[English] 日本語
Yorodumi
- PDB-4o4l: Tubulin-Peloruside A-Epothilone A complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4o4l
TitleTubulin-Peloruside A-Epothilone A complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-tyrosine ligase
KeywordsCELL CYCLE/INHIBITOR / ALPHA-TUBULIN / BETA-TUBULIN / LIGASE / GTPASE / MICROTUBULE / STATHMIN / PELORUSIDE A / EPOTHILONE A / TUBULIN FOLD / CYTOSKELETON / CELL CYCLE-INHIBITOR complex
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / mitotic cell cycle / double-stranded RNA binding / nervous system development / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / nucleotide binding / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / 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, A domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 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 / Dna Ligase; domain 1 / 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
EPOTHILONE A / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Peloruside A / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.2 Å
AuthorsProta, A.E. / Bargsten, K. / Northcote, P.T. / Marsh, M. / Altmann, K.H. / Miller, J.H. / Diaz, J.F. / Steinmetz, M.O.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Structural basis of microtubule stabilization by laulimalide and peloruside a.
Authors: Prota, A.E. / Bargsten, K. / Northcote, P.T. / Marsh, M. / Altmann, K.H. / Miller, J.H. / Diaz, J.F. / Steinmetz, M.O.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
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)266,06122
Polymers261,6316
Non-polymers4,43016
Water10,106561
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.400, 156.330, 180.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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 / Details: BRAIN / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: BRAIN / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q6B856
#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) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

-
Non-polymers , 8 types, 577 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.: 3 / 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-POU / Peloruside A / (1R,3R,4S,7S,9S,11S,13R,14R,15R)-4,11,13,14-tetrahydroxy-7-[(2Z,4R)-4-(hydroxymethyl)hex-2-en-2-yl]-3,9,15-trimethoxy-12,12-dimethyl-6,17-dioxabicyclo[11.3.1]heptadecan-5-one


Mass: 548.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H48O11
#10: Chemical ChemComp-EP / EPOTHILONE A


Mass: 493.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H39NO6S
#11: 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
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 293 K / pH: 6.7
Details: 6% PEG, 16% glycerol, 30 mM magnesium chloride, 30 mM calcium chloride, 0.1M MES/0.1M imidazole, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97976
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 2, 2013
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR, SAGITTALLY - HORIZONTALLY FOCUSSED
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 2.2→59.1 Å / Num. obs: 149698 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 15.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 12.4 % / Rmerge(I) obs: 4.112 / Mean I/σ(I) obs: 0.75 / % possible all: 99

-
Processing

Software
NameVersionClassification
DA+data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: 404J

