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- PDB-3d2e: Crystal structure of a complex of Sse1p and Hsp70, Selenomethioni... -

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Basic information

Entry
Database: PDB / ID: 3d2e
TitleCrystal structure of a complex of Sse1p and Hsp70, Selenomethionine-labeled crystals
Components
  • Heat shock 70 kDa protein 1
  • Heat shock protein homolog SSE1Heat shock response
KeywordsCHAPERONE / nucleotide exchange factor / protein folding / ATP-binding / Calmodulin-binding / Nucleotide-binding / Phosphoprotein / Stress response
Function / homology
Function and homology information


: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / adenyl-nucleotide exchange factor activity / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / : ...: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / adenyl-nucleotide exchange factor activity / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / : / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / proteasomal ubiquitin-independent protein catabolic process / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein complex assembly / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / protein folding chaperone / vesicle-mediated transport / inclusion body / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / positive regulation of interleukin-8 production / ATP-dependent protein folding chaperone / peptide binding / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / autophagy / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / virus receptor activity / cellular response to heat / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / protein refolding / proteasome-mediated ubiquitin-dependent protein catabolic process / vesicle / ficolin-1-rich granule lumen / blood microparticle / receptor ligand activity / protein stabilization / calmodulin binding / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Heat shock 70 kDa protein 1B / Heat shock 70 kDa protein 1A / Heat shock protein homolog SSE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsPolier, S. / Bracher, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structural basis for the cooperation of Hsp70 and Hsp110 chaperones in protein folding.
Authors: Polier, S. / Dragovic, Z. / Hartl, F.U. / Bracher, A.
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein homolog SSE1
B: Heat shock 70 kDa protein 1
C: Heat shock protein homolog SSE1
D: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,4379
Polymers236,2824
Non-polymers1,1555
Water7,710428
1
A: Heat shock protein homolog SSE1
B: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7645
Polymers118,1412
Non-polymers6243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Heat shock protein homolog SSE1
D: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6724
Polymers118,1412
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.840, 141.649, 150.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Heat shock protein homolog SSE1 / Heat shock response / Chaperone protein MSI3


Mass: 75821.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSE1, MSI3, YPL106C, LPG3C / Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) cod+ RLI / References: UniProt: P32589
#2: Protein Heat shock 70 kDa protein 1 / HSP70.1 / HSP70-1/HSP70-2


Mass: 42319.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSPA1, HSPA1B / Plasmid: pProEx-HtB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) cod+ RLI / References: UniProt: P08107, UniProt: P0DMV8*PLUS

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Non-polymers , 4 types, 433 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE AGSD LINKER WAS INTRODUCED ON PURPOSE BY PCR TO REPLACE THE LOOP RESIDUES ...AUTHORS STATE THAT THE AGSD LINKER WAS INTRODUCED ON PURPOSE BY PCR TO REPLACE THE LOOP RESIDUES VEEPIPLPEDAPEDAEQEFKKV OF UNP ENTRY P32589 AND WAS FOUND DISORDERED IN COORDINATE DEPOSITED.

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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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 17 % (w/v) polyethyleneglycol-6000, 50 mM KCl, 100 mM HEPES-KOH pH 7.5, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9719, 0.9792, 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: May 3, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97191
20.97921
30.97951
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 8.8 / Number: 311015 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / D res high: 2.6 Å / D res low: 103.142 Å / Num. obs: 85497 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.2280.8598.510.030.033.6
5.818.2299.510.0440.0443.7
4.755.8199.810.0610.0613.8
4.114.7599.910.0440.0443.8
3.684.1110010.0450.0453.8
3.363.6810010.0630.0633.8
3.113.3610010.1030.1033.8
2.913.1110010.1610.1613.8
2.742.9199.910.2440.2443.6
2.62.749910.3530.3533.1
ReflectionResolution: 2.35→103.142 Å / Num. obs: 115684 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 50.11 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.35-2.483.40.4721.656550166640.47299.7
2.48-2.633.80.3112.159996158980.311100
2.63-2.813.80.1963.956392149250.196100
2.81-3.033.80.1226.252504139090.122100
3.03-3.323.80.0741048626128630.074100
3.32-3.723.80.04415.643949116510.044100
3.72-4.293.80.03815.738808103230.038100
4.29-5.253.80.04313.23289287690.04399.9
5.25-7.433.70.03417.12541468340.03499.6
7.43-80.853.60.02221.41380838480.02298.3

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Phasing

PhasingMethod: MAD
Phasing dmFOM centric: 0.6 / Reflection centric: 8156
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.7-80.7670.970.970.9451994295904
4.2-6.70.930.940.8415550140171533
3.4-4.20.860.860.7719443179611482
2.9-3.40.680.690.5819515182571258
2.5-2.90.410.420.3334575326471928
2.4-2.50.250.250.221356203051051

