[English] 日本語
Yorodumi
- PDB-5jqg: An apo tubulin-RB-TTL complex structure used for side-by-side com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jqg
TitleAn apo tubulin-RB-TTL complex structure used for side-by-side comparison
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Uncharacterized protein
KeywordsSTRUCTURAL PROTEIN / apo structure
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
Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family ...Rossmann fold - #11480 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 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. / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsWang, Y.X. / Naismith, J.H. / Zhu, X.
CitationJournal: Nat Commun / Year: 2016
Title: Pironetin reacts covalently with cysteine-316 of alpha-tubulin to destabilize microtubule
Authors: Yang, J. / Wang, Y.X. / Wang, T. / Jiang, J. / Botting, C.H. / Liu, H. / Chen, Q. / Yang, J. / Naismith, J.H. / Zhu, X. / Chen, L.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_detector / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,60821
Polymers261,4476
Non-polymers3,16115
Water5,999333
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22750 Å2
ΔGint-127 kcal/mol
Surface area79520 Å2
Unit cell
Length a, b, c (Å)105.050, 158.120, 180.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA1 - 4361 - 436
21METMETGLYGLYCC1 - 4361 - 436
12ARGARGALAALABB2 - 4282 - 428
22ARGARGALAALADD2 - 4282 - 428

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: 50204.445 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 / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1 / Fragment: UNP residues 49-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63043
#4: Protein Uncharacterized 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 BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: E1BQ43

-
Non-polymers , 8 types, 348 molecules

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


Mass: 523.180 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / 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-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
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 0.1M MES, 6% PEG4000, 5% Glycerol, 30mM CaCl2, 30mM MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.24→35.22 Å / Num. obs: 144729 / % possible obs: 100 % / Redundancy: 6.7 % / Net I/σ(I): 14.9
Reflection shellResolution: 2.24→2.3 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I55

