098445620250.5847191359560.103488100893-1.11676315680.315530966877-0.507153821471-0.8704183785950.298603077577-0.3212873593540.654722182438-0.1510724980380.1237415260230.53917713356-0.1630169803030.32694157894128.475100945587.618486482142.7396406328
30.585936763684-0.0313349245536-0.1954904532872.856525788731.151656124491.60879291474-0.01248746789260.255848387587-0.159531698531-0.09150716737690.541328344637-0.738717096361-0.178859981210.721069738608-0.293646504120.34073739472-0.06023242540640.04626738265970.541217854622-0.327026457830.4676487821135.017711707678.488298136155.0421822302
46.08770386388-1.281402420251.749744164784.890929282380.5942129036794.700171259790.2792104632980.013669723373-0.524731807714-0.0329991948240.05078186930450.4614675200050.122890730418-0.507310780515-0.1732524715740.265671462678-0.007906328517160.03617440974630.289123818274-0.1428434050550.25945192470113.33522756979.872033694360.5614228364
51.3615283358-0.1340230377310.4229283039573.033396649990.7949610871733.01409961059-0.1791007361150.1500198824850.03906208129140.1057456506360.219541908952-0.293976109172-0.572411976960.247271857436-0.04864166683350.379104588372-0.04054048710190.08845683982630.309475397314-0.1294946562210.2695988628925.218347758190.755062752365.7436159002
61.595387390110.844464708674-0.6959805198793.03386293631.76059661764.620924690870.270563166952-0.2011562793110.06259295588170.2709903206430.001764057303050.0976407958133-0.33375269137-0.215000105606-0.1948032234450.424254773006-0.05124010770090.1054422317330.331842638124-0.1249716638160.17870057735715.026995749686.132709930769.4043672787
71.32916338695-0.871098097345-0.02438389139924.127370399051.638479961611.316732468130.039244378054-0.2301783970070.004501488949430.785277513913-0.02098034333170.304069443034-0.01226808569860.0914477157099-0.04096824032820.5507194972120.02068634309340.1365524353610.316441474085-0.08201889963310.33592510258815.244462530585.646567844378.362268605
81.02954731618-0.478052504936-0.4017650206313.245673102861.580635658032.78135278801-0.0873672761522-0.0869367959526-0.1241930938740.7672524491460.273128977549-0.1256640590880.3527365343150.481566707021-0.2048633222350.3113943315340.0375710814638-0.05056170678630.331578175533-0.1424915685780.3014652991324.487235212773.643440472267.2878591762
94.91124723316-2.252857404880.005000466846247.52529801360.4074062580743.320184533160.2678988914660.2508634246290.915837301043-0.664400358352-0.1808192581780.000980579858962-0.9046862824-0.152354014567-0.04602975004470.433492097660.02666237071940.09564246053160.2865563443250.003394637136350.41416613297916.180041295470.452939617418.648760466
102.04984490092-0.951219637182-0.5066814520672.204162786970.8596816778892.703329276160.0434371706780.1069588861430.195925875437-0.0593168045274-0.08110276495880.111639464367-0.2638309435110.004662049870160.01488034835470.193069484407-0.01551212428380.01898814835420.270189806642-0.1242439004770.27008139913720.121388420154.522506062423.0837536444
112.548529492-0.853593137794-0.715016564324.268972639880.3802797894182.47234690681-0.03565299176950.00992086051494-0.01558479917260.06660591331180.05764007010460.526831019894-0.236299670256-0.6464937790680.0570895478920.3218691886060.06410384121390.04903840529040.491842743101-0.2390057311840.3532143132667.3949415130662.299779491340.1084214101
120.943124240759-1.03959819694-0.4261374019793.835562096632.452652387513.23017283696-0.0571265750936-0.2186582128250.1029768848930.5711219703870.01679899980080.07603692114360.3095073140430.0482677830408-0.005728897208080.185864941368-0.02968392927320.01681125687830.316598059023-0.04696897257550.26398921853317.152451920847.120065307135.7810489935
133.5237654396-2.83181849897-0.566475409176.140596889960.714277522541.860275426840.005925476182230.4218620080210.24658201573-0.610512957108-0.1062769527270.130089165832-0.340830242566-0.01672024518330.07350526979240.325787225237-0.100966769381-0.01586044500750.3106556721130.06161420761490.16951246939415.471393120239.1153664679-16.1478382279
141.4950917061-0.463136850897-0.4641250430294.91255214626-0.01446525806123.28166986837-0.16525955520.1631684641590.104511067128-0.285775474860.177496368139-0.2479581733740.0506865753250.254630386806-0.02304186565090.120626970585-0.04113476601220.01614024092410.248321471027-0.05437618827420.16516472584424.667466962726.3726392508-7.82281584898