404j


Resolution: 2.2→59.1 Å / SU ML: 0.33 / σ(F): 1.33 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 7515 5.02 %
Rwork0.186 --
obs0.188 149671 99.9 %
all-149869 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→59.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17498 0 283 561 18342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318560
X-RAY DIFFRACTIONf_angle_d0.83725291
X-RAY DIFFRACTIONf_dihedral_angle_d15.4317032
X-RAY DIFFRACTIONf_chiral_restr0.0582794
X-RAY DIFFRACTIONf_plane_restr0.0033279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.22510.37462560.38854592X-RAY DIFFRACTION98
2.2251-2.25130.3742310.34254694X-RAY DIFFRACTION100
2.2513-2.27870.38472710.32554648X-RAY DIFFRACTION100
2.2787-2.30760.35432270.3164713X-RAY DIFFRACTION100
2.3076-2.33790.34662580.30764674X-RAY DIFFRACTION100
2.3379-2.370.30732270.29694772X-RAY DIFFRACTION100
2.37-2.40380.3222580.28744622X-RAY DIFFRACTION100
2.4038-2.43970.32492830.2764723X-RAY DIFFRACTION100
2.4397-2.47780.29292520.2634677X-RAY DIFFRACTION100
2.4778-2.51840.32712760.26444636X-RAY DIFFRACTION100
2.5184-2.56190.31542450.2454721X-RAY DIFFRACTION100
2.5619-2.60850.26392520.22924749X-RAY DIFFRACTION100
2.6085-2.65860.29572280.23444714X-RAY DIFFRACTION100
2.6586-2.71290.29582330.22624711X-RAY DIFFRACTION100
2.7129-2.77190.29272680.21734685X-RAY DIFFRACTION100
2.7719-2.83640.24222470.21024726X-RAY DIFFRACTION100
2.8364-2.90730.26842450.20484739X-RAY DIFFRACTION100
2.9073-2.98590.24262380.19914756X-RAY DIFFRACTION100
2.9859-3.07380.24512380.18964737X-RAY DIFFRACTION100
3.0738-3.1730.21282540.18194735X-RAY DIFFRACTION100
3.173-3.28640.22982270.19284736X-RAY DIFFRACTION100
3.2864-3.41790.23652720.18384762X-RAY DIFFRACTION100
3.4179-3.57350.21542510.17564718X-RAY DIFFRACTION100
3.5735-3.76180.19782610.16314770X-RAY DIFFRACTION100
3.7618-3.99750.18582570.15424768X-RAY DIFFRACTION100
3.9975-4.3060.1832300.14774785X-RAY DIFFRACTION100
4.306-4.73920.15992550.13814851X-RAY DIFFRACTION100
4.7392-5.42460.19692500.15294800X-RAY DIFFRACTION100
5.4246-6.83280.22442500.18444885X-RAY DIFFRACTION100
6.8328-59.13720.19872750.1785057X-RAY DIFFRACTION100
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)
11.9175-0.4543-0.7563.7795-0.48671.5890.20860.03290.45-0.16460.0324-0.3818-0.80150.0977-0.23580.7182-0.0330.10780.4221-0.12080.441928.139598.439354.6697
21.73380.0217-0.11022.40851.0542.59310.00440.2105-0.0493-0.40950.2762-0.3584-0.40490.3939-0.2590.4019-0.05990.08590.4108-0.16030.375134.406783.0248.3955
31.4025-0.9041-0.80772.75290.66922.54170.0547-0.03380.02990.24280.0634-0.1457-0.01750.0885-0.10460.35290.0626-0.01310.3267-0.09490.324624.163779.978162.684
41.18781.3721-0.42052.45370.53865.04690.0079-0.0802-0.04920.2604-0.15810.93870.1535-0.75240.12820.41890.03730.11530.4591-0.15340.43189.469783.038571.8071
51.99590.11020.38161.6496-0.64031.3945-0.1942-0.17280.34570.73340.31470.3454-0.1795-0.3964-0.00090.62980.12630.03740.4456-0.1650.381316.820589.064480.6082
62.42350.02290.5722.35590.12622.110.019-0.00790.03790.3077-0.05850.14440.11270.13950.040.50190.07910.030.396-0.13650.28917.814788.769573.6637
70.5737-0.0453-0.03932.82110.93191.7539-0.10710.0129-0.22130.75090.13930.10710.63520.111-0.0460.38820.0727-0.01010.3805-0.11050.358622.954368.741466.5167
81.7866-0.10610.90842.47441.85394.2937-0.018-0.0123-0.12650.50220.3579-0.38930.51640.7085-0.25240.43350.1466-0.10880.3278-0.10160.41333.275661.54462.0279
91.2684-0.0973-0.21720.85330.66211.81760.01510.07570.2187-0.1366-0.0660.1008-0.3397-0.1577-0.08170.23310.0188-0.00540.2391-0.09380.283716.923959.048425.9655
100.68610.51710.68450.94320.12431.5311-0.1291-0.4013-0.0370.72010.25060.5906-0.0823-0.65840.44530.0132-0.0842-0.0205-0.0238-0.2641-0.006615.686249.750838.4297
112.3352-0.9738-0.20862.9345-0.37281.6916-0.06940.10410.335-0.11520.17040.079-0.35440.0261-0.08090.3027-0.083-0.00140.3206-0.01240.291314.858841.791-13.0193
122.0466-0.74340.02442.5928-0.07492.28150.03810.2231-0.0312-0.32460.1349-0.2539-0.09260.2318-0.13750.2393-0.08790.06790.3312-0.07290.305625.257930.084-14.6326
130.775-0.6796-0.65514.43750.28522.1465-0.06670.0906-0.03140.09070.01560.25210.20190.16950.01310.21340.00890.0130.2756-0.07760.269920.943720.0869-3.8184
142.2522-0.84590.41941.32880.67442.51030.04080.01740.0054-0.0007-0.1170.22770.0104-0.49870.05690.2308-0.04020.02930.3327-0.03420.27634.10428.03220.5709
