[English] 日本語
Yorodumi
- PDB-4yee: beta2 carbohydrate binding module (CBM) of AMP-activated protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yee
Titlebeta2 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclodextrin
Components5'-AMP-activated protein kinase subunit beta-2
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding module (CBM) / AMP-activated protein kinase (AMPK) / glycogen
Function / homology
Function and homology information


AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process ...AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / apical plasma membrane / protein kinase binding / enzyme binding / signal transduction / nucleoplasm / nucleus / 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 / Immunoglobulin-like ...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
6-O-alpha-D-Glucosyl-beta-cyclodextrin / 5'-AMP-activated protein kinase subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / diffrn_source / entity / entity_src_gen / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Oct 14, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_branch_scheme / pdbx_molecule_features / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_seq_id / _chem_comp.pdbx_synonyms ..._atom_site.auth_seq_id / _chem_comp.pdbx_synonyms / _pdbx_branch_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id
Revision 3.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-AMP-activated protein kinase subunit beta-2
B: 5'-AMP-activated protein kinase subunit beta-2
C: 5'-AMP-activated protein kinase subunit beta-2
D: 5'-AMP-activated protein kinase subunit beta-2
E: 5'-AMP-activated protein kinase subunit beta-2
F: 5'-AMP-activated protein kinase subunit beta-2
G: 5'-AMP-activated protein kinase subunit beta-2
H: 5'-AMP-activated protein kinase subunit beta-2
I: 5'-AMP-activated protein kinase subunit beta-2
J: 5'-AMP-activated protein kinase subunit beta-2
K: 5'-AMP-activated protein kinase subunit beta-2
L: 5'-AMP-activated protein kinase subunit beta-2
M: 5'-AMP-activated protein kinase subunit beta-2
N: 5'-AMP-activated protein kinase subunit beta-2
O: 5'-AMP-activated protein kinase subunit beta-2
P: 5'-AMP-activated protein kinase subunit beta-2
Q: 5'-AMP-activated protein kinase subunit beta-2
R: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,82255
Polymers180,40018
Non-polymers25,42237
Water30,2111677
1
A: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5224
Polymers10,0221
Non-polymers1,4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5224
Polymers10,0221
Non-polymers1,4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5224
Polymers10,0221
Non-polymers1,4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4293
Polymers10,0221
Non-polymers1,4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4293
Polymers10,0221
Non-polymers1,4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4293
Polymers10,0221
Non-polymers1,4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3372
Polymers10,0221
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5224
Polymers10,0221
Non-polymers1,4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5224
Polymers10,0221
Non-polymers1,4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3372
Polymers10,0221
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4293
Polymers10,0221
Non-polymers1,4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4293
Polymers10,0221
Non-polymers1,4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4293
Polymers10,0221
Non-polymers1,4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5224
Polymers10,0221
Non-polymers1,4993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3372
Polymers10,0221
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4293
Polymers10,0221
Non-polymers1,4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
Q: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3372
Polymers10,0221
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
R: 5'-AMP-activated protein kinase subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3372
Polymers10,0221
Non-polymers1,3151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)204.538, 96.432, 118.724
Angle α, β, γ (deg.)90.00, 125.46, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
5'-AMP-activated protein kinase subunit beta-2 / AMPK subunit beta-2


