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- PDB-6qlb: Calpain small subunit 1, RNA-binding protein Hfq -

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Basic information

Entry
Database: PDB / ID: 6qlb
TitleCalpain small subunit 1, RNA-binding protein Hfq
Components
  • Calpain small subunit 1
  • RNA-binding protein Hfq
KeywordsDNA BINDING PROTEIN / Calpain-1 / PEF(S) / Hfq / E.coli / Chaperone / Calcium binding / EF-Hand / Complex / 3D Structure Determination / Contamination / Contaminant / RNA binding / DNA binding / Cysteine / Protease / Nucleotide
Function / homology
Function and homology information


sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / calpain complex / regulation of translation, ncRNA-mediated / RNA folding chaperone / bent DNA binding / regulation of RNA stability / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models ...sRNA-mediated post-transcriptional gene silencing / positive regulation of translation, ncRNA-mediated / calpain complex / regulation of translation, ncRNA-mediated / RNA folding chaperone / bent DNA binding / regulation of RNA stability / calcium-dependent cysteine-type endopeptidase activity / Formation of the cornified envelope / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / regulation of macroautophagy / Degradation of the extracellular matrix / calcium ion binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / proteolysis / DNA binding / RNA binding / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / EF-hand / Recoverin; domain 1 / SH3 type barrels. / EF-Hand 1, calcium-binding site ...RNA-binding protein Hfq / Hfq protein / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / EF-hand / Recoverin; domain 1 / SH3 type barrels. / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
GUANINE / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / : / Calpain small subunit 1 / RNA-binding protein Hfq
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsRizkallah, P.J. / Cresser-Brown, J.O.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Calpain small subunit 1, RNA-binding protein Hfq
Authors: Rizkallah, P.J. / Cresser-Brown, J.O.
History
DepositionJan 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _citation.year / _database_2.pdbx_DOI ..._citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calpain small subunit 1
B: Calpain small subunit 1
C: Calpain small subunit 1
D: Calpain small subunit 1
E: RNA-binding protein Hfq
F: RNA-binding protein Hfq
G: RNA-binding protein Hfq
H: RNA-binding protein Hfq
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,04435
Polymers108,2518
Non-polymers1,79327
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21300 Å2
ΔGint-297 kcal/mol
Surface area41210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.607, 147.607, 147.607
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUMETMETAA2 - 1712 - 171
21GLUGLUMETMETBB2 - 1712 - 171
12GLUGLUTYRTYRAA2 - 1722 - 172
22GLUGLUTYRTYRCC2 - 1722 - 172
13GLUGLUTYRTYRAA2 - 1722 - 172
23GLUGLUTYRTYRDD2 - 1722 - 172
14GLUGLUMETMETBB1 - 1711 - 171
24GLUGLUMETMETCC1 - 1711 - 171
15GLUGLUMETMETBB1 - 1711 - 171
25GLUGLUMETMETDD1 - 1711 - 171
16GLUGLUSERSERCC1 - 1731 - 173
26GLUGLUSERSERDD1 - 1731 - 173
17GLYGLYALAALAEE1 - 631 - 63
27GLYGLYALAALAFF1 - 631 - 63
18GLYGLYALAALAEE1 - 631 - 63
28GLYGLYALAALAGG1 - 631 - 63
19GLYGLYALAALAEE1 - 631 - 63
29GLYGLYALAALAHH1 - 631 - 63
110GLYGLYALAALAFF1 - 631 - 63
210GLYGLYALAALAGG1 - 631 - 63
111GLYGLYALAALAFF1 - 631 - 63
211GLYGLYALAALAHH1 - 631 - 63
112GLYGLYALAALAGG1 - 631 - 63
212GLYGLYALAALAHH1 - 631 - 63

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
Calpain small subunit 1 / / CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent ...CSS1 / Calcium-activated neutral proteinase small subunit / CANP small subunit / Calcium-dependent protease small subunit / CDPS / Calcium-dependent protease small subunit 1 / Calpain regulatory subunit


