[English] 日本語
Yorodumi
- PDB-6y6d: Tubulin-7-Aminonoscapine complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y6d
TitleTubulin-7-Aminonoscapine complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine Ligase
KeywordsCELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-OBQ / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsOliva, M.A. / Prota, A.E. / Rodriguez-Salarichs, J. / Gu, W. / Bennani, Y.L. / Jimenez-Barbero, J. / Canales, A. / Steinmetz, M.O. / Diaz, J.F.
Funding support Spain, Switzerland, 4items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2013-47014-P Spain
Spanish Ministry of Economy and CompetitivenessBFU2016-75319-R Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2011-07900 Spain
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis of Noscapine Activation for Tubulin Binding.
Authors: Oliva, M.A. / Prota, A.E. / Rodriguez-Salarichs, J. / Bennani, Y.L. / Jimenez-Barbero, J. / Bargsten, K. / Canales, A. / Steinmetz, M.O. / Diaz, J.F.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Jan 24, 2024Group: 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: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin-Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,35522
Polymers261,6316
Non-polymers3,72416
Water9,116506
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22940 Å2
ΔGint-127 kcal/mol
Surface area79070 Å2
Unit cell
Length a, b, c (Å)104.360, 157.150, 180.370
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

-
Protein , 4 types, 6 molecules ACBDEF

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


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: Q6B856
#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.) Rattus norvegicus (Norway rat) / Tissue: Brain / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#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 , 9 types, 522 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.: 5 / 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-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
#9: Chemical ChemComp-OBQ / (3~{S})-7-azanyl-6-methoxy-3-[(5~{R})-4-methoxy-6-methyl-7,8-dihydro-5~{H}-[1,3]dioxolo[4,5-g]isoquinolin-5-yl]-3~{H}-2-benzofuran-1-one


Mass: 398.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N2O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 5% PEG 4K, 11% glycerol, 30 mM MgCl2, 30 mM CaCl2, 100 mM MES/Imidazole, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→43.34 Å / Num. obs: 150529 / % possible obs: 99.95 % / Redundancy: 13.4 % / Biso Wilson estimate: 50.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1382 / Rpim(I) all: 0.03905 / Rrim(I) all: 0.1437 / Net I/σ(I): 14.42
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 13.2 % / Rmerge(I) obs: 3.394 / Mean I/σ(I) obs: 0.74 / Num. unique obs: 14882 / CC1/2: 0.259 / Rpim(I) all: 0.9606 / Rrim(I) all: 3.529 / % possible all: 99.95