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
SHELXphasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 17.676 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.262 5797 5 %RANDOM
Rwork0.21 ---
obs0.213 115424 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.668 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---1.91 Å20 Å2
3---2.06 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15327 0 70 428 15825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02215681
X-RAY DIFFRACTIONr_angle_refined_deg1.431.96621297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11952010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36225694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.562152584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9691578
X-RAY DIFFRACTIONr_chiral_restr0.1050.22454
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211849
X-RAY DIFFRACTIONr_nbd_refined0.2030.26956
X-RAY DIFFRACTIONr_nbtor_refined0.2980.210631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2720
X-RAY DIFFRACTIONr_metal_ion_refined0.0520.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.218
X-RAY DIFFRACTIONr_mcbond_it0.5631.510282
X-RAY DIFFRACTIONr_mcangle_it0.903216070
X-RAY DIFFRACTIONr_scbond_it1.46936034
X-RAY DIFFRACTIONr_scangle_it2.2834.55227
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 417 -
Rwork0.284 7870 -
all-8287 -
obs--100 %
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)
11.53870.02940.18461.369-0.34681.3458-0.08080.0408-0.0518-0.06450.11630.16120.074-0.0437-0.0354-0.2138-0.0040.014-0.2996-0.0014-0.183888.539977.252182.948
23.59341.90030.65724.3469-0.41122.16160.2141-0.5083-0.69240.3026-0.1325-0.15110.8328-0.1239-0.08160.1389-0.0090.0748-0.17340.08920.066786.192345.3625198.3048
30.32260.8681-0.14437.59811.63170.84010.1871-0.25520.16030.481-0.07540.280.04840.1537-0.1117-0.1003-0.0140.0472-0.0538-0.0909-0.033699.4513105.166210.0443
41.6106-0.94560.09232.16830.33392.5781-0.06660.04420.24930.0140.22430.0582-0.4007-0.2323-0.1577-0.17590.04470.0307-0.18230.133-0.025471.179106.2813183.3528
53.9714-0.7966-2.65029.68991.26174.45120.2940.32820.3443-2.3871-0.0263-1.0334-0.54760.3403-0.26770.4445-0.01540.1708-0.1261-0.08750.1251103.9829107.3796185.9787
62.1532-0.14990.45341.5831-0.40591.2679-0.210.3418-0.0999-0.0686-0.0027-0.2775-0.03810.22820.2127-0.1853-0.08960.0116-0.0904-0.0096-0.201274.5669136.6109119.4957
73.2934-0.2517-2.27231.12-0.19894.26490.20161.39390.5624-0.7791-0.0988-0.2689-0.3435-0.2972-0.10280.2629-0.19130.02060.80360.32610.058876.2912155.374190.0559
80.76830.4656-0.13940.7271.16387.40480.141-0.19430.28980.0027-0.12590.2056-0.48350.0534-0.0152-0.0316-0.012-0.0361-0.0827-0.11350.025963.0026160.8291150.1681
92.39770.28610.99292.94990.28842.1788-0.0817-0.2699-0.27030.3798-0.2183-0.5352-0.03010.13360.3-0.2006-0.0702-0.0966-0.05750.19880.028591.4976133.6687148.6076
105.21662.60220.86795.05582.966610.17360.517-0.4545-0.53590.8743-0.081-0.08772.7569-0.6324-0.43590.6085-0.0835-0.2540.0387-0.0246-0.105959.4296136.159149.6244
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 396
2X-RAY DIFFRACTION1A1001
3X-RAY DIFFRACTION1A2001
4X-RAY DIFFRACTION1A2002
5X-RAY DIFFRACTION1A2003 - 2081
6X-RAY DIFFRACTION1B383
7X-RAY DIFFRACTION1A2097 - 2132
8X-RAY DIFFRACTION1B415 - 417
9X-RAY DIFFRACTION2A397 - 500
10X-RAY DIFFRACTION2A525 - 540
11X-RAY DIFFRACTION2A2082 - 2085
12X-RAY DIFFRACTION2A2133 - 2143
13X-RAY DIFFRACTION3A541 - 654
14X-RAY DIFFRACTION3A2086 - 2094
15X-RAY DIFFRACTION3B384
16X-RAY DIFFRACTION3A2144 - 2158
17X-RAY DIFFRACTION3B418
18X-RAY DIFFRACTION4B4 - 229
19X-RAY DIFFRACTION4B308 - 382
20X-RAY DIFFRACTION4A2095
21X-RAY DIFFRACTION4B385 - 413
22X-RAY DIFFRACTION4A2159 - 2161
23X-RAY DIFFRACTION4B419 - 441
24X-RAY DIFFRACTION5B230 - 307
25X-RAY DIFFRACTION5A2096
26X-RAY DIFFRACTION5B414
27X-RAY DIFFRACTION5B442 - 445
28X-RAY DIFFRACTION6C2 - 396
29X-RAY DIFFRACTION6C1001
30X-RAY DIFFRACTION6C2001
31X-RAY DIFFRACTION6C2002 - 2079
32X-RAY DIFFRACTION6D1064 - 1071
33X-RAY DIFFRACTION6A2162
34X-RAY DIFFRACTION6C2095 - 2129
35X-RAY DIFFRACTION6D1127 - 1158
36X-RAY DIFFRACTION7C397 - 498
37X-RAY DIFFRACTION7C526 - 540
38X-RAY DIFFRACTION7C2080 - 2083
39X-RAY DIFFRACTION7C2130 - 2131
40X-RAY DIFFRACTION8C541 - 655
41X-RAY DIFFRACTION8C2084 - 2093
42X-RAY DIFFRACTION8C2132 - 2143
43X-RAY DIFFRACTION9D4 - 229
44X-RAY DIFFRACTION9D308 - 382
45X-RAY DIFFRACTION9C2094
46X-RAY DIFFRACTION9D1096 - 1124
47X-RAY DIFFRACTION9C2144 - 2146
48X-RAY DIFFRACTION9D1182 - 1197
49X-RAY DIFFRACTION10D230 - 307
50X-RAY DIFFRACTION10D1125 - 1126
51X-RAY DIFFRACTION10C2147
52X-RAY DIFFRACTION10D1198 - 1205

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