152.47781194711-0.9165585398450.7300636550811.425407726620.04882789821492.299095324850.0859090028120.0928732730651-0.140838619524-0.0156773289027-0.1451271377490.3007430723430.0616180585331-0.4786009367480.02806176447430.186775652153-0.04397577066150.04198369668530.271663657816-0.07561829101680.2590286186613.4008532878729.09625642420.422081242308
161.98323766417-0.959265812875-0.2003210351082.674289592990.7821643722041.62000971915-0.176030223166-0.0607244572946-0.03508470511620.1663361874770.02556428784170.1599064232140.181664823006-0.08557103893360.1326257372070.182323173913-0.08591890073950.01160247860370.161759455167-0.05501434473920.18587343754510.804601530623.67391662035.92614332428
173.17682522892-0.987965666081-1.47656630513.095797989342.553591634163.18200049734-0.1000566081810.686079005158-0.182608791139-0.6965920347530.01366603129990.217303732902-0.0147417229985-0.6596852609310.1130374567531.02423447902-0.421217447590.002492710767051.08220112739-0.1165210915140.2649771868818.05763139463.68215944434-39.9557937199
184.95476110042-2.17439659828-2.521288316495.217462946274.391117351653.815432567250.09830144533151.264878537480.774896744216-1.66956890101-0.1860314048120.391487940418-0.602332691274-0.9623787165890.04751363690021.19765470405-0.223672674649-0.1172227712681.326251694140.1683449159340.55974228268213.592870396116.243969309-42.193595093
190.419784263062-0.241551102732-0.1197173565090.341164059462-0.08513709208260.1555670091930.08327677878220.723795168002-0.279988756734-0.675246558063-0.155729659567-0.02647221415830.177041188145-0.2043235223420.007988696509411.48125585926-0.4227231237540.3959974292981.27309493195-0.585940537350.42209829389529.7368781362-1.10648315019-45.5984723409
201.932353991010.3472049364370.2021759240291.70811688071.456754949572.80414290359-0.3479164935280.478284237012-0.292948267169-0.4697193482210.299128985931-0.3025169652530.2166475992970.0388374778222-0.1428615069660.909231245543-0.2879349378070.2207429408310.767891086882-0.2997384330730.39915261822627.1680465052-1.69754595199-33.4030977948
211.09195748558-0.01098802144660.866183251551.657239973651.303468615832.63135496021-0.1413495590950.457449191218-0.54553297197-0.217615086106-0.03572636700950.1314050535370.751666830723-0.310394774905-0.04376201899490.945143799454-0.2884873401870.3047097961780.687246619679-0.4729963742190.57460111483220.5677015524-12.0680141677-30.2651473029
221.717048815941.045870953862.21540349922.620310743463.096573256755.08842952002-0.3727273413460.622884993336-0.34572427383-0.8893436964030.1327753236680.3430051631330.00592740754356-0.5377187958140.3424362995210.725511081952-0.2752024168020.07886407960010.757884053911-0.2316048083370.40208777392713.47100356580.313225996062-29.3103334195
230.632876077129-1.48239501354-0.2817326267344.22925725919-0.3333585040191.44121571506-0.1285730355190.277052652181-0.3861752257-0.5342257756380.09337171512551.066833061070.690131532369-0.7305609779910.07405590747930.706761607265-0.314638577644-0.02396772156850.747906219451-0.2895053938220.6925334668474.72232892371-6.49374850148-23.0569577329
247.61725985243-2.51199786181-1.469462712548.959890952890.955009302938.52037239681-0.6413961775530.8032260800880.005597142203220.00193706089250.6266614189621.33972067607-0.353686012193-1.34982374853-0.003893375148060.41802889113-0.121047209589-0.06335898121870.6087865785560.03868951754090.4910108604541.202979011614.03508989253-18.2180644845
252.67126500324-0.668549550624-0.4632938670164.285579789161.104293440882.10344779069-0.1261407311440.673811869791-0.0338339828728-0.4117375227390.05247227883050.5056892715580.490310125116-0.6455262277920.1753189510170.362067384042-0.1285163992520.03153240219860.560524704129-0.1011839435110.3863187117016.434689136972.60875720368-19.1050852571
261.94857118853-1.08919597972-0.8765907786422.489358699810.9695986759651.26004413394-0.1459456979630.485634124741-0.792461517035-0.3567120085990.053326772301-0.2479948747030.8584287708340.235553279015-0.0279367305941.03168656317-0.02360470453750.3463206102120.52808758798-0.4822756444170.76338094133325.6587031977-16.334036499-23.3514676605
274.15294254744-2.70180852556-0.05297303814646.808326064030.9502947676261.021448350490.238590932253-0.2700913314210.2011293105161.23485750920.319213341503-0.4791395848680.3113062802550.603567710091-0.5250681253430.73697251592-0.0951211825834-0.1368442710530.570882669428-0.2016647986240.40036340516227.640401733192.854268657982.5438990002