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4I4T

4i4t


Resolution: 2.2→43.34 Å / SU ML: 0.3451 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.5596
RfactorNum. reflection% reflection
Rfree0.2238 7565 5.03 %
Rwork0.1838 --
obs0.1858 150500 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 70.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17236 0 234 506 17976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002417912
X-RAY DIFFRACTIONf_angle_d0.51824297
X-RAY DIFFRACTIONf_chiral_restr0.04112639
X-RAY DIFFRACTIONf_plane_restr0.00283141
X-RAY DIFFRACTIONf_dihedral_angle_d18.80616621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.41572590.38034718X-RAY DIFFRACTION99.88
2.23-2.250.36382780.34354695X-RAY DIFFRACTION100
2.25-2.280.36472640.33074669X-RAY DIFFRACTION99.98
2.28-2.310.36392250.32554733X-RAY DIFFRACTION100
2.31-2.340.3332490.30834714X-RAY DIFFRACTION99.96
2.34-2.370.31932510.30164769X-RAY DIFFRACTION99.96
2.37-2.40.33242440.28794675X-RAY DIFFRACTION99.94
2.4-2.440.31282550.26754752X-RAY DIFFRACTION99.98
2.44-2.480.31612310.25724731X-RAY DIFFRACTION100
2.48-2.520.3162670.25384704X-RAY DIFFRACTION100
2.52-2.560.28172590.24414716X-RAY DIFFRACTION100
2.56-2.610.25762940.22624720X-RAY DIFFRACTION100
2.61-2.660.26262250.22084745X-RAY DIFFRACTION100
2.66-2.710.26392280.2234757X-RAY DIFFRACTION100
2.71-2.770.27422310.22844769X-RAY DIFFRACTION100
2.77-2.840.27322500.21954715X-RAY DIFFRACTION100
2.84-2.910.25812360.20984778X-RAY DIFFRACTION100
2.91-2.990.25792270.20554787X-RAY DIFFRACTION99.98
2.99-3.070.25432360.19834759X-RAY DIFFRACTION100
3.07-3.170.22922600.19334729X-RAY DIFFRACTION100
3.17-3.290.23522670.19464746X-RAY DIFFRACTION100
3.29-3.420.22542660.18934770X-RAY DIFFRACTION99.98
3.42-3.570.21342700.17544766X-RAY DIFFRACTION99.98
3.57-3.760.21592750.15974742X-RAY DIFFRACTION100
3.76-40.20032590.14834792X-RAY DIFFRACTION100
4-4.310.18062460.14714805X-RAY DIFFRACTION100
4.31-4.740.16162430.12864871X-RAY DIFFRACTION100
4.74-5.420.17922570.14344834X-RAY DIFFRACTION100
5.42-6.830.20942410.1774909X-RAY DIFFRACTION99.98
6.83-43.340.19442720.16195065X-RAY DIFFRACTION99.63
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)
12.51896598861-0.371113884586-0.2490172836345.04019496970.1089170344791.90209775870.006700079789720.007996948166260.509202842436-0.6010549316040.239836165323-0.375579943087-1.084898095160.395548898735-0.2393062965440.850522264736-0.1725622561490.1606049149340.549651511424-0.1272718462360.54099976299628.434374464195.901459576952.3286126267
22.13686006358-0.598506784455-0.002007471310632.11903174967-0.08896780887993.68480307013-0.02351967414780.2184858743460.254664146273-1.694051237970.0905021443761-0.525561040719-0.9683192631030.190501814727-0.1036255244410.967163339511-0.09874620549110.08248515937770.68166575677-0.1038128851680.56796692287228.981650909586.902943126542.9528475147
31.773758122750.47686957167-0.4140994956464.135330412750.9004538785972.98020536739-0.09494564330.11129671786-0.0227541540572-0.2431730258720.429199844019-0.707078836083-0.2607383959490.707962481109-0.2947482829450.460711171248-0.07565102568620.07662011174860.626680605605-0.2516688859730.56534898392235.088724004477.920083319955.1073926213
42.09792087313-1.156194118732.725432106235.83978555834-0.4538019287336.739218309010.4496408945460.00996426759886-0.6196646073450.03982803693990.0006897085695851.074068818160.328908731393-0.872453563397-0.4607492724930.4714679916410.02560401600880.04982431572510.494613527326-0.1245908594090.61698394714311.684097954178.775145807760.002438178
51.09157743441-0.0579955203910.3521010559383.498734030160.8128334604934.105839424160.0823679530214-0.1076471167160.1629482023290.530610302367-0.04514388131060.145904695355-0.4379026853410.0429199110489-0.0913906368860.4987550918150.01161468444980.09575045277250.42403046689-0.132511600010.47923805300218.757254272386.472902410668.436860394
60.4606755981310.9226132435610.4453185499893.8936308950.07744403124170.8655491194260.0626342943959-0.1016957777940.2108618653871.051123490910.07794832582060.64814605008-0.303598450081-0.266346004294-0.15408245780.8745885367410.04312225855020.1981714478070.502419932128-0.09912123500580.47594848408717.253408293787.214937680280.3187248698
70.866508986158-0.296941081534-0.2611169703223.802172423721.767705546843.007206374530.0107054167966-0.0660282880712-0.06988410661730.6443131053340.1573421682740.09160731860210.1825761647390.340911236487-0.1794771473620.451225581486-0.01214395596590.04009568961440.49069204094-0.1131132875550.47206189784324.605093545872.905385530567.5257019025
