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- PDB-3q6n: Crystal Structure of Human MC-HSP90 in P21 space group -

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Basic information

Entry
Database: PDB / ID: 3q6n
TitleCrystal Structure of Human MC-HSP90 in P21 space group
ComponentsHeat shock protein HSP 90-alpha
KeywordsCHAPERONE / three domains / trimer of dimer / hexamer
Function / homology
Function and homology information


positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane ...positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / telomere maintenance via telomerase / protein unfolding / HSF1-dependent transactivation / response to unfolded protein / positive regulation of cell size / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of defense response to virus by host / eNOS activation / positive regulation of lamellipodium assembly / axonal growth cone / DNA polymerase binding / activation of innate immune response / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Signaling by ERBB2 / response to salt stress / cardiac muscle cell apoptotic process / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of cardiac muscle contraction / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / protein tyrosine kinase binding / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / lysosomal lumen / ESR-mediated signaling / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / neuron migration / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / tau protein binding / Regulation of necroptotic cell death / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Aggrephagy / Chaperone Mediated Autophagy / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / Regulation of PLK1 Activity at G2/M Transition / positive regulation of nitric oxide biosynthetic process / unfolded protein binding / melanosome
Similarity search - Function
Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein ...Heat shock protein 90, C-terminal domain / Rossmann fold - #11260 / Ribosomal Protein S5; domain 2 - #80 / Ribosomal Protein S5; domain 2 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock protein HSP 90-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLee, C.C. / Lin, T.W. / Ko, T.P. / Wang, A.H.-J.
CitationJournal: Plos One / Year: 2011
Title: The hexameric structures of human heat shock protein 90
Authors: Lee, C.C. / Lin, T.W. / Ko, T.P. / Wang, A.H.-J.
History
DepositionJan 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 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 / 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 / _struct_ref_seq_dif.details / _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: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
D: Heat shock protein HSP 90-alpha
E: Heat shock protein HSP 90-alpha
F: Heat shock protein HSP 90-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,80612
Polymers314,2296
Non-polymers5766
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.897, 90.868, 167.093
Angle α, β, γ (deg.)90.00, 115.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP 86 / HSP86 / Renal carcinoma antigen NY-REN-38