4i55


Resolution: 2.24→35.22 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 9.577 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21247 7246 5 %RANDOM
Rwork0.18081 ---
obs0.18238 137397 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.06 Å
Displacement parametersBiso mean: 49.326 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20 Å2
2--0.14 Å2-0 Å2
3----1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.24→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16999 0 187 333 17519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01917731
X-RAY DIFFRACTIONr_bond_other_d0.0060.0216473
X-RAY DIFFRACTIONr_angle_refined_deg1.691.96224041
X-RAY DIFFRACTIONr_angle_other_deg1.299337952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6452175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72924.327855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.642152980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.65615107
X-RAY DIFFRACTIONr_chiral_restr0.0970.22621
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02120114
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024142
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2632.148658
X-RAY DIFFRACTIONr_mcbond_other2.2612.148657
X-RAY DIFFRACTIONr_mcangle_it3.1373.19710815
X-RAY DIFFRACTIONr_mcangle_other3.1373.19810816
X-RAY DIFFRACTIONr_scbond_it3.5732.5599073
X-RAY DIFFRACTIONr_scbond_other3.5732.569074
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.153.68913216
X-RAY DIFFRACTIONr_long_range_B_refined6.89517.66719207
X-RAY DIFFRACTIONr_long_range_B_other6.89917.5819122
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A495600.13
12C495600.13
21B501000.08
22D501000.08
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 504 -
Rwork0.24 10048 -
obs--99.96 %
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)
11.69340.1496-0.33713.57490.94991.41540.0040.13340.2437-0.36170.11350.0213-0.74140.2199-0.11750.5481-0.14390.07640.1669-0.06970.197328.51397.86754.659
21.2698-1.10840.50249.0241-0.10241.9294-0.09170.30050.2434-0.71450.2785-0.0242-0.66920.1427-0.18680.3364-0.11660.09280.254-0.06920.247429.32983.68843.713
31.03270.115-0.37772.13151.16031.92080.01710.0581-0.01360.0540.1697-0.1418-0.17730.2365-0.18680.1672-0.03010.0350.1039-0.10530.191527.69880.99559.848
41.4971-0.4704-0.64363.51930.89172.05860.0695-0.02070.02510.2554-0.05610.2847-0.0961-0.229-0.01340.2489-0.00960.08820.1078-0.0730.213512.67286.45875.458
50.5964-0.2675-0.26172.83181.78652.5026-0.0497-0.0992-0.020.59760.0920.05450.29880.14-0.04230.1922-0.02480.02930.1081-0.07630.204823.06274.09968.672
62.276-1.2009-0.44963.29680.76171.61120.13750.29040.3503-0.4507-0.09950.0693-0.6268-0.0622-0.0380.27950.00940.01890.1883-0.03490.249720.34365.11517.947
71.14380.00670.05512.47581.72932.49190.002-0.08930.12570.0399-0.12630.2342-0.1175-0.1650.12430.047900.0240.1217-0.09280.187517.34955.06428.189
82.0756-0.49220.27741.76170.90182.5377-0.1297-0.0669-0.00210.1762-0.15940.35730.0286-0.65690.28910.1372-0.02350.06620.2849-0.16340.30897.28358.72243.985
90.8267-0.35450.0331.07811.44143.2827-0.1735-0.0249-0.01210.2162-0.08460.26560.1134-0.31730.25810.0816-0.03760.07470.2599-0.08080.355510.06154.05535.284
100.3351-0.03630.7392.58232.00683.4064-0.00110.0158-0.01210.57570.0313-0.02930.48090.2123-0.03020.185-0.0067-0.00750.2885-0.03820.243624.49236.28930.206
112.0761-0.6498-0.19913.3881-0.38251.3128-0.09270.13980.1866-0.26190.04760.1273-0.24080.04190.04510.1351-0.0545-0.02180.10080.03130.151514.7440.746-14.691
121.16230.0965-0.10551.77570.43151.3426-0.05670.16810.0456-0.15790.1202-0.0058-0.05760.1008-0.06350.0662-0.02280.01320.0671-0.01120.115118.27227.262-9.522
134.0801-1.50692.30260.9428-0.47722.64410.03540.04550.2201-0.0551-0.07230.0529-0.108-0.16780.03690.0388-0.01070.02780.073-0.0120.14456.88832.9734.139
147.2866-4.1434-0.38844.53771.2670.71540.04260.1895-0.2778-0.0126-0.20230.45620.0806-0.17890.15960.0943-0.11020.03440.2435-0.00990.2375-1.77325.7646.676
151.0264-0.50680.03451.65580.90931.5103-0.0682-0.07190.02010.173-0.00610.12550.1709-0.12140.07430.0708-0.04420.0310.0537-0.02350.162210.49123.6635.34
163.5021-1.1510.29423.12770.17772.6169-0.06370.6590.105-0.7670.05370.0179-0.2183-0.07930.01010.4737-0.08710.03780.4295-0.06470.174618.3559.3-44.787
171.94080.0025-0.31412.03070.52561.4511-0.11010.3385-0.1789-0.4250.1524-0.15520.26250.074-0.04230.4316-0.04520.07720.3084-0.17530.192322.686-3.225-35.75
182.1694-0.4289-0.151.36970.66461.8552-0.07850.2844-0.3917-0.2105-0.07050.2920.2933-0.36390.14890.2801-0.06240.00450.2346-0.13820.270610.9920.148-22.994
192.2158-0.3086-0.59871.64560.34692.0415-0.18210.3173-0.2518-0.22060.06020.16610.3103-0.15220.12190.3005-0.08150.0190.1728-0.10920.22459.876-4.044-22.134
204.3944-1.0697-4.12531.38111.87677.3681-0.08530.0433-0.3686-0.010.0864-0.23560.53830.3798-0.0010.41550.08680.06770.1927-0.16710.39329.679-15.419-23.695
212.76180.1270.336510.688-6.93319.90740.1226-0.32940.11460.6017-0.00740.1265-0.17630.3653-0.11520.3403-0.0599-0.0020.2187-0.12730.220124.2399.36382.955
221.7502-1.4641-1.84653.81993.75673.8613-0.3597-0.3568-0.03310.95010.9118-0.61990.82780.9237-0.55210.64770.2556-0.02590.6633-0.25240.488338.35878.36868.711
230.67471.54552.1664.69416.874110.1410.0240.00610.04240.17830.1349-0.11410.28240.2458-0.15890.18220.0148-0.00990.2981-0.10450.320841.54951.5230.97
240.1895-1.0857-1.008614.68712.641511.40360.0404-0.0221-0.09640.15650.1081-0.3020.31940.2596-0.14850.19520.01810.06130.3221-0.13350.336540.68812.958-13.343
2511.23280.1131-0.33540.5209-2.501718.7243-0.1346-0.1278-0.2208-0.06210.057-0.0110.03360.28640.07770.31770.06330.08630.3173-0.12140.374848.121-16.265-41.726
261.79910.4898-1.39922.4744-0.41634.6153-0.30910.2442-0.5604-0.23120.0133-0.02221.0389-0.26260.29580.5115-0.07190.1120.1384-0.11590.36896.43954.56270.737
272.04431.5789-0.59833.5368-1.28985.0698-0.0343-0.5774-0.330.3574-0.317-0.6779-0.03731.18320.35130.4350.0364-0.0640.56050.16220.512614.49360.845102.242
282.10331.1647-2.29292.0887-1.42244.2685-0.3441-0.3594-0.76150.1931-0.0498-0.33050.83020.34360.39390.60650.0650.08460.16090.13440.5419-0.46948.567102.112
291.72170.4598-2.79341.3486-0.67715.228-0.19940.1313-0.27560.10050.14460.03450.379-0.24620.05480.31760.00480.03680.10660.02630.3375-1.6259.33289.162
301.7323-2.01980.112112.9950.98130.12360.11680.61340.1292-0.0857-0.1288-0.14780.02020.09950.01210.4017-0.00850.03510.32820.00510.3538-8.11676.38794.281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 65
2X-RAY DIFFRACTION2A66 - 107
3X-RAY DIFFRACTION3A108 - 279
4X-RAY DIFFRACTION4A280 - 331
5X-RAY DIFFRACTION5A332 - 437
6X-RAY DIFFRACTION6B2 - 125
7X-RAY DIFFRACTION7B126 - 254
8X-RAY DIFFRACTION8B255 - 351
9X-RAY DIFFRACTION9B352 - 387
10X-RAY DIFFRACTION10B388 - 428
11X-RAY DIFFRACTION11C1 - 81
12X-RAY DIFFRACTION12C82 - 244
13X-RAY DIFFRACTION13C245 - 283
14X-RAY DIFFRACTION14C284 - 311
15X-RAY DIFFRACTION15C312 - 440
16X-RAY DIFFRACTION16D2 - 93
17X-RAY DIFFRACTION17D94 - 248
18X-RAY DIFFRACTION18D249 - 297
19X-RAY DIFFRACTION19D298 - 394
20X-RAY DIFFRACTION20D395 - 431
21X-RAY DIFFRACTION21E6 - 18
22X-RAY DIFFRACTION22E19 - 55
23X-RAY DIFFRACTION23E56 - 85
24X-RAY DIFFRACTION24E86 - 134
25X-RAY DIFFRACTION25E135 - 141
26X-RAY DIFFRACTION26F1 - 69
27X-RAY DIFFRACTION27F70 - 180
28X-RAY DIFFRACTION28F181 - 277
29X-RAY DIFFRACTION29F278 - 378
30X-RAY DIFFRACTION30F379 - 384

+
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