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- PDB-2pf4: Crystal structure of the full-length simian virus 40 small t anti... -

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Basic information

Entry
Database: PDB / ID: 2pf4
TitleCrystal structure of the full-length simian virus 40 small t antigen complexed with the protein phosphatase 2A Aalpha subunit
Components
  • Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
  • Small T antigen
KeywordsHYDROLASE REGULATOR/VIRAL PROTEIN / PP2A / SV40 / small t / DnaJ / Aalpha subunit / HYDROLASE REGULATOR-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Cyclin A/B1/B2 associated events during G2/M transition / CTLA4 inhibitory signaling / Beta-catenin phosphorylation cascade / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling ...Inhibition of replication initiation of damaged DNA by RB1/E2F1 / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Cyclin A/B1/B2 associated events during G2/M transition / CTLA4 inhibitory signaling / Beta-catenin phosphorylation cascade / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / meiotic spindle elongation / RAF activation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin D associated events in G1 / PKR-mediated signaling / mitotic sister chromatid separation / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of meiotic cell cycle process involved in oocyte maturation / Resolution of Sister Chromatid Cohesion / Degradation of beta-catenin by the destruction complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / DARPP-32 events / RHO GTPases Activate Formins / Separation of Sister Chromatids / Platelet sensitization by LDL / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / ERK/MAPK targets / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / female meiotic nuclear division / protein antigen binding / AURKA Activation by TPX2 / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase regulator activity / Regulation of PLK1 Activity at G2/M Transition / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / protein serine/threonine phosphatase activity / T cell homeostasis / chromosome, centromeric region / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / chromosome segregation / host cell cytoplasm / neuron projection / protein heterodimerization activity / symbiont-mediated suppression of host gene expression / dendrite / neuronal cell body / glutamatergic synapse / synapse / host cell nucleus / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Small t-antigen, unique domain / Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / DnaJ domain / HEAT repeat / HEAT repeat / HEAT repeat profile. / HEAT, type 2 / HEAT repeats ...Small t-antigen, unique domain / Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / DnaJ domain / HEAT repeat / HEAT repeat / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Four Helix Bundle (Hemerythrin (Met), subunit A) / Armadillo-like helical / Alpha Horseshoe / Helix Hairpins / Armadillo-type fold / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Small t antigen / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Small t antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
Simian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / Resolution: 3.1 Å
AuthorsCho, U. / Morrone, S. / Xu, W.
CitationJournal: Plos Biol. / Year: 2007
Title: Structural basis of PP2A inhibition by small t antigen.
Authors: Cho, U.S. / Morrone, S. / Sablina, A.A. / Arroyo, J.D. / Hahn, W.C. / Xu, W.
History
DepositionApr 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
B: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
C: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
E: Small T antigen
F: Small T antigen
G: Small T antigen
H: Small T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,16916
Polymers343,6468
Non-polymers5238
Water0
1
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
E: Small T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0424
Polymers85,9122
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
F: Small T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0424
Polymers85,9122
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
G: Small T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0424
Polymers85,9122
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
H: Small T antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0424
Polymers85,9122
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.711, 105.501, 111.937
Angle α, β, γ (deg.)115.64, 109.55, 94.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / PP2A / subunit A / PR65-alpha isoform / PP2A / subunit A / R1-alpha isoform


Mass: 65392.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppp2r1a / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 star / References: UniProt: Q76MZ3
#2: Protein
Small T antigen


Mass: 20519.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: PolyomavirusPolyomaviridae / Strain: VA45-54-2 / Gene: small t antigen / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: Q9W9P1, UniProt: P03081*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / pH: 8
Details: 16% PEG 3350, 0.2 M Ammonium formate, 30 mM spermine, 6% 6-aminocaproic acid, 10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2007
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7.1 % / Av σ(I) over netI: 12 / Number: 441399 / Rmerge(I) obs: 0.071 / Χ2: 1.77 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 62490 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.675099.210.0383.1547.1
5.36.6799.510.0692.537.3
4.635.399.510.0712.3127.4
4.214.6399.210.0882.2137.5
3.914.2199.110.1151.6447.6
3.683.9199.110.1551.3727.6
3.493.6898.910.2271.1557.5
3.343.4998.810.3531.0017.3
3.213.3497.610.5150.9146.3
3.13.2189.710.7520.8724.8
ReflectionResolution: 3.1→50 Å / Num. obs: 62693 / % possible obs: 98 % / Observed criterion σ(I): 1.8 / Redundancy: 7.1 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 12.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.758 / % possible all: 88.7

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Phasing

PhasingMethod: MAD
Phasing MR
Highest resolutionLowest resolution
Rotation5 Å15 Å
Translation5 Å15 Å
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 62465
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
13.73-10040.70.63503
10.64-13.7332.70.773842
8.99-10.6432.70.7331061
7.93-8.9935.40.7381204
7.17-7.9340.10.7241355
6.6-7.1741.80.6991471
6.14-6.643.10.6821618
5.77-6.1438.70.7071709
5.46-5.7738.20.721790
5.19-5.4633.50.7621937
4.96-5.1931.50.7861998
4.76-4.9627.60.8072082
4.58-4.7628.30.82169
4.42-4.58280.812256
4.27-4.4228.70.7942320
4.14-4.2729.10.7942402
4.02-4.1429.90.7882451
3.91-4.0229.90.7822559
3.81-3.9129.20.7842642
3.71-3.81280.8012704
3.63-3.7130.20.7932703
3.55-3.6331.70.7782863
3.47-3.5531.60.7862884
3.4-3.4731.80.782881
3.33-3.433.70.7783027
3.27-3.3334.90.7593017
3.21-3.2736.50.723017
3.1-3.2142.70.6625000