152.6522-0.40441.29991.693-0.21152.3619-0.0765-0.30160.1068-0.01890.08910.18950.1042-0.5042-0.0380.2577-0.03730.04860.3553-0.05110.31881.864234.27728.8589
161.3009-0.4771-0.30291.38560.77431.4523-0.01460.0595-0.15090.23810.1333-0.11630.37120.1167-0.09160.3239-0.0065-0.05510.2409-0.06150.385720.98712.78512.6027
172.6347-0.2669-1.24215.48911.00972.2743-0.05870.83590.1203-0.24670.20620.32540.1152-0.1083-0.06650.4287-0.1466-0.00430.7005-0.08870.290315.472810.7887-41.1236
181.9981-0.5926-0.96432.95170.40622.8628-0.17241.1578-0.0615-0.43470.3186-0.59810.20460.4299-0.19730.6092-0.06870.13921.0016-0.41030.577629.10071.994-43.2421
191.7307-0.19690.00780.5552-0.87391.4821-0.01350.2765-0.5176-0.0780.1194-0.15860.68830.1125-0.08880.7318-0.02940.00950.6143-0.33450.657122.5769-9.2229-32.135
202.10040.67581.20371.81441.25221.1703-0.10020.7596-0.51-0.03790.07150.37920.9414-0.74260.03280.7709-0.29430.01550.809-0.21140.60367.2287-8.5912-38.2528
212.13170.83740.20141.0015-0.34093.74360.04850.33540.03660.03690.2556-0.2930.0803-0.1049-0.31940.4057-0.04510.05410.4608-0.19680.445718.76615.7626-23.2196
222.07890.0780.43752.68830.86072.36510.2080.5856-0.5909-0.0871-0.02210.49241.0229-0.9248-0.240.6756-0.3181-0.02960.8528-0.12090.58291.6253-6.847-26.3067
233.47870.5333-0.67531.977-0.13654.84980.03350.26160.03370.08710.08450.4158-0.352-1.0817-0.13210.419-0.06530.02540.6596-0.07620.44822.49584.2994-18.5376
240.30380.03210.0980.4425-0.10580.67390.08850.1687-0.4544-0.12350.24340.04790.9599-0.3320.91130.8215-0.048-0.0570.2859-0.33940.48118.9409-10.1609-25.5837
254.3463-0.5777-2.422.23930.2594.7622-0.2736-0.2503-0.57950.44430.2058-0.33510.73290.48770.00450.89250.0714-0.11610.4449-0.21470.824127.9563-13.9233-17.0002
261.7895-1.9695-0.4272.820.6040.3734-0.1569-0.20140.0920.86420.3555-0.1957-0.11930.46410.00810.8959-0.0307-0.1180.7046-0.19360.585927.590392.247181.7489
270.2937-0.2212-0.16020.17930.08310.2741-0.07790.0572-0.09230.13660.5094-0.39070.32630.7625-0.54130.46980.04510.05190.6463-0.29540.663743.559727.56233.4293
280.1759-0.2186-0.11230.3726-1.01352.2939-0.1808-0.2309-0.35790.1909-0.08-0.06990.5793-0.02580.19351.095-0.0070.10140.74620.10340.660315.839454.157891.2051
290.35060.04030.02261.5442-0.56141.2325-0.2979-0.2152-0.70590.490.265-0.43060.87510.01590.12251.6750.01520.22811.08330.13151.29825.288941.794100.6125
303.1103-0.0815-0.01371.36540.2942.0275-0.0191-0.6247-0.65760.67610.00340.0360.5832-0.2411-0.05881.384-0.17640.34670.9176-0.010.71851.575855.978690.0531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 160 )
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 273 )
4X-RAY DIFFRACTION4chain 'A' and (resid 274 through 311 )
5X-RAY DIFFRACTION5chain 'A' and (resid 312 through 338 )
6X-RAY DIFFRACTION6chain 'A' and (resid 339 through 372 )
7X-RAY DIFFRACTION7chain 'A' and (resid 373 through 401 )
8X-RAY DIFFRACTION8chain 'A' and (resid 402 through 439 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 311 )
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 438 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 72 )
12X-RAY DIFFRACTION12chain 'C' and (resid 73 through 161 )
13X-RAY DIFFRACTION13chain 'C' and (resid 162 through 199 )
14X-RAY DIFFRACTION14chain 'C' and (resid 200 through 311 )
15X-RAY DIFFRACTION15chain 'C' and (resid 312 through 372 )
16X-RAY DIFFRACTION16chain 'C' and (resid 373 through 440 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 56 )
18X-RAY DIFFRACTION18chain 'D' and (resid 57 through 160 )
19X-RAY DIFFRACTION19chain 'D' and (resid 161 through 214 )
20X-RAY DIFFRACTION20chain 'D' and (resid 215 through 238 )
21X-RAY DIFFRACTION21chain 'D' and (resid 239 through 268 )
22X-RAY DIFFRACTION22chain 'D' and (resid 269 through 311 )
23X-RAY DIFFRACTION23chain 'D' and (resid 312 through 337 )
24X-RAY DIFFRACTION24chain 'D' and (resid 338 through 415 )
25X-RAY DIFFRACTION25chain 'D' and (resid 416 through 441 )
26X-RAY DIFFRACTION26chain 'E' and (resid 6 through 46 )
27X-RAY DIFFRACTION27chain 'E' and (resid 47 through 143 )
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 207 )
29X-RAY DIFFRACTION29chain 'F' and (resid 208 through 275 )
30X-RAY DIFFRACTION30chain 'F' and (resid 276 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