[English] 日本語
Yorodumi
- PDB-4yef: beta1 carbohydrate binding module (CBM) of AMP-activated protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yef
Titlebeta1 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclododextrin
Components5'-AMP-activated protein kinase subunit beta-1
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding module / CBM / AMPK / AMP-activated protein kinase / cyclodextrin
Function / homology
Function and homology information


Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / nucleotide-activated protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / protein kinase activity ...Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nail development / nucleotide-activated protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / protein kinase activity / positive regulation of gene expression / protein kinase binding / signal transduction / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold ...Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cyclodextrin / 5'-AMP-activated protein kinase subunit beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMobbs, J. / Gorman, M.A. / Parker, M.W. / Gooley, P.R. / Griffin, M.
CitationJournal: Biochem.J. / Year: 2015
Title: Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase.
Authors: Mobbs, J.I. / Koay, A. / Di Paolo, A. / Bieri, M. / Petrie, E.J. / Gorman, M.A. / Doughty, L. / Parker, M.W. / Stapleton, D.I. / Griffin, M.D. / Gooley, P.R.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_ls_restr_ncs
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _refine_ls_restr_ncs.pdbx_auth_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _refine_hist.d_res_low / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Apr 13, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_value_order
Revision 3.1Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-AMP-activated protein kinase subunit beta-1
B: 5'-AMP-activated protein kinase subunit beta-1
C: 5'-AMP-activated protein kinase subunit beta-1
D: 5'-AMP-activated protein kinase subunit beta-1
E: 5'-AMP-activated protein kinase subunit beta-1
F: 5'-AMP-activated protein kinase subunit beta-1
G: 5'-AMP-activated protein kinase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,20122
Polymers69,3707
Non-polymers8,83215
Water12,322684
1
A: 5'-AMP-activated protein kinase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1553
Polymers9,9101
Non-polymers1,2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-AMP-activated protein kinase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2554
Polymers9,9101
Non-polymers1,3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5'-AMP-activated protein kinase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1553
Polymers9,9101
Non-polymers1,2452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5'-AMP-activated protein kinase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1593
Polymers9,9101
Non-polymers1,2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 5'-AMP-activated protein kinase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2554
Polymers9,9101
Non-polymers1,3453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 5'-AMP-activated protein kinase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1593
Polymers9,9101
Non-polymers1,2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: 5'-AMP-activated protein kinase subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0632
Polymers9,9101
Non-polymers1,1531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.718, 68.394, 92.211
Angle α, β, γ (deg.)111.72, 95.56, 90.06
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11GA
21A
31B
41C
51D
61E
71F
12GB
22A
32B
42C
52D
62E
72F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114GA79 - 201
2114A79 - 201
3114B79 - 201
4114C79 - 201
5114D79 - 201
6114E79 - 201
7114F79 - 201
1124GB79 - 201
2124A79 - 201
3124B79 - 201
4124C79 - 201
5124D79 - 201
6124E79 - 201
7124F79 - 201

NCS ensembles :
ID
1
2

-
Components

#1: Protein
5'-AMP-activated protein kinase subunit beta-1 / AMPKb / 5'-AMP-activated protein kinase 40 kDa subunit


Mass: 9909.985 Da / Num. of mol.: 7 / Fragment: UNP residues 76-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkab1 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P80386
#2: Polysaccharide
Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 684 / 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: 3.42 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M lithium sulphate, 25 % w/v PEG 8000 and 0.1 M sodium acetate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.72→43.71 Å / Num. obs: 95126 / % possible obs: 97.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.043 / Rsym value: 0.06 / Net I/σ(I): 18.6
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1.9 / % possible all: 92.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z0M

