[English] 日本語
Yorodumi
- PDB-3vux: Crystal structure of A20 ZF7 in complex with linear ubiquitin, form II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vux
TitleCrystal structure of A20 ZF7 in complex with linear ubiquitin, form II
Components
  • Polyubiquitin-C
  • Tumor necrosis factor alpha-induced protein 3
KeywordsPROTEIN BINDING/METAL BINDING PROTEIN / zinc finger / PROTEIN BINDING-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of B cell activation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway ...regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of B cell activation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / negative regulation of toll-like receptor 2 signaling pathway / protein K11-linked deubiquitination / negative regulation of chronic inflammatory response / negative regulation of toll-like receptor 4 signaling pathway / : / regulation of germinal center formation / B-1 B cell homeostasis / protein K48-linked deubiquitination / regulation of defense response to virus by host / regulation of tumor necrosis factor-mediated signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / protein K63-linked deubiquitination / positive regulation of hepatocyte proliferation / negative regulation of bone resorption / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of interleukin-2 production / negative regulation of interleukin-1 beta production / K63-linked deubiquitinase activity / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of interleukin-6 production / response to muramyl dipeptide / positive regulation of Wnt signaling pathway / negative regulation of tumor necrosis factor production / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of protein ubiquitination / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of innate immune response / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin
Similarity search - Function
Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / OTU domain / OTU domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain ...Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / OTU domain / OTU domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Polyubiquitin-C / Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsNishimasu, H. / Ishitani, R. / Nureki, O.
CitationJournal: Embo J. / Year: 2012
Title: Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-kappaB regulation
Authors: Tokunaga, F. / Nishimasu, H. / Ishitani, R. / Goto, E. / Noguchi, T. / Mio, K. / Kamei, K. / Ma, A. / Iwai, K. / Nureki, O.
History
DepositionJul 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyubiquitin-C
B: Polyubiquitin-C
C: Polyubiquitin-C
E: Tumor necrosis factor alpha-induced protein 3
F: Tumor necrosis factor alpha-induced protein 3
G: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,03613
Polymers37,6606
Non-polymers3767
Water5,783321
1
A: Polyubiquitin-C
G: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7205
Polymers12,5532
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-15 kcal/mol
Surface area6350 Å2
MethodPISA
2
B: Polyubiquitin-C
E: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6584
Polymers12,5532
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-18 kcal/mol
Surface area6350 Å2
MethodPISA
3
C: Polyubiquitin-C
F: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6584
Polymers12,5532
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-19 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.329, 62.329, 85.180
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

-
Protein / Protein/peptide , 2 types, 6 molecules ABCEFG

#1: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 3 / Fragment: Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P0CG48
#2: Protein/peptide Tumor necrosis factor alpha-induced protein 3 / TNF alpha-induced protein 3 / OTU domain-containing protein 7C / Putative DNA-binding protein A20 / ...TNF alpha-induced protein 3 / OTU domain-containing protein 7C / Putative DNA-binding protein A20 / Zinc finger protein A20


Mass: 3976.549 Da / Num. of mol.: 3 / Fragment: A20-type 7 Zinc finger domain, residues 757-790
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P21580

-
Non-polymers , 4 types, 328 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.54 Å3/Da / Density % sol: 51.51 % / Mosaicity: 0.26 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.276
ReflectionResolution: 1.699→50 Å / Num. all: 40121 / Num. obs: 40121 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Χ2: 2.619 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.732.20.3718261.044189.6
1.73-1.762.60.36519251.026195.2
1.76-1.792.80.33719671.023196.1
1.79-1.832.90.33220021.096197.4
1.83-1.8730.3119771.133198.2
1.87-1.913.20.2720171.252198
1.91-1.963.40.26120411.408198.7
1.96-2.023.60.23920221.446199.1
2.02-2.073.80.21420071.579199.3
2.07-2.1440.19820161.792199.3
2.14-2.224.10.17420461.882199.9
2.22-2.314.10.15820322.079199.6
2.31-2.414.30.14720402.407199.9
2.41-2.544.30.13420092.634199.8
2.54-2.74.50.12120693.003199.6
2.7-2.914.50.10819993.551199.7
2.91-3.24.40.10320404.512199.3
3.2-3.664.30.08220414.893199.8
3.66-4.614.40.06620214.638199.6
4.61-504.40.05920244.396198.6