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
SHARPphasing
DM6phasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IAE-A

2iae


Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.906 / SU B: 66.726 / SU ML: 0.527 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.601 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.304 3159 5.1 %RANDOM
Rwork0.244 ---
obs0.247 59306 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.44 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å2-0.5 Å21.94 Å2
2---2.8 Å2-1.19 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22794 0 8 0 22802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02223214
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.98331440
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85552888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.30124.708975
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.662154282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.11115136
X-RAY DIFFRACTIONr_chiral_restr0.0910.23704
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216959
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.211869
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.216124
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2738
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0180.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3911.514903
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.704223483
X-RAY DIFFRACTIONr_scbond_it0.93339283
X-RAY DIFFRACTIONr_scangle_it1.5634.57957
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 181 -
Rwork0.328 3486 -
obs--79 %
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)
13.62042.0250.63233.27530.31111.9962-0.0755-0.11590.0316-0.26530.09270.1117-0.2936-0.0363-0.0173-0.7860.22090.0403-0.23370.0186-0.3398-45.914741.719623.6664
22.34071.04230.55234.7629-2.56196.1764-0.1396-0.16490.4193-0.04990.41850.6022-0.5149-0.84-0.2790.02570.207-0.1269-0.205-0.02840.071-30.182182.6418-9.1192
31.86011.1121-0.11843.03390.43361.6349-0.10170.04740.0192-0.1143-0.0117-0.02850.54050.16120.1134-0.67860.11470.0373-0.28410.0376-0.437814.855530.503324.4571
43.19380.20570.05854.94882.07982.3345-0.01690.1963-0.5147-0.13660.071-0.38120.62010.5294-0.05410.0549-0.00960.0787-0.3007-0.0507-0.02730.8889-10.2585-9.7242
51.6373-0.27260.34094.00070.21471.72090.1429-0.0105-0.1844-0.0094-0.10260.13610.3045-0.1629-0.0403-0.3274-0.0615-0.0071-0.19650.079-0.2644-43.155144.0397-25.4976
62.29690.8244-1.58432.6192-2.0836.1714-0.0598-0.1362-0.30640.2206-0.00950.7520.2829-1.11780.06930.31540.0568-0.05190.1069-0.09030.5155-45.919-0.87531.8639
71.03230.4096-0.25183.3273-0.57811.023-0.11240.3003-0.0837-0.2558-0.0314-0.2509-0.00760.17590.1439-0.31490.00740.0441-0.0409-0.0783-0.306816.15127.85-23.4715
80.79530.49060.4963.38162.51293.93220.1214-0.60690.6931.01670.0529-0.4071-1.08780.2949-0.17420.49190.0152-0.03140.4967-0.02830.585617.512873.11748.8981
93.37410.71020.64743.96421.0046.602-0.0337-0.0972-0.3793-0.14670.0512-0.08210.54130.0508-0.0175-0.68870.2412-0.02-0.35440.0319-0.2869-23.829821.484520.4066
106.8131-0.2558-0.4485.7546-0.04438.8878-0.00890.26390.4572-0.2964-0.08160.152-0.5832-0.42660.0906-0.8910.1835-0.083-0.28130.0483-0.2638-7.445650.010622.9672
115.3656-1.5582-0.18414.68430.31046.963-0.19260.47170.1949-0.27720.3619-0.3402-0.25920.7336-0.1693-0.2971-0.0893-0.0526-0.14190.0058-0.0148-16.676753.775-25.7009
124.2135-1.209-1.10614.1577-1.12895.3431-0.24950.658-0.1093-0.29220.23150.17010.4014-0.30570.018-0.3134-0.1549-0.0923-0.1664-0.0325-0.152-11.519620.7126-24.3323
1310.37158.4974-11.09116.9619-9.086911.8605-0.1838-0.43520.6453-1.2808-0.9850.891-1.5453-1.06241.16880.00540.0062-0.00720.0012-0.00320.0015-25.326127.02887.6953
1416.95675.6945-6.54195.26683.562912.41370.7121.71620.7612-0.6699-0.30430.3192-1.9282-1.1786-0.40770.00610.0208-0.00950.01130.0042-0.0135-6.54245.900910.3077
153.9206-5.87834.6378.8133-6.95235.4842-0.32220.3724-1.6124-0.66130.4637-0.7942-0.16420.8451-0.14150.0035-0.00770.00370.002-0.0002-0.001-18.270349.4359-12.9577
163.9571-5.6483-5.36268.06227.65457.2673-0.0958-0.03120.8090.382-1.0015-0.5389-0.66431.12291.09730.0016-0.0036-0.0020.0001-0.0011-0.0013-10.133223.7838-11.3887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 39513 - 395
2X-RAY DIFFRACTION2AA396 - 587396 - 587
3X-RAY DIFFRACTION3BB15 - 39515 - 395
4X-RAY DIFFRACTION4BB396 - 589396 - 589
5X-RAY DIFFRACTION5CC13 - 39513 - 395
6X-RAY DIFFRACTION6CC396 - 589396 - 589
7X-RAY DIFFRACTION7DD13 - 39513 - 395
8X-RAY DIFFRACTION8DD396 - 589396 - 589
9X-RAY DIFFRACTION9EE1 - 1721 - 172
10X-RAY DIFFRACTION10FF1 - 1721 - 172
11X-RAY DIFFRACTION11GG1 - 1721 - 172
12X-RAY DIFFRACTION12HH1 - 1721 - 172
13X-RAY DIFFRACTION13EI - J601 - 6021
14X-RAY DIFFRACTION14FK - L701 - 7021
15X-RAY DIFFRACTION15GM - N801 - 8021
16X-RAY DIFFRACTION16HO - P901 - 9021

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Major update of PDB

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  • 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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