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- PDB-4d0l: Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Ra... -

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Basic information

Entry
Database: PDB / ID: 4d0l
TitlePhosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS
Components
  • PHOSPHATIDYLINOSITOL 4-KINASE BETA
  • RAS-RELATED PROTEIN RAB-11A
KeywordsTRANSFERASE/HYDROLASE / TRANSFERASE-HYDROLASE COMPLEX / TRANSFERASE / PHOSPHATIDYLINOSITOL 4-KINASE / PI4K / NUCLEOTIDE / GTP / RAB11 / PIK93 / SIGNALING / GTPASE / SIGNAL TRANSDUCTION / GOLGI / RECYCLING ENDOSOME / PI4P / PHOSPHOINOSITIDE / PTDINS4P / PI4KB
Function / homology
Function and homology information


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / regulation of endocytic recycling / postsynaptic recycling endosome / establishment of protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / regulation of cilium assembly / exosomal secretion / amyloid-beta clearance by transcytosis / rough endoplasmic reticulum membrane / melanosome transport / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / Synthesis of PIPs at the Golgi membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / protein localization to cilium / multivesicular body assembly / phosphatidylinositol biosynthetic process / dynein light intermediate chain binding / phosphatidylinositol-mediated signaling / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / lysosome organization / positive regulation of epithelial cell migration / exocytosis / inner ear development / cleavage furrow / phosphatidylinositol phosphate biosynthetic process / centriolar satellite / mitotic spindle assembly / phagocytic vesicle / transport vesicle / vesicle-mediated transport / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / receptor-mediated endocytosis / centriole / multivesicular body / small monomeric GTPase / G protein activity / 14-3-3 protein binding / trans-Golgi network membrane / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / Vasopressin regulates renal water homeostasis via Aquaporins / spindle pole / recycling endosome membrane / neuron projection development / endocytic vesicle membrane / cytoplasmic vesicle / microtubule binding / vesicle / mitochondrial outer membrane / endosome / phosphorylation / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / small GTPase Rab1 family profile. / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily ...: / PI4KB/PIK1, accessory (PIK) domain / small GTPase Rab1 family profile. / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-093 / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Ras-related protein Rab-11A / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsBurke, J.E. / Inglis, A.J. / Perisic, O. / Masson, G.R. / McLaughin, S.H. / Rutaganira, F. / Shokat, K.M. / Williams, R.L.
CitationJournal: Science / Year: 2014
Title: Structures of Pi4Kiiibeta Complexes Show Simultaneous Recruitment of Rab11 and its Effectors.
Authors: Burke, J.E. / Inglis, A.J. / Perisic, O. / Masson, G.R. / Mclaughlin, S.H. / Rutaganira, F. / Shokat, K.M. / Williams, R.L.
History
DepositionApr 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn
Item: _pdbx_data_processing_status.task_name
Revision 1.4Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / 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 / _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_label_asym_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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: PHOSPHATIDYLINOSITOL 4-KINASE BETA
B: RAS-RELATED PROTEIN RAB-11A
C: PHOSPHATIDYLINOSITOL 4-KINASE BETA
D: RAS-RELATED PROTEIN RAB-11A
E: PHOSPHATIDYLINOSITOL 4-KINASE BETA
F: RAS-RELATED PROTEIN RAB-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,71515
Polymers267,8556
Non-polymers2,8609
Water32418
1
A: PHOSPHATIDYLINOSITOL 4-KINASE BETA
B: RAS-RELATED PROTEIN RAB-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2385
Polymers89,2852
Non-polymers9533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-27.2 kcal/mol
Surface area29970 Å2
MethodPISA
2
C: PHOSPHATIDYLINOSITOL 4-KINASE BETA
D: RAS-RELATED PROTEIN RAB-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2385
Polymers89,2852
Non-polymers9533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-27.4 kcal/mol
Surface area30280 Å2
MethodPISA
3
E: PHOSPHATIDYLINOSITOL 4-KINASE BETA
F: RAS-RELATED PROTEIN RAB-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2385
Polymers89,2852
Non-polymers9533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-26.8 kcal/mol
Surface area30500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.795, 146.925, 188.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13B
23D
14B
24F
15C
25E
16D
26F

NCS domain segments:

Component-ID: 0 / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA128 - 78410 - 566
21SERSERCC128 - 78410 - 566
12SERSERAA128 - 78410 - 566
22SERSEREE128 - 78410 - 566
13ASPASPBB6 - 1779 - 180
23ASPASPDD6 - 1779 - 180
14ASPASPBB6 - 1779 - 180
24ASPASPFF6 - 1779 - 180
15SERSERCC128 - 78410 - 566
25SERSEREE128 - 78410 - 566
16ASPASPDD6 - 1829 - 185
26ASPASPFF6 - 1829 - 185

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.9992, 0.00955, -0.03844), (0.01053, 0.9996, -0.02546), (0.03818, -0.02585, -0.9989)-7.48, 26.8, 103.1
2given(-0.9943, 0.01597, -0.1058), (0.01522, 0.9999, 0.007889), (0.1059, 0.006233, -0.9944)-5.273, -24.54, 91.44
3given(-0.9994, 0.007342, 0.03435), (0.008588, 0.9993, 0.03625), (-0.03406, 0.03652, -0.9988)-9.92, 24.01, 82.22
4given(-0.9924, 0.02412, -0.1206), (0.02146, 0.9995, 0.02335), (0.1211, 0.02058, -0.9924)-6.009, -24.32, 86.28

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein PHOSPHATIDYLINOSITOL 4-KINASE BETA / PHOSPHATIDYLINOSITOL 4-KINASE IIIBETA / PI4K-BETA / PI4KBETA / PTDINS 4-KINASE BETA / NPIK / PI4K92


Mass: 64593.141 Da / Num. of mol.: 3 / Fragment: RESIDUES 121-407,508-784 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HDX-OPTIMISED DELETION VARIANT / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACEBAC1-HSPI4KIIIBETA / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9UBF8, 1-phosphatidylinositol 4-kinase
#2: Protein RAS-RELATED PROTEIN RAB-11A / RAB11A / RAB-11 / YL8


Mass: 24691.818 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PJB88 HSRAB11A-Q70L IN POPTG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62491, small monomeric GTPase

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Non-polymers , 4 types, 27 molecules

#3: Chemical ChemComp-093 / N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE / PIK-93 / N-[(2Z)-5-(4-CHLORO-3-{[(2-HYDROXYETHYL)AMINO]SULFONYL}PHENYL)-4-METHYL-1,3-THIAZOL-2(3H)-YLIDENE]ACETAMIDE


Mass: 389.878 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H16ClN3O4S2
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHREE HDX-OPTIMIZED DELETIONS AND S294A MUTATION. ISOFORM 2 OF UNIPROT Q9UBF8 (CHAINS ACE)

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 5.6
Details: 15% (W/V) PEG 4000, 0.1 M NA CITRATE PH 5.6, AND 0.2 M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2013 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.8→48.51 Å / Num. obs: 70875 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.9
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.04 / Mean I/σ(I) obs: 1.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3IHY AND 1OIW

3ihy

1oiw


Resolution: 2.94→115.84 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU B: 22.398 / SU ML: 0.386 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 3095 5.1 %RANDOM
Rwork0.21626 ---
obs0.21843 58056 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.221 Å2
Baniso -1Baniso -2Baniso -3
1-6 Å20 Å20 Å2
2--0.74 Å20 Å2
3----6.75 Å2
Refinement stepCycle: LAST / Resolution: 2.94→115.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15675 0 171 18 15864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01916155
X-RAY DIFFRACTIONr_bond_other_d0.0050.0215613
X-RAY DIFFRACTIONr_angle_refined_deg1.491.97421852
X-RAY DIFFRACTIONr_angle_other_deg1.225335826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45951935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02323.758745
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.591152903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.47315115
X-RAY DIFFRACTIONr_chiral_restr0.0810.22447
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217947
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023774
X-RAY DIFFRACTIONr_nbd_refined0.2480.23764
X-RAY DIFFRACTIONr_nbd_other0.2130.215514
X-RAY DIFFRACTIONr_nbtor_refined0.1910.28021
X-RAY DIFFRACTIONr_nbtor_other0.0910.28170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3040.211
X-RAY DIFFRACTIONr_metal_ion_refined0.3050.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2980.29
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0530.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1726.7247791
X-RAY DIFFRACTIONr_mcbond_other4.1726.7237790
X-RAY DIFFRACTIONr_mcangle_it6.610.0729709
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4347.1388364
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.13910.53112143
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A286500.14
12C286500.14
21A280100.15
22E280100.15
31B97570.15
32D97570.15
41B96810.15
42F96810.15
51C283510.14
52E283510.14
61D103960.14
62F103960.14
LS refinement shellResolution: 2.94→3.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 223 -
Rwork0.354 4161 -
obs--99.1 %

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