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.7.2_869refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.699→26.989 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 2.11 / Phase error: 30.87 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2015 5.02 %random
Rwork0.1654 ---
all0.1671 40113 --
obs0.1671 40113 98.4 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.911 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 94.87 Å2 / Biso mean: 31.128 Å2 / Biso min: 13.11 Å2
Baniso -1Baniso -2Baniso -3
1-5.8668 Å2-0 Å2-0 Å2
2--5.8668 Å2-0 Å2
3----11.7335 Å2
Refinement stepCycle: LAST / Resolution: 1.699→26.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 10 321 2878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092610
X-RAY DIFFRACTIONf_angle_d0.923489
X-RAY DIFFRACTIONf_chiral_restr0.058381
X-RAY DIFFRACTIONf_plane_restr0.003464
X-RAY DIFFRACTIONf_dihedral_angle_d14.588992
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7003-1.74280.32791380.28562531266986
1.7428-1.790.25741250.25272640276592
1.79-1.84260.29731370.24442692282993
1.8426-1.90210.25661470.22182718286593
1.9021-1.970.23141450.20312719286494
1.97-2.04890.23521460.19772697284394
2.0489-2.14210.21041480.17532783293194
2.1421-2.25490.23991380.17832772291095
2.2549-2.39610.20411580.17592762292094
2.3961-2.58090.22731450.17412740288595
2.5809-2.84040.22031440.16722772291695
2.8404-3.25060.18511410.16032719286095
3.2506-4.09260.17731330.12892759289295
4.0926-25.13170.15521400.12612761290195
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)
11.7062-0.5047-0.61912.39150.1841.9880.0094-0.0064-0.08510.00170.0324-0.19810.09430.3287-0.04190.14590.0469-0.00850.2406-0.00950.19583.963928.22513.334
21.4867-0.92330.18852.9657-0.03122.0035-0.10150.1487-0.15570.10840.05650.13480.091-0.1740.03530.0715-0.00430.01380.2079-0.02590.2104-28.313610.3203-8.1527
32.98560.3312-0.01221.91880.55122.4481-0.19320.1019-0.27840.0920.10690.22940.2936-0.1720.06960.1946-0.00240.02510.2281-0.03150.248-6.8979-2.3788-7.3113
41.6466-0.014-0.8620.35070.02022.10230.0484-0.1210.17860.0926-0.0211-0.2395-0.51030.41110.0420.2381-0.1439-0.03020.1931-0.00130.2633-24.358520.2373-24.3684
52.8270.7514-0.38833.20760.44723.19650.02250.34610.07660.04720.07210.116-0.1301-0.2261-0.08390.1960.02330.02140.11030.02040.2092-3.4547.29349.1133
61.2472-0.4741-0.33431.28650.36141.352-0.03420.1821-0.20880.0635-0.02930.1806-0.0332-0.2445-0.08080.16860.1361-0.01710.2417-0.02280.2449-5.773231.871529.9904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:76)A1 - 76
2X-RAY DIFFRACTION2(CHAIN B AND RESID 1:76)B1 - 76
3X-RAY DIFFRACTION3(CHAIN C AND RESID 1:76)C1 - 76
4X-RAY DIFFRACTION4(CHAIN E AND (RESID 758:790 OR RESID 801:802) )E758 - 790
5X-RAY DIFFRACTION4(CHAIN E AND (RESID 758:790 OR RESID 801:802) )E801 - 802
6X-RAY DIFFRACTION5(CHAIN F AND (RESID 759:790 OR RESID 801:802) )F759 - 790
7X-RAY DIFFRACTION5(CHAIN F AND (RESID 759:790 OR RESID 801:802) )F801 - 802
8X-RAY DIFFRACTION6(CHAIN G AND (RESID 757:790 OR RESID 801:802) )G757 - 790
9X-RAY DIFFRACTION6(CHAIN G AND (RESID 757:790 OR RESID 801:802) )G801 - 802

+
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