Mass: 10022.198 Da / Num. of mol.: 18 / Fragment: UNP residues 74-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkab2 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QZH4
#2: Polysaccharide
Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1315.142 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: 6-O-alpha-D-Glucosyl-beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,8,8/[a2122h-1a_1-5]/1-1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1_g6-h1WURCSPDB2Glycan 1.1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1677 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: in 0.2 M lithium chloride, 20% w/v PEG 6000 and 0.1 M sodium HEPES pH 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→48.38 Å / Num. obs: 127116 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.098 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.8 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F15
Resolution: 2→43.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.721 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22463 6385 5 %RANDOM
Rwork0.16872 ---
obs0.1715 120729 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.2 Å2
2--0.51 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11966 0 1698 1677 15341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212478
X-RAY DIFFRACTIONr_angle_refined_deg1.682.06319551
X-RAY DIFFRACTIONr_angle_other_deg0.785329262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88251493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33624.966590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.503151892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5491532
X-RAY DIFFRACTIONr_chiral_restr0.1130.22572
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022987
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_it1.2811.7566008
X-RAY DIFFRACTIONr_mcbond_other1.2811.7566007
X-RAY DIFFRACTIONr_mcangle_it2.0962.6197480
X-RAY DIFFRACTIONr_mcangle_other2.0962.627481
X-RAY DIFFRACTIONr_scbond_it1.972.3718163
X-RAY DIFFRACTIONr_scbond_other1.972.3728164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0173.49812069
X-RAY DIFFRACTIONr_long_range_B_refined7.49418.09416025
X-RAY DIFFRACTIONr_long_range_B_other7.49318.09516026
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 486 -
Rwork0.237 8833 -
obs--98.49 %
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)
10.84220.36370.17932.32070.18641.0063-0.12730.03970.008-0.04690.0044-0.0820.0065-0.0030.12290.0730.0059-0.05020.03340.00290.136546.5913-14.19728.354
21.504-0.54110.38281.14420.34492.10250.0183-0.0494-0.0496-0.00510.04350.04770.1589-0.0138-0.06180.10550.0325-0.03460.06590.03240.062280.7416-10.6268-7.7423
31.06320.26080.2191.67340.00470.8024-0.0148-0.0623-0.0423-0.090.03590.0933-0.0397-0.0123-0.02120.10110.0129-0.0240.0276-0.00060.123255.03419.78037.0712
40.69890.25420.12271.32340.35872.06270.0641-0.08880.04230.0091-0.0051-0.0079-0.0704-0.0539-0.0590.06570.0304-0.03110.1076-0.01630.067283.4867-32.022338.6194
51.6695-0.4816-0.3790.6639-0.18751.30180.0186-0.14990.05960.00380.0279-0.00440.04890.1264-0.04640.050.0073-0.02960.1069-0.01080.088471.72990.322324.1846
61.6747-0.3415-1.21271.56970.13211.33430.1346-0.09670.2506-0.09490.0804-0.0327-0.1140.1696-0.2150.0976-0.0142-0.00510.0461-0.04650.130685.692214.7243-9.1694
72.7216-1.0169-0.22761.85-0.0330.6447-0.0044-0.03180.11450.06080.0196-0.0292-0.03-0.1492-0.01520.02990.0444-0.05010.0948-0.05380.207228.4516-3.078322.2418
81.8693-1.2834-0.72281.99870.74612.5094-0.11680.2302-0.02450.0701-0.0964-0.07930.1937-0.25090.21320.03630.0051-0.00920.1086-0.0770.085383.6766-15.6799-39.3329
91.8362-0.353-0.98711.55430.42941.70090.2409-0.26410.23710.0982-0.1030.1021-0.04860.3062-0.13790.0973-0.04380.02270.1439-0.10760.105554.032111.086237.1028
102.0227-0.1378-1.39990.40540.2561.57290.08760.29660.213-0.00260.1051-0.0855-0.0514-0.4339-0.19270.04950.0215-0.01120.24280.04690.1364101.34023.351521.9451
113.66180.8670.42991.05260.38371.71850.0032-0.5057-0.2055-0.0894-0.2161-0.0218-0.1326-0.31150.21290.0551-0.028-0.04430.27950.02780.116265.1923-48.987931.3705
122.9072-0.26430.2631.0084-0.12441.59570.02070.33110.04610.17620.0065-0.071-0.0872-0.4191-0.02730.09020.0344-0.04840.26720.03660.102664.8037-4.0819-26.1552
130.61210.48190.10171.0219-0.46112.14030.0648-0.14830.06310.0304-0.09950.19450.01270.05080.03470.08450.0141-0.01330.0761-0.00490.12245.2042-12.542838.459
141.1514-0.31280.661.4248-1.08944.67530.15530.0403-0.05970.07660.0892-0.0346-0.2366-0.3758-0.24450.13530.06450.00370.0930.06320.131485.5293-30.075213.3252
152.3564-0.5504-0.37331.80280.24360.9418-0.0325-0.0364-0.0794-0.08990.0814-0.15810.06250.0867-0.0490.05610.0551-0.01770.0931-0.00430.104102.5762-46.560419.2985
161.4013-1.33-0.93972.22120.63621.7155-0.0265-0.1319-0.13470.09160.09370.1803-0.21390.0691-0.06720.0924-0.03690.0440.0902-0.05020.1344116.91768.795740.9917
173.00291.0093-0.79030.92930.64623.0743-0.2145-0.2012-0.4781-0.0797-0.0597-0.17120.128-0.02060.27410.1041-0.00250.00070.02510.04520.174384.441632.981513.6761
181.8402-1.3641-0.191.4210.85253.2613-0.42210.0169-0.0240.37750.2310.28270.57920.23480.19110.2992-0.00190.01430.33730.32120.369583.706131.493838.5789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 156
2X-RAY DIFFRACTION2B74 - 156
3X-RAY DIFFRACTION3C74 - 156
4X-RAY DIFFRACTION4D78 - 156
5X-RAY DIFFRACTION5E72 - 156
6X-RAY DIFFRACTION6F72 - 156
7X-RAY DIFFRACTION7G74 - 156
8X-RAY DIFFRACTION8H72 - 156
9X-RAY DIFFRACTION9I72 - 156
10X-RAY DIFFRACTION10J72 - 156
11X-RAY DIFFRACTION11K75 - 156
12X-RAY DIFFRACTION12L75 - 156
13X-RAY DIFFRACTION13M72 - 156
14X-RAY DIFFRACTION14N73 - 156
15X-RAY DIFFRACTION15O73 - 156
16X-RAY DIFFRACTION16P72 - 156
17X-RAY DIFFRACTION17Q73 - 156
18X-RAY DIFFRACTION18R73 - 156

+
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://pdbjlvh1.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