Mass: 52371.547 Da / Num. of mol.: 6
Fragment: Middle and C-terminal domain, UNP residues 293-732
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSP90AA1, HSP90A, HSPC1, HSPCA / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07900
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.43 Å3/Da / Density % sol: 64.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.0M ammonium sulfate, 0.04M Tris-sodium citrate, 0.04 mM cisplatin, pH 5.4-5.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
PH range: 5.4-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. all: 83280 / Num. obs: 82281 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 19.6
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 5.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q6M
Resolution: 3.05→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / SU B: 37.284 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 1.38 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25921 4017 5 %RANDOM
Rwork0.20447 ---
obs0.20721 76434 98.69 %-
all-77861 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.835 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17827 0 30 277 18134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218146
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.97824363
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5452132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23424.893887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.651153662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.73515104
X-RAY DIFFRACTIONr_chiral_restr0.0990.22704
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213253
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.691.510750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.339217455
X-RAY DIFFRACTIONr_scbond_it1.56537396
X-RAY DIFFRACTIONr_scangle_it2.8824.56908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.05→3.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 305 -
Rwork0.274 5580 -
obs--99.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.66211.17492.33161.9262-0.615.6594-0.0432-0.20220.6475-0.1918-0.18730.1134-0.12610.50260.23050.6488-0.124-0.16441.1098-0.16940.5791-53.57627.99735.877
25.77440.12510.03063.3505-0.63782.7053-0.1404-0.641-0.0960.11730.0584-0.21230.21410.08450.0820.63510.1244-0.01411.09050.05630.4921-36.872-28.20811.269
33.226-0.6361-0.40441.70351.1416.6415-0.35830.3711-0.2786-0.0089-0.1862-0.12110.3152-0.01030.54450.6672-0.02330.03671.163-0.24750.4817-52.599-27.88434.893
43.1452-1.5511-0.01542.5577-1.68117.3386-0.20690.25990.5116-0.11530.0348-0.0627-0.1538-0.16670.17210.66570.0068-0.14070.99950.10830.589-25.5927.57533.357
53.49711.4096-0.14953.8431-1.04715.25650.10670.0758-0.31730.16560.17440.15750.2489-0.128-0.28110.7795-0.0058-0.11020.82340.07630.6255-24.54-27.49638.189
65.256-0.07220.31843.3141.06012.7955-0.1503-0.3120.34440.18760.08640.1412-0.0478-0.04930.06390.78140.0644-0.14540.83610.0290.5559-42.04427.3399.882
717.46775.75810.75852.3889-0.53187.46460.4954-0.5478-0.9193-0.505-0.2535-0.4530.2285-0.0086-0.24190.48240.0052-0.30141.1668-0.08940.7102-50.85116.86540.026
89.8016-2.54245.63833.3787-1.45176.2531-0.2275-0.64250.79750.45780.02150.0332-0.40180.07390.2060.62390.0323-0.16121.0762-0.13740.6769-32.598-16.59412.483
9-3.815-2.8935-1.48637.5233.673435.7082-0.22170.31190.5009-0.1752-1.1278-1.1362-1.4117-0.38781.34940.76960.13370.0181.32480.08410.1698-54.768-16.73330.535
102.5836-1.37382.78392.3616-3.778617.82350.02230.1789-0.1785-0.4432-0.4430.47551.18510.09790.42070.9324-0.0203-0.16451.0312-0.00950.4211-24.00216.18728.861
1115.38734.3006-7.03653.33710.46012.14960.2751-0.64270.788-0.3863-0.1350.2042-0.27140.1872-0.14010.72420.0533-0.10280.91920.09190.7185-27.255-15.30940.757
1215.50820.8051-8.0073.07083.2644.58160.0421-0.1535-0.67750.3603-0.1604-0.0160.3059-0.10040.11830.82640.0283-0.07140.85090.15340.6282-46.57615.7810.941