1z0m


Resolution: 1.72→43.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.342 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21312 4768 5 %RANDOM
Rwork0.17766 ---
obs0.17944 90357 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.179 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20.03 Å2-0.3 Å2
2--0.73 Å2-0.07 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.72→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 586 684 5668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025829
X-RAY DIFFRACTIONr_bond_other_d0.0020.024987
X-RAY DIFFRACTIONr_angle_refined_deg1.6052.0578057
X-RAY DIFFRACTIONr_angle_other_deg0.812311656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17924.713244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7515734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4641517
X-RAY DIFFRACTIONr_chiral_restr0.1050.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021293
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_it1.0231.2492528
X-RAY DIFFRACTIONr_mcbond_other1.0231.2492527
X-RAY DIFFRACTIONr_mcangle_it1.7521.8593145
X-RAY DIFFRACTIONr_mcangle_other1.7511.8593146
X-RAY DIFFRACTIONr_scbond_it1.3491.4613301
X-RAY DIFFRACTIONr_scbond_other1.3481.4613302
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0912.1554910
X-RAY DIFFRACTIONr_long_range_B_refined7.96512.4425886
X-RAY DIFFRACTIONr_long_range_B_other7.96712.4365883
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11G1129MEDIUM POSITIONAL0.660.5
12A1129MEDIUM POSITIONAL0.530.5
13B1129MEDIUM POSITIONAL0.750.5
14C1129MEDIUM POSITIONAL0.530.5
15D1129MEDIUM POSITIONAL0.50.5
16E1129MEDIUM POSITIONAL0.750.5
17F1129MEDIUM POSITIONAL0.490.5
11G1129MEDIUM THERMAL4.342
12A1129MEDIUM THERMAL4.752
13B1129MEDIUM THERMAL5.142
14C1129MEDIUM THERMAL4.62
15D1129MEDIUM THERMAL5.612
16E1129MEDIUM THERMAL5.232
17F1129MEDIUM THERMAL5.592
21G1180MEDIUM POSITIONAL0.610.5
22A1180MEDIUM POSITIONAL0.570.5
23B1180MEDIUM POSITIONAL0.760.5
24C1180MEDIUM POSITIONAL0.570.5
25D1180MEDIUM POSITIONAL0.550.5
26E1180MEDIUM POSITIONAL0.770.5
27F1180MEDIUM POSITIONAL0.530.5
21G1180MEDIUM THERMAL3.362
22A1180MEDIUM THERMAL4.522
23B1180MEDIUM THERMAL5.162
24C1180MEDIUM THERMAL4.382
25D1180MEDIUM THERMAL5.862
26E1180MEDIUM THERMAL5.252
27F1180MEDIUM THERMAL5.832
LS refinement shellResolution: 1.718→1.763 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 307 -
Rwork0.302 6554 -
obs--93.81 %
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)
11.8927-0.3450.3431.3164-0.86551.52850.0296-0.02940.0637-0.0733-0.0486-0.0457-0.01410.01340.0190.04-0.00110.00870.07310.01070.12050.2075-3.1566.2051
21.13620.4960.23851.5790.53971.31790.0130.0713-0.00130.1097-0.01290.03450.0194-0.0749-0.00010.0499-0.01250.00550.078-0.00030.10970.0175-28.14075.2434
31.89160.37920.37151.24420.92891.55190.02990.03810.06240.0751-0.04540.043-0.0026-0.00190.01560.0438-0.02370.00720.0714-0.00050.121-18.1806-37.6183-2.7638
44.3295-0.5231-1.61210.98030.14234.0892-0.1706-0.5904-0.08790.06650.0065-0.07810.16030.47810.16420.02330.0151-0.00870.19820.03540.0264-27.4213-10.061326.4859
51.2107-0.56830.15961.5262-0.6441.29270.0162-0.07350.0102-0.1029-0.0284-0.03860.01740.07970.01220.0519-0.01690.00270.0820.01070.1119-18.44345.887-1.9606
64.17640.4972-1.64830.9117-0.10764.1769-0.14590.5889-0.0983-0.0613-0.01520.09160.1448-0.49860.16110.0188-0.0294-0.00910.1956-0.03070.039.1246-44.2593-23.0941
72.7711-0.8440.05830.6625-0.15412.39660.06460.0087-0.1655-0.0733-0.0615-0.00270.1616-0.1739-0.00320.0737-0.0501-0.01320.21670.00730.0224-10.4026-17.062843.6395
82.62040.491-0.24210.7180.15683.03880.0254-0.0211-0.1950.0755-0.0384-0.00440.20990.23570.0130.10230.0251-0.02410.2210.00560.0318-16.7657-17.384644.9595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A77 - 156
2X-RAY DIFFRACTION2B71 - 156
3X-RAY DIFFRACTION3C78 - 156
4X-RAY DIFFRACTION4D79 - 155
5X-RAY DIFFRACTION5E72 - 156
6X-RAY DIFFRACTION6F79 - 155
7X-RAY DIFFRACTION7GA79 - 153
8X-RAY DIFFRACTION8GB79 - 153

+
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