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- PDB-6f7c: TUBULIN-Compound 12 complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6f7c
TitleTUBULIN-Compound 12 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 / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / tubulin binding / spindle microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / 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-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Tubulin/FtsZ, GTPase domain / 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-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Tubulin/FtsZ, GTPase domain / 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; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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 / Chem-CVT / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 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: 2.002 Å
AuthorsMuehlethaler, T. / Prota, A.E. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Iscience / Year: 2019
Title: Structural Basis of Colchicine-Site targeting Acylhydrazones active against Multidrug-Resistant Acute Lymphoblastic Leukemia.
Authors: Cury, N.M. / Muhlethaler, T. / Laranjeira, A.B.A. / Canevarolo, R.R. / Zenatti, P.P. / Lucena-Agell, D. / Barasoain, I. / Song, C. / Sun, D. / Dovat, S. / Yunes, R.A. / Prota, A.E. / ...Authors: Cury, N.M. / Muhlethaler, T. / Laranjeira, A.B.A. / Canevarolo, R.R. / Zenatti, P.P. / Lucena-Agell, D. / Barasoain, I. / Song, C. / Sun, D. / Dovat, S. / Yunes, R.A. / Prota, A.E. / Steinmetz, M.O. / Diaz, J.F. / Yunes, J.A.
History
DepositionDec 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 17, 2024Group: 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
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)264,87121
Polymers261,6316
Non-polymers3,23915
Water12,845713
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22150 Å2
ΔGint-140 kcal/mol
Surface area77800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.810, 157.900, 180.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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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) / 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

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Non-polymers , 8 types, 728 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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-CVT / 3,4,5-trimethoxy-~{N}-[(~{E})-naphthalen-1-ylmethylideneamino]benzamide


Mass: 364.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N2O4
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 5% PEG 4K, 16% GLYCEROL, 30 MM MAGNESIUM CHLORIDE, 30 MM CALCIUM CHLORIDE, 0.1M MES/0.1M IMIDAZOLE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 199860 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.109 / Net I/σ(I): 17.81
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.2 % / Rmerge(I) obs: 3.984 / Mean I/σ(I) obs: 0.73 / Num. unique obs: 14518 / CC1/2: 0.254 / Rrim(I) all: 4.131 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2863: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT

