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- PDB-4ap4: Rnf4 - ubch5a - ubiquitin heterotrimeric complex -

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Basic information

Entry
Database: PDB / ID: 4ap4
TitleRnf4 - ubch5a - ubiquitin heterotrimeric complex
Components
  • E3 UBIQUITIN LIGASE RNF4
  • UBIQUITIN C
  • UBIQUITIN-CONJUGATING ENZYME E2 D1
KeywordsLIGASE/SIGNALLING PROTEIN / LIGASE-SIGNALLING PROTEIN COMPLEX / CHIMERA
Function / homology
Function and homology information


regulation of spindle assembly / regulation of kinetochore assembly / SUMO polymer binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein polyubiquitination / response to human chorionic gonadotropin / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects ...regulation of spindle assembly / regulation of kinetochore assembly / SUMO polymer binding / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of protein polyubiquitination / response to human chorionic gonadotropin / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / cellular response to hydroxyurea / Phosphorylation of the APC/C / cellular response to arsenic-containing substance / protein K6-linked ubiquitination / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / cellular response to testosterone stimulus / response to arsenic-containing substance / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / negative regulation of protein localization to chromatin / E2 ubiquitin-conjugating enzyme / nuclear androgen receptor binding / cellular response to cytokine stimulus / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / negative regulation of BMP signaling pathway / protein K63-linked ubiquitination / protein K48-linked ubiquitination / nucleosome binding / protein autoubiquitination / negative regulation of TORC1 signaling / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / TBP-class protein binding / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / nuclear estrogen receptor binding / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D
Similarity search - Function
RNF4, RING finger, HC subclass / : / Zinc finger, C3HC4 type (RING finger) / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 ...RNF4, RING finger, HC subclass / : / Zinc finger, C3HC4 type (RING finger) / Ring finger domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / E3 ubiquitin-protein ligase RNF4 / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPlechanovova, A. / Hay, R.T. / Tatham, M.H. / Jaffray, E. / Naismith, J.H.
CitationJournal: Nature / Year: 2012
Title: Structure of a Ring E3 Ligase and Ubiquitin-Loaded E2 Primed for Catalysis
Authors: Plechanovova, A. / Jaffray, E. / Tatham, M.H. / Naismith, J.H. / Hay, R.T.
History
DepositionMar 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references / Structure summary
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: E3 UBIQUITIN LIGASE RNF4
B: UBIQUITIN-CONJUGATING ENZYME E2 D1
C: UBIQUITIN C
E: UBIQUITIN-CONJUGATING ENZYME E2 D1
F: UBIQUITIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0759
Polymers66,8145
Non-polymers2624
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-42.4 kcal/mol
Surface area32240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.480, 65.090, 189.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 UBIQUITIN LIGASE RNF4 / RING FINGER PROTEIN 4 / SMALL NUCLEAR RING FINGER PROTEIN / PROTEIN SNURF


Mass: 14758.155 Da / Num. of mol.: 1 / Fragment: RESIDUES 131-195,131-195
Source method: isolated from a genetically manipulated source
Details: THE RING DOMAIN IS DUPLICATED BUT AS A FUSED DIMER. THAT IS THE SEQUENCE OF THE RING DOMAIN FROM RNF4 (RESIDUES 131 TO 194) IS LINKED BY A SINGLE GLYCINE RESIDUE TO ANOTHER RING DOMAIN (RESIDUES 131 TO 194).
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O88846, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein UBIQUITIN-CONJUGATING ENZYME E2 D1 / UBCH5A / STIMULATOR OF FE TRANSPORT / SFT / UBC4/5 HOMOLOG / UBCH5 / UBIQUITIN CARRIER PROTEIN D1 / ...UBCH5A / STIMULATOR OF FE TRANSPORT / SFT / UBC4/5 HOMOLOG / UBCH5 / UBIQUITIN CARRIER PROTEIN D1 / UBIQUITIN-CONJUGATING ENZYME E2(17)KB 1 / UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 1 / UBIQUITIN-PROTEIN LIGASE D1


Mass: 17134.553 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ISOPEPTIDE AMIDE LINKAGE OF C85K ON UBCH5A TO G76 OF UBIQUITIN CHAIN B LINKED TO CHAIN C (UBIQUITIN) CHAIN E LINKED TO CHAIN F (UBIQUITIN)
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P51668, ubiquitin-protein ligase
#3: Protein UBIQUITIN C


Mass: 8893.206 Da / Num. of mol.: 2 / Fragment: RESIDUES 76-152
Source method: isolated from a genetically manipulated source
Details: ISOPEPTIDE AMIDE LINKED TO UBCH5A (CHAIN B AND CHAIN E)
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: F5H7Y5, UniProt: P0CG48*PLUS
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, SER 22 TO ARG ENGINEERED RESIDUE IN CHAIN B, CYS 85 TO LYS ...ENGINEERED RESIDUE IN CHAIN B, SER 22 TO ARG ENGINEERED RESIDUE IN CHAIN B, CYS 85 TO LYS ENGINEERED RESIDUE IN CHAIN E, SER 22 TO ARG ENGINEERED RESIDUE IN CHAIN E, CYS 85 TO LYS
Sequence detailsTHE PROTEIN IS A FUSION DIMER OF TWO MOLECULES OF RNF4. EACH DOMAIN IS SER 131 TO ILE 194. THE N- ...THE PROTEIN IS A FUSION DIMER OF TWO MOLECULES OF RNF4. EACH DOMAIN IS SER 131 TO ILE 194. THE N-TERMINUS HAS A GAMG EXTENSION. GLY 195 LINKS THE TWO SEQUENCES. THUS SER 196 CORRESPONDS TO SER 131 OF THE SEQUENCE N-TERMINAL GAGSGS FROM CLONING S22R AND C85K MUTATION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.2 / Details: pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 31, 2012 / Details: MIRROR
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→190 Å / Num. obs: 32159 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 43.9
Reflection shellResolution: 2.21→2.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.17 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
xia2data reduction
xia2data scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2YH0 1UBQ 2XEU