83.45060580862-1.4405460412-2.29178117018.327399110181.827237501254.559450927120.03951524315380.3101644911960.0625466682687-0.3083716670240.1047783552640.601656481528-0.413014364176-0.169795136606-0.1537181354490.3885302105770.01708525834040.02582768722220.451462709375-0.04191348088140.49280869522515.565386346264.255633581921.9485784601
94.55072150795-3.48135140446-1.188955330247.478191594012.640037354285.206082442770.2083939203820.3471088845960.607214351363-0.540954865261-0.2836652561860.012744171395-0.988316878545-0.2938353790770.06674702912440.6191933498560.005220677450380.03576246347320.4738621646430.03776619693090.60197281890216.065264506372.16334623518.1743651524
101.85178215646-0.216333405452-0.6273108309032.714988764081.072916458653.39204504431-0.03733767912350.1816168169530.0894934052539-0.182933998550.157574443076-0.133773492219-0.330323034710.263309640396-0.09983109808150.378922375134-0.01549173380460.04188452548680.537240066736-0.1183194476320.46335891020626.412032324356.123529413620.9238614472
111.29485058868-0.569879141378-0.4290446931882.032699823470.6594982411313.379541295180.0386828662947-0.1410999005690.03988629519480.118475983639-0.1320423040350.183033595544-0.00787049882229-0.3680655885450.07482379027950.2794170397550.002119425444230.04951915736380.439864421683-0.1590849646690.43082727052514.537273450355.055332756431.6059510651
124.07496438322-2.379678149512.073642289424.28673423593-0.5568217036393.08188184254-0.38399069167-0.378456296416-0.02761031305720.1466158938120.1355977097440.365196262212-0.154263191885-1.095699872210.1450225820920.519702052268-0.04247260435790.05939370669120.89375091308-0.2171118516860.6259495246971.4745341206956.148472272638.9026953052
134.26959996371-2.07442947283-2.639013017931.501040149431.672958976611.94825606204-0.770426097773-0.8520488264090.2877022023620.9790450535650.4333790225810.396402164983-0.700058634629-1.305740690760.2423016425850.6820153897650.2778118712570.01348060487430.954733363905-0.2731549070850.6869794724494.6354206612864.861711884747.1389900244
144.16027057341-2.080503739243.888876832223.15642531352-1.4167516726.50290260477-0.367720477059-0.5105084618990.3494128174470.1946250265680.0802187267774-0.0415443814532-0.100471016074-1.118857973650.1888126648080.4123984637170.04775398146020.06272631983630.729930201939-0.1836016469840.5142462601148.9172000535762.142542251844.9800143114
151.45352637145-1.95311676751-0.596390406274.944991452663.128008414853.85158261285-0.0900396591233-0.19704445592-0.03875270499260.2443104591860.02564876646220.5387865674830.413452048164-0.1088669001330.1115310236790.324789002329-0.06301256032240.09290727215430.46719057014-0.08268505957760.44195280347814.697382300242.942679399734.1765245869
161.61309663211-0.375424935813-1.070173367745.000072865933.936918889593.95241450764-0.226262501485-0.147778518858-0.2247924840990.8148517622820.158651394299-0.1195711693571.26442474870.839605557706-0.0375131053010.4328113081710.0105898319216-0.05759542005040.508190823757-0.0259416443810.45981405444125.634454663537.869870688530.875600612
171.49818388431-0.580698342309-0.1303781942123.29557331906-0.1006819136581.991856956650.02525712264890.152439889570.143243724786-0.2495595856840.0474716216852-0.0517893214493-0.1863894072250.0986200682859-0.06679329135520.314490811286-0.05811683973980.03680553820230.404856478618-0.0373768003750.33479130005520.120688948132.7556026024-11.9661661994
180.984211899067-0.510139080637-0.1058997992161.445619903480.9595685379391.855404892520.0080414947103-0.01429801101950.1216181505440.0765126914527-0.06758284648070.09985124204310.0469565886371-0.2570299425130.05828317071120.300813208544-0.07489046189080.0332734596420.37215166872-0.04516870509890.3753841242437.7124845294725.68600783623.13669071537
194.06383255977-1.41308111201-0.2694490916324.402417300190.6566672156923.01911887782-0.02472506326310.9531849506460.115580118202-0.8444509820880.08962797110320.1380862026-0.0203728794164-0.377635779342-0.04162533846040.680994951802-0.1405209620180.02769483562210.854668403341-0.02768149769810.37419171355217.41662174289.62502223705-43.7839027573
202.273941196850.125894070352-0.4761089075651.55018974335-0.258644819072.77151744411-0.1799435685820.464211951549-0.28757981462-0.3945903552910.192524165043-0.2436276634040.5302987858060.077446036444-0.02791695880550.648127889621-0.0384275546220.06606331308590.651636706067-0.2289962872430.49353300456224.261133965-4.36650391652-36.8643834719
211.45946134692-0.0832789021495-0.7400353558940.9044460431170.8373864794061.357415269390.04727985575130.562747523642-0.00369466132419-0.3697511314130.118328839947-0.0570455669020.1312805332060.105646970593-0.1422919979730.502395639119-0.02425679743060.04697356649730.549488144078-0.1370928992350.50956483920918.2037348316.55261556682-22.9900446315