5lxt


Resolution: 2.002→59.542 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.74
RfactorNum. reflection% reflection
Rfree0.2431 10119 5.06 %
Rwork0.2117 --
obs0.2133 199845 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.002→59.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16722 0 198 713 17633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617340
X-RAY DIFFRACTIONf_angle_d0.77323521
X-RAY DIFFRACTIONf_dihedral_angle_d15.1636417
X-RAY DIFFRACTIONf_chiral_restr0.0462569
X-RAY DIFFRACTIONf_plane_restr0.0043042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.002-2.02480.39992580.39675157X-RAY DIFFRACTION82
2.0248-2.04860.35293030.36126358X-RAY DIFFRACTION100
2.0486-2.07360.35573370.35016228X-RAY DIFFRACTION99
2.0736-2.09980.36853290.34556299X-RAY DIFFRACTION99
2.0998-2.12750.36543410.34196330X-RAY DIFFRACTION100
2.1275-2.15660.36853350.32886243X-RAY DIFFRACTION99
2.1566-2.18740.3343180.31326313X-RAY DIFFRACTION99
2.1874-2.22010.32563610.30676289X-RAY DIFFRACTION100
2.2201-2.25480.33453450.29246294X-RAY DIFFRACTION100
2.2548-2.29170.32093360.28676306X-RAY DIFFRACTION100
2.2917-2.33130.3343530.28316287X-RAY DIFFRACTION100
2.3313-2.37370.31973650.27586319X-RAY DIFFRACTION100
2.3737-2.41930.30083620.2636261X-RAY DIFFRACTION100
2.4193-2.46870.30863470.25796334X-RAY DIFFRACTION100
2.4687-2.52240.3023570.25886308X-RAY DIFFRACTION100
2.5224-2.58110.27323460.24616328X-RAY DIFFRACTION100
2.5811-2.64560.27973420.23886331X-RAY DIFFRACTION100
2.6456-2.71710.28573130.2446381X-RAY DIFFRACTION100
2.7171-2.79710.26983210.2386360X-RAY DIFFRACTION100
2.7971-2.88740.27473520.23966354X-RAY DIFFRACTION100
2.8874-2.99060.26753140.236410X-RAY DIFFRACTION100
2.9906-3.11030.27673160.2236413X-RAY DIFFRACTION100
3.1103-3.25180.26813450.22476354X-RAY DIFFRACTION100
3.2518-3.42330.26473380.20936414X-RAY DIFFRACTION100
3.4233-3.63770.22153390.1936417X-RAY DIFFRACTION100
3.6377-3.91850.20943780.17976381X-RAY DIFFRACTION100
3.9185-4.31280.19613110.16116489X-RAY DIFFRACTION100
4.3128-4.93660.17713460.14346477X-RAY DIFFRACTION100
4.9366-6.21850.20723370.18026537X-RAY DIFFRACTION100
6.2185-59.56830.21383740.20296754X-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)
11.36490.0306-0.07474.38131.69412.9235-0.02560.25250.123-0.63280.3864-0.4625-0.69310.562-0.30080.5383-0.13750.11930.5671-0.1980.481531.749386.281653.1874
22.54960.04660.57253.73881.36963.92930.113-0.16190.14690.485-0.10160.1855-0.1257-0.132-0.01420.5128-0.01890.10970.4105-0.14920.458917.690886.330871.1946
32.0433-0.2843-0.32914.7532.25764.15580.05060.0335-0.21070.93590.266-0.43580.90980.5237-0.2480.52430.1205-0.08950.4527-0.15120.493829.590862.070361.8838
42.4357-0.5168-0.24993.71261.44642.81580.10060.19450.4059-0.41750.0113-0.0566-0.55480.0516-0.11680.4003-0.0060.06260.3977-0.0620.428321.456961.024921.1641
52.0881-0.8731-0.10591.54720.63123.568-0.0385-0.21930.11480.1552-0.1440.3276-0.0887-0.75320.12340.3384-0.00240.07050.546-0.21520.5357.118359.889238.6324
61.4039-0.005-0.19434.74193.10136.5976-0.0289-0.224-0.2210.8787-0.03870.09980.81850.14990.06990.36450.02-0.03220.3616-0.04250.335422.699337.436630.8351
71.9638-0.23590.16943.3350.09232.2845-0.05090.21110.1321-0.28550.1394-0.0869-0.20410.2214-0.07860.2936-0.08510.0520.4004-0.04730.312720.131632.7918-11.4899
82.3672-0.58471.07691.8131.06543.3717-0.0041-0.02590.101-0.0057-0.16670.28810.0074-0.51990.14710.2659-0.07060.04580.346-0.04370.37782.470331.07973.5236
92.696-1.2016-3.05784.6845.21967.58710.00320.0692-0.18210.4480.1978-0.20380.59320.3762-0.1910.35630.0694-0.06470.2707-0.02070.322622.63510.76042.0923
102.7156-0.3015-0.25462.6533-0.46832.3762-0.18960.8994-0.1341-0.63490.3101-0.18070.30870.0311-0.13750.6832-0.14120.09950.866-0.19680.439324.24972.4257-39.9396
112.34620.2091-0.30872.23620.48483.336-0.14550.5003-0.1019-0.18780.22330.27570.3404-0.5187-0.08430.5158-0.12180.00280.5955-0.12530.41097.7961-0.7427-24.852
122.345-2.0798-2.45421.99911.80243.5622-0.11460.31-1.0643-0.10880.1227-0.1850.86480.40030.24420.98950.04490.11140.7098-0.39080.818829.0049-18.5268-26.5757
134.0705-3.33721.06455.0283-0.48150.3651-0.4103-0.3610.46061.90560.3678-1.1747-0.93080.6732-0.11021.1623-0.1173-0.03310.6751-0.23710.68325.337995.179684.1598
141.62082.68692.77114.42184.70645.6575-0.0727-0.37360.43950.29250.3968-0.1890.18520.6391-0.39020.475-0.00390.03891.0516-0.38810.810143.740155.248734.5911
150.2315-0.678-0.95138.83678.33888.3285-0.0984-0.0855-0.1240.36390.3469-0.34980.56730.7912-0.26280.62520.11440.1170.9485-0.30370.848442.57627.6139-18.6845
164.09131.624-0.61745.5250.1395.1228-0.22630.6811-0.87010.0974-0.0622-0.07331.3914-0.29570.19120.8732-0.07360.14320.5975-0.1980.63596.144354.61370.0623
172.5239-0.4447-1.27194.7491-1.85524.735-0.1025-0.9578-0.32890.6387-0.2345-0.55530.07821.36590.36240.8190.1523-0.13691.0030.12730.671211.951759.6747104.5933
182.80370.4721-1.90110.7878-0.45982.7719-0.42360.066-0.80020.21950.20220.01970.7408-0.23920.09830.88270.02180.13850.43190.02810.6734-3.388656.602691.5751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 205)
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 381)
3X-RAY DIFFRACTION3chain 'A' and (resid 382 through 436)
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 205)
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 381)
6X-RAY DIFFRACTION6chain 'B' and (resid 382 through 436)
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 205)
8X-RAY DIFFRACTION8chain 'C' and (resid 206 through 381)
9X-RAY DIFFRACTION9chain 'C' and (resid 382 through 440)
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 205)
11X-RAY DIFFRACTION11chain 'D' and (resid 206 through 381)
12X-RAY DIFFRACTION12chain 'D' and (resid 382 through 436)
13X-RAY DIFFRACTION13chain 'E' and (resid 7 through 28)
14X-RAY DIFFRACTION14chain 'E' and (resid 45 through 89)
15X-RAY DIFFRACTION15chain 'E' and (resid 90 through 140)
16X-RAY DIFFRACTION16chain 'F' and (resid 1 through 66)
17X-RAY DIFFRACTION17chain 'F' and (resid 67 through 198)
18X-RAY DIFFRACTION18chain 'F' and (resid 199 through 379)

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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

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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

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