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- PDB-1xda: STRUCTURE OF INSULIN -

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Basic information

Entry
Database: PDB / ID: 1xda
TitleSTRUCTURE OF INSULIN
Components(FATTY ACID ACYLATED ...) x 2
KeywordsHORMONE / METABOLIC ROLE / CHEMICAL ACTIVITY / INSULIN ALBUMIN / FATTY ACID / GLUCOSE METABOLISM / DIABETES
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
PHENOL / MYRISTIC ACID / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWhittingham, J.L. / Havelund, S. / Jonassen, I.
Citation
Journal: Biochemistry / Year: 1997
Title: Crystal structure of a prolonged-acting insulin with albumin-binding properties.
Authors: Whittingham, J.L. / Havelund, S. / Jonassen, I.
#1: Journal: Diabetologia / Year: 1996
Title: Soluble, Fatty Acid Acylated Insulins Bind to Albumin and Show Protracted Action in Pigs
Authors: Markussen, J. / Havelund, S. / Kurtzhals, P. / Andersen, A.S. / Halstrom, J. / Hasselager, E. / Larsen, U.D. / Ribel, U. / Schaffer, L. / Vad, K. / Jonassen, I.
#2: Journal: Biopolymers / Year: 1992
Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol
Authors: Smith, G.D. / Dodson, G.G.
History
DepositionDec 18, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,56024
Polymers22,8668
Non-polymers1,69316
Water2,774154
1
A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1406
Polymers5,7172
Non-polymers4234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-7 kcal/mol
Surface area3980 Å2
MethodPISA
2
C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1406
Polymers5,7172
Non-polymers4234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-2 kcal/mol
Surface area4400 Å2
MethodPISA
3
E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1406
Polymers5,7172
Non-polymers4234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-11 kcal/mol
Surface area4110 Å2
MethodPISA
4
G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1406
Polymers5,7172
Non-polymers4234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-7 kcal/mol
Surface area4240 Å2
MethodPISA
5
E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules

E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules

E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,83936
Polymers34,29912
Non-polymers2,54024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area21680 Å2
ΔGint-332 kcal/mol
Surface area12240 Å2
MethodPISA
6
A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
hetero molecules

A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
hetero molecules

A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,83936
Polymers34,29912
Non-polymers2,54024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area23900 Å2
ΔGint-287 kcal/mol
Surface area12440 Å2
MethodPISA
7
A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
hetero molecules

A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
hetero molecules

A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,42018
Polymers17,1506
Non-polymers1,27012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7540 Å2
ΔGint-137 kcal/mol
Surface area9770 Å2
MethodPISA
8
E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
hetero molecules

E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
hetero molecules

E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,42018
Polymers17,1506
Non-polymers1,27012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5500 Å2
ΔGint-156 kcal/mol
Surface area10530 Å2
MethodPISA
9
G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules

G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules

G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,42018
Polymers17,1506
Non-polymers1,27012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7450 Å2
ΔGint-149 kcal/mol
Surface area10440 Å2
MethodPISA
10
C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
hetero molecules

C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
hetero molecules

C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,42018
Polymers17,1506
Non-polymers1,27012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8150 Å2
ΔGint-129 kcal/mol
Surface area10880 Å2
MethodPISA
11
E: FATTY ACID ACYLATED INSULIN
F: FATTY ACID ACYLATED INSULIN
G: FATTY ACID ACYLATED INSULIN
H: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,28012
Polymers11,4334
Non-polymers8478
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-25 kcal/mol
Surface area6630 Å2
MethodPISA
12
A: FATTY ACID ACYLATED INSULIN
B: FATTY ACID ACYLATED INSULIN
C: FATTY ACID ACYLATED INSULIN
D: FATTY ACID ACYLATED INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,28012
Polymers11,4334
Non-polymers8478
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-14 kcal/mol
Surface area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.752, 78.752, 79.199
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-30-

ZN

21B-31-

CL

31D-30-

ZN

41D-31-

CL

51F-30-

ZN

61F-31-

CL

71H-30-

ZN

81H-31-

CL

91B-57-

HOH

101D-53-

HOH

111F-51-

HOH

121H-47-

HOH

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Components

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FATTY ACID ACYLATED ... , 2 types, 8 molecules ACEGBDFH

#1: Protein/peptide
FATTY ACID ACYLATED INSULIN / NN304 INSULIN


Mass: 2383.698 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308
#2: Protein/peptide
FATTY ACID ACYLATED INSULIN / NN304 INSULIN


Mass: 3332.849 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P01308

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Non-polymers , 5 types, 170 molecules

#3: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsAT THE END OF CHAINS B, D, F, AND H, ATOM C1 OF A FATTY ACID (RESIDUE 30) IS COVALENTLY LINKED TO ...AT THE END OF CHAINS B, D, F, AND H, ATOM C1 OF A FATTY ACID (RESIDUE 30) IS COVALENTLY LINKED TO THE NZ ATOM OF A LYS SIDE CHAIN (RESIDUE 29).

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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: 2.07 Å3/Da / Density % sol: 40 %
Crystal growpH: 8.2
Details: HANGING DROP, 0.1M TRI-SODIUM CITRATE, 6% (W/V) TRIS, 0.02% (W/V) ZINC ACETATE, PH 8.2.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17.5 mg/mlNN304 insulin1drop
20.02 M1dropHCl
30.1 Mtrisodium citrate1reservoir
46 %(w/v)Tris1reservoir
50.02 %(w/v)zinc acetate1reservoir
65 %(w/v)phenol solution1reservoir
7ethanol1reservoir0.010-0.060ml

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 16624 / % possible obs: 98 % / Redundancy: 2.4 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.278 / % possible all: 73
Reflection
*PLUS
Num. measured all: 40024
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4-IODOPHENOL INSULIN DIMER

Resolution: 1.8→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.174 --
obs-16624 98 %
Displacement parametersBiso mean: 19.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 96 154 1842
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.632
X-RAY DIFFRACTIONp_mcangle_it2.273
X-RAY DIFFRACTIONp_scbond_it1.992
X-RAY DIFFRACTIONp_scangle_it3.033
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.080.1
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.280.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.270.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor15.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.720
X-RAY DIFFRACTIONp_special_tor

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