222.28034748341-0.67528257603-0.04774811862762.265258846010.3569469229032.82358912295-0.1967948022290.34560709041-0.2436365796580.06150007157230.115280089570.2335204316090.334337520736-0.4630006616160.05993702943950.505124786317-0.1343155160510.04271665508730.535392579115-0.1050609376640.4265947197977.33807804163-3.23105675672-21.6219285525
233.80577353099-0.119265082873-1.541421467862.572493677240.2553094384953.31583773915-0.3296615646480.141145782415-0.9178871990370.06316112839230.0338522051242-0.1037417598880.5798739298670.5349147203790.01283440599260.8373998595270.07303624743150.05000958780180.609558042085-0.2439665808990.75039503970530.406872415-17.4227504631-24.4473837095
243.05482292245-1.14036447331-0.4914027665054.217841961511.057046909860.7023701951170.00629174040787-0.3094007421020.09575947379811.06707061120.251000167195-0.1983541413990.04414052612750.801258015652-0.2210991225311.15181446893-0.0697552243245-0.08925897762140.863225483253-0.2343321100830.71063530767927.616759503292.818379468681.6468584254
250.34958997404-0.122164849751-0.2880084650270.3790162913030.3868436534290.620447304699-0.0826655428766-0.00169596404161-0.01768004134310.4029557268230.536568581615-0.4820345280730.6080156314720.776753335897-0.5404022754670.5839274542020.08943747257920.01750798007930.82369967795-0.2783817025530.74598450690142.984952788827.73406508444.01661752749
263.471374504981.71332169407-1.884871680024.933022131010.3610033342463.23898626163-0.6204463909160.667618381474-0.785619563495-0.05855574504950.1766971957580.0977085052711.46627943859-0.7191766000510.3899762147641.20392181703-0.1665988325630.2211923253860.699030905036-0.1672126687530.654859716316.3118893077354.328269727769.8369153249
276.82396135172.42428202129-0.538772980125.54810475077-3.615744980912.62990786278-0.114542673608-0.714548008935-0.2444248918590.376345830928-0.0368416951046-0.535389663137-0.3134245868231.255022495060.204205578920.7339226209620.0930520820448-0.03987914025110.7424168202730.05798734830290.57664902217511.157991337465.045864141896.829447291
284.244126211921.492590394160.7477813527263.13422759352-0.6408851189981.779849145470.26684675771-0.398963326074-0.09259620225860.364698798543-0.731528526115-1.117633766350.5474370732372.084992403470.3985865460841.030569568150.245568690621-0.1629567263572.094788792460.4917666651151.2472997575619.967130180357.0361025286109.306647436
291.234558824770.699031595975-0.9992512977663.03154906671-0.7746815647922.38902795066-0.501441779657-0.158413535167-0.8707622665570.0237764057330.0824113543478-0.3547532225721.452744998820.2944299458910.2250232038121.316036684960.1556013027960.2635545657360.6532890179440.1972761972940.941383180838-1.689606387647.1825302188101.100736899
303.203877392890.236448609581-2.850834257261.08182306487-0.5062192931454.90433587915-0.3349276770940.133411175708-0.291908137742-0.002936830044240.3237258256030.09835174949750.92180349646-0.230046935866-0.06756955864210.763571867704-0.03098254327360.08058311980260.4389117913130.0123349432030.514419389564-0.81078694996959.297603083787.3913613116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 223 )
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 306 )
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 337 )
7X-RAY DIFFRACTION7chain 'A' and (resid 338 through 439 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 27 )
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 88 )
10X-RAY DIFFRACTION10chain 'B' and (resid 89 through 180 )
11X-RAY DIFFRACTION11chain 'B' and (resid 181 through 268 )
12X-RAY DIFFRACTION12chain 'B' and (resid 269 through 311 )
13X-RAY DIFFRACTION13chain 'B' and (resid 312 through 338 )
14X-RAY DIFFRACTION14chain 'B' and (resid 339 through 372 )
15X-RAY DIFFRACTION15chain 'B' and (resid 373 through 401 )
16X-RAY DIFFRACTION16chain 'B' and (resid 402 through 438 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 199 )
18X-RAY DIFFRACTION18chain 'C' and (resid 200 through 440 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 88 )
20X-RAY DIFFRACTION20chain 'D' and (resid 89 through 238 )
21X-RAY DIFFRACTION21chain 'D' and (resid 239 through 268 )
22X-RAY DIFFRACTION22chain 'D' and (resid 269 through 399 )
23X-RAY DIFFRACTION23chain 'D' and (resid 400 through 441 )
24X-RAY DIFFRACTION24chain 'E' and (resid 6 through 46 )
25X-RAY DIFFRACTION25chain 'E' and (resid 47 through 143 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 66 )
27X-RAY DIFFRACTION27chain 'F' and (resid 67 through 96 )
28X-RAY DIFFRACTION28chain 'F' and (resid 97 through 184 )
29X-RAY DIFFRACTION29chain 'F' and (resid 185 through 283 )
30X-RAY DIFFRACTION30chain 'F' and (resid 284 through 378 )

+
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