2yh0

1ubq

2xeu


Resolution: 2.21→94.82 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.981 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24175 1625 5.1 %RANDOM
Rwork0.2075 ---
obs0.20926 30468 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.21→94.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 4 137 4722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024736
X-RAY DIFFRACTIONr_bond_other_d0.0030.023309
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9726406
X-RAY DIFFRACTIONr_angle_other_deg0.9763.0038091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46324.098205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.41915839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8381529
X-RAY DIFFRACTIONr_chiral_restr0.0730.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215171
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02900
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.206→2.263 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 116 -
Rwork0.262 1887 -
obs--91.05 %
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)
16.7172-0.1728-1.51592.77950.36588.2229-0.0248-0.24820.0807-0.1320.1125-0.41130.55510.8478-0.08770.14260.08250.04110.1024-0.02460.1306-17.732-8.75131.343
24.8383-2.0592-4.644315.9537-1.902819.4474-0.0428-0.58820.19692.18360.0887-0.5242-0.76021.1804-0.04590.4209-0.01290.08340.1306-0.00410.2415-18.5175.96917.67
33.1936-0.6905-1.69513.8248-1.12715.06420.0240.159-0.12550.20670.11980.60280.1323-0.5153-0.14390.0728-0.00460.10990.05440.0310.223-24.348-4.33713.086
410.5697-0.1022-4.23393.41590.7133.15040.1828-0.90720.78750.00240.10880.125-0.2560.2372-0.29160.03910.00140.02260.098-0.06660.1608-12.96314.4794.402
53.0283-0.1572-1.77572.26920.06672.0232-0.02410.1332-0.0899-0.32370.0140.00010.106-0.02180.01010.05670-0.00720.0107-0.00930.0491-7.2122.884-7.734
63.3342-3.1212-0.870617.21412.09943.8508-0.01150.0149-0.2022-0.86480.1144-0.89490.23170.5206-0.10290.2098-0.0330.15220.1547-0.07370.15928.26-0.302-17.367
75.15061.0785-1.35296.37770.54462.419-0.1552-0.7035-0.22370.71560.0707-0.58390.33130.52640.08450.12110.0943-0.04510.20360.02470.14640.226-5.73412.558
813.5319-5.440112.997630.957-19.375922.03260.74750.4892-1.0517-1.9292-0.3666-0.53581.86110.6636-0.38090.27290.15620.06040.2848-0.06470.53126.356-10.4234.156
93.9522-1.5445-0.47984.5508-0.55136.0763-0.2643-0.6003-0.17960.30790.2159-1.027-0.11411.08670.04840.08270.0402-0.03370.2901-0.01690.34565.788-2.4198.58
104.59291.99151.012514.5592-0.062210.90990.2188-0.87580.3109-0.280.2812-0.4924-0.94941.9375-0.50.2844-0.1625-0.01980.6984-0.24890.2842-17.6123.06450.307
112.5454-0.2971-1.62452.20270.7256.3143-0.0276-0.2519-0.03230.32360.0956-0.19590.8069-0.0465-0.0680.2752-0.0006-0.06420.09770.02440.0408-31.776-4.96153.829
125.72721.0507-0.6818.88023.48216.7846-0.094-0.04510.09470.4711-0.19111.16320.4883-1.53250.2850.3525-0.12780.04110.56450.03920.171-47.731-3.5363
1317.8351-1.68683.21427.67390.52098.0639-0.03170.57121.2318-0.7409-0.216-0.3694-0.8785-0.80480.24780.2570.10060.0510.18760.02790.1065-35.8849.5433.103
144.7068-3.2047-4.4286.45754.070711.87970.0630.343-0.11890.1427-0.33340.29630.2106-1.30610.27040.0401-0.00370.01430.25180.01340.0599-39.7520.39835.944
153.98694.48951.15235.30591.72538.3009-0.0098-0.20730.62180.0361-0.34210.3356-1.2781-1.49220.35190.39560.2419-0.13510.4857-0.00650.7499-41.33110.34238.96
1621.28722.6575-25.402536.0867-9.250856.7639-0.41241.01090.3523-0.04590.11130.91591.1284-2.55440.3010.4440.0935-0.17010.559-0.26930.5812-35.852-8.20743.277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A131 - 193
2X-RAY DIFFRACTION2A194 - 210
3X-RAY DIFFRACTION3A211 - 259
4X-RAY DIFFRACTION4B-3 - 28
5X-RAY DIFFRACTION5B29 - 126
6X-RAY DIFFRACTION6B127 - 147
7X-RAY DIFFRACTION7C0 - 48
8X-RAY DIFFRACTION8C49 - 56
9X-RAY DIFFRACTION9C57 - 76
10X-RAY DIFFRACTION10E1 - 32
11X-RAY DIFFRACTION11E33 - 119
12X-RAY DIFFRACTION12E120 - 147
13X-RAY DIFFRACTION13F0 - 22
14X-RAY DIFFRACTION14F23 - 54
15X-RAY DIFFRACTION15F55 - 70
16X-RAY DIFFRACTION16F71 - 76

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  • 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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