280.6377792068940.0875305096553-0.2227640610060.137485257465-0.151337125250.234121488864-0.191848923676-0.0197105510088-0.0404512957530.1779147582940.680737851712-0.5861414727960.3782502508780.849675886072-0.598004540950.44140883070.1022717691780.07539469123980.627845226818-0.2294407110870.62620898874242.725194562727.45698137174.61380347017
293.447063474550.315368737589-0.5529253909052.38458609199-0.2788085631652.47580836905-0.304465162516-0.114227215142-0.758413459016-0.05148814666230.0553400418325-0.2143985692361.21645700913-0.05809157827280.03383765906090.786032621780.005203974748650.1687282970840.337387061847-0.01646616775890.5419077472468.0978369811358.05851665979.4750400043
300.110376029582-0.0865436627874-0.690566286651.355229226540.3586901612654.43199975597-0.187167250083-0.485784267024-0.5136070681440.6107513692020.123600377556-0.8034319153590.6668672159261.553834248540.155093463841.037909835770.396757390794-0.05116490690721.181717115850.3564432787870.850299838215.235361815555.247238373111.329260645
311.578714225431.046359426530.5402164234582.3804754001-1.606250658222.5191293621-0.30935793285-0.303867494913-0.9124226861940.3837757701420.219867029797-0.2068728882610.8548007521820.177030231532-0.2465741748171.204823317760.2566306173010.3064604343930.44161314210.2167530776150.814333068052-0.16482555099650.253300829397.8863069605
320.5592320132391.24394354588-0.3900695038462.86128356154-0.683322407590.624770797838-0.649054380057-0.339344335938-1.43692853625-0.348969313090.0981297278542-0.4790346516130.95882137720.5559111908580.5364297915791.590787697530.1584508428270.5631168919920.6724651985520.230997037111.40240244394-2.9097566494241.6618102147101.007260316
333.357225949391.68188867937-2.514480114131.32305477553-0.4347599746223.46356525234-0.420309605725-0.0732702801454-0.5239987344980.1818338257480.3089761334720.05839450956910.5626002014070.03371161741440.08551460191280.8032613326860.1010645294480.1721478359750.3586123876110.1126396888830.507651898313-0.91455493480959.413303262290.6543779843
347.59132368406-3.18192611255-2.326237828664.2818243635-1.199946760814.97838769672-0.1749752513290.74830596231-0.2123550170060.06488137460030.04923549049970.81932387340.770419195957-1.498900407450.1924688007940.411555581063-0.2204629079580.05895327291130.6133216846280.06209003997090.608188205058-9.5927604924661.992781295477.3959011876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 197 )
4X-RAY DIFFRACTION4chain 'A' and (resid 198 through 223 )
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 259 )
6X-RAY DIFFRACTION6chain 'A' and (resid 260 through 287 )
7X-RAY DIFFRACTION7chain 'A' and (resid 288 through 338 )
8X-RAY DIFFRACTION8chain 'A' and (resid 339 through 438 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 86 )
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 236 )
11X-RAY DIFFRACTION11chain 'B' and (resid 237 through 336 )
12X-RAY DIFFRACTION12chain 'B' and (resid 337 through 429 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 102 )
14X-RAY DIFFRACTION14chain 'C' and (resid 103 through 197 )
15X-RAY DIFFRACTION15chain 'C' and (resid 198 through 311 )
16X-RAY DIFFRACTION16chain 'C' and (resid 312 through 441 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 27 )
18X-RAY DIFFRACTION18chain 'D' and (resid 28 through 62 )
19X-RAY DIFFRACTION19chain 'D' and (resid 63 through 125 )
20X-RAY DIFFRACTION20chain 'D' and (resid 126 through 178 )
21X-RAY DIFFRACTION21chain 'D' and (resid 179 through 213 )
22X-RAY DIFFRACTION22chain 'D' and (resid 214 through 264 )
23X-RAY DIFFRACTION23chain 'D' and (resid 265 through 309 )
24X-RAY DIFFRACTION24chain 'D' and (resid 310 through 336 )
25X-RAY DIFFRACTION25chain 'D' and (resid 337 through 362 )
26X-RAY DIFFRACTION26chain 'D' and (resid 363 through 431 )
27X-RAY DIFFRACTION27chain 'E' and (resid 4 through 44 )
28X-RAY DIFFRACTION28chain 'E' and (resid 45 through 141 )
29X-RAY DIFFRACTION29chain 'F' and (resid 1 through 115 )
30X-RAY DIFFRACTION30chain 'F' and (resid 116 through 192 )
31X-RAY DIFFRACTION31chain 'F' and (resid 193 through 236 )
32X-RAY DIFFRACTION32chain 'F' and (resid 237 through 275 )
33X-RAY DIFFRACTION33chain 'F' and (resid 276 through 354 )
34X-RAY DIFFRACTION34chain 'F' and (resid 355 through 380 )

+
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