135.70391.98192.7349-0.68390.93712.80.1939-0.44070.1227-0.0698-0.14620.03640.1811-0.0759-0.04760.7778-0.058-0.30420.8759-0.05570.7512-78.37815.62928.385
145.6949-1.9622.48961.413-1.17872.3140.03720.19360.3498-0.1081-0.1018-0.00050.18480.19330.06460.650.009-0.05910.87690.06260.6305-54.812-15.823-7.867
151.09960.0916-0.49840.1652.33317.9584-0.13160.11840.0220.0335-0.2879-0.0469-0.0424-0.47540.41950.86910.1275-0.10711.0204-0.09860.4565-59.601-15.62859.976
160.82730.2980.5091.1475-1.91037.9346-0.08720.0341-0.01540.021-0.2902-0.0580.12170.35290.37750.71340.1003-0.09881.01090.0690.5242-17.74615.65758.448
176.25352.6956-3.53650.1364-1.37013.03540.1345-0.433-0.113-0.1208-0.1738-0.0207-0.09330.28590.03930.70970.0203-0.02060.85110.15530.79420.452-15.11629.382
184.3124-2.0704-2.6841.69571.06531.8003-0.03370.1703-0.1863-0.2148-0.0310.0145-0.1824-0.07340.06470.81-0.0368-0.04480.88020.00020.6056-23.50214.802-8.693
195.45650.7712.72012.50190.62711.21420.3995-0.5191-0.26220.4959-0.3063-0.13250.3514-0.2531-0.09310.8313-0.2472-0.1180.91670.00440.6509-96.347-2.17916.259
202.2085-0.81240.38822.16840.38655.81490.4660.55850.6007-0.2041-0.0735-0.5287-0.0639-0.152-0.39250.63020.1990.03990.90710.40570.9175-72.4432.347-18.706
211.35090.887-1.51682.16861.92124.3771-0.01330.10580.0928-0.3349-0.66140.3214-0.5993-0.53560.67470.83320.1753-0.19641.0511-0.22560.6028-58.0513.25681.358
222.39711.12770.07412.6512-1.61893.6929-0.1884-0.3906-0.3457-0.3634-0.2496-0.4060.34190.20110.4380.78470.2041-0.06540.99960.30530.6354-18.55-2.76278.833
235.91210.3004-2.43062.4477-3.29912.1770.3024-0.806-0.15710.4647-0.40890.303-0.71640.74850.10650.6978-0.2386-0.01061.13240.03070.65718.0942.08716.165
243.1502-1.9999-2.96452.3484-0.94784.43220.03580.51-0.5555-0.01670.15270.49860.0318-0.132-0.18850.69970.0083-0.07150.9127-0.25570.8151-5.833-4.338-16.374
254.14850.0442-0.61371.7855-0.5462.66410.32660.14170.18350.0353-0.1998-0.22890.5347-0.099-0.12690.748-0.0395-0.19130.7734-0.02360.7297-93.163-5.0941.526
263.5154-0.4539-2.95860.7034-0.3472.55610.50780.43840.94890.0857-0.3768-0.3282-0.0878-0.3619-0.1310.62570.1691-0.05680.89890.27550.9893-85.0164.815-10.353
273.2711-1.1919-0.41860.71910.29612.7413-0.1181-0.19120.2961-0.2272-0.374-0.2311-0.1606-0.18470.49210.9861-0.0318-0.13070.8575-0.07960.5572-45.5845.23686.703
284.8929-0.2678-1.91970.6510.02311.7391-0.1547-0.1476-0.42940.1149-0.4620.06110.46380.25360.61660.97890.06530.03170.8920.21740.6052-30.645-4.60486.462
292.73231.47290.55132.1530.49262.15540.06920.0773-0.11650.00180.02870.2198-0.25540.2914-0.0980.6457-0.06590.06280.94360.09870.73214.8554.0591.628
304.069-0.57791.38381.59190.35942.87450.22880.1889-0.49290.0486-0.29180.01690.24910.19130.0630.67770.10120.0030.869-0.06090.85276.325-6.147-9.862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A297 - 349
2X-RAY DIFFRACTION2B297 - 349
3X-RAY DIFFRACTION3C297 - 349
4X-RAY DIFFRACTION4D297 - 349
5X-RAY DIFFRACTION5E297 - 348
6X-RAY DIFFRACTION6F297 - 349
7X-RAY DIFFRACTION7A360 - 393
8X-RAY DIFFRACTION8B358 - 394
9X-RAY DIFFRACTION9C360 - 393
10X-RAY DIFFRACTION10D360 - 394
11X-RAY DIFFRACTION11E358 - 394
12X-RAY DIFFRACTION12F358 - 395
13X-RAY DIFFRACTION13A407 - 552
14X-RAY DIFFRACTION14B408 - 552
15X-RAY DIFFRACTION15C407 - 552
16X-RAY DIFFRACTION16D407 - 552
17X-RAY DIFFRACTION17E408 - 552
18X-RAY DIFFRACTION18F408 - 552
19X-RAY DIFFRACTION19A553 - 611
20X-RAY DIFFRACTION20B553 - 611
21X-RAY DIFFRACTION21C557 - 611
22X-RAY DIFFRACTION22D556 - 613
23X-RAY DIFFRACTION23E553 - 611
24X-RAY DIFFRACTION24F557 - 614
25X-RAY DIFFRACTION25A631 - 698
26X-RAY DIFFRACTION26B631 - 698
27X-RAY DIFFRACTION27C631 - 696
28X-RAY DIFFRACTION28D631 - 698
29X-RAY DIFFRACTION29E631 - 697
30X-RAY DIFFRACTION30F630 - 698

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