Mass: 19997.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CAPNS1-deltaGR gene / Source: (gene. exp.) Homo sapiens (human) / Gene: CAPNS1, CAPN4, CAPNS / Production host: Escherichia coli (E. coli) / References: UniProt: P04632
#2: Protein
RNA-binding protein Hfq


Mass: 7065.178 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hfq, NCTC13125_02619 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A376T1I0, UniProt: P0A6X3*PLUS

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Non-polymers , 5 types, 183 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Chemical
ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5O
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / Diethylene glycol diethyl ether


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Molecular Dimensions Pact premier screen condition D06: 0.1 M MMT, 25% PEG1500, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.32→66.02 Å / Num. obs: 46565 / % possible obs: 100 % / Redundancy: 22.1 % / Biso Wilson estimate: 42.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.116 / Net I/σ(I): 19.2
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 22.2 % / Rmerge(I) obs: 1.115 / Num. unique obs: 3416 / CC1/2: 0.632 / Rrim(I) all: 1.141 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PHJ
Resolution: 2.32→66.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 18.513 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.382 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 2337 5.1 %RANDOM
Rwork0.20093 ---
obs0.20328 43741 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.223 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.32→66.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7591 0 90 156 7837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137851
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177227
X-RAY DIFFRACTIONr_angle_refined_deg1.8551.63910582
X-RAY DIFFRACTIONr_angle_other_deg1.3931.58716731
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3065944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18822.417451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.456151399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9421556
X-RAY DIFFRACTIONr_chiral_restr0.0990.21001
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028820
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021736
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_it1.9552.7193788
X-RAY DIFFRACTIONr_mcbond_other1.9522.7193787
X-RAY DIFFRACTIONr_mcangle_it3.0674.0674728
X-RAY DIFFRACTIONr_mcangle_other3.0674.0684729
X-RAY DIFFRACTIONr_scbond_it2.4043.0764063
X-RAY DIFFRACTIONr_scbond_other2.43.0754061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7684.4845855
X-RAY DIFFRACTIONr_long_range_B_refined5.84931.8078889
X-RAY DIFFRACTIONr_long_range_B_other5.84131.7568879
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)
11A53520.12
12B53520.12
21A53130.13
22C53130.13
31A53760.12
32D53760.12
41B54700.1
42C54700.1
51B53870.12
52D53870.12
61C53860.13
62D53860.13
71E16750.13
72F16750.13
81E17190.12
82G17190.12
91E17050.13
92H17050.13
101F16970.14
102G16970.14
111F17560.1
112H17560.1
121G16920.14
122H16920.14
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 161 -
Rwork0.321 3167 -
obs--97.51 %
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)
12.99470.59490.23251.53630.44894.0179-0.1286-0.10320.40670.18720.0958-0.0602-0.60180.1430.03290.28970.0605-0.08370.0807-0.04610.2623177.82210.7681108.3851
22.9621-0.6428-0.02880.9096-0.6032.3767-0.0144-0.0888-0.01870.11340.04980.09380.1665-0.1084-0.03540.15860.0206-0.04840.0544-0.03850.1526181.6366-11.89104.3382
32.34260.50190.76353.3144-0.25751.6083-0.00110.1096-0.23290.14990.14090.12370.34830.0457-0.13980.1864-0.04050.01440.2220.0810.2089146.5436-40.844997.1324
41.5186-0.59620.33473.0775-1.24183.8803-0.218-0.25890.03650.73840.50090.3463-0.18890.1202-0.28290.280.12020.06560.23650.07820.2082148.0824-24.0302113.9579
56.1541-1.16082.06937.09640.70883.7203-0.0592-0.205-0.3670.04550.171-0.71050.12890.7007-0.11180.0559-0.0387-0.03440.340.10740.1642174.1041-9.965273.7431
63.8367-0.99631.56887.4110.02414.14030.165-0.3855-0.80340.1173-0.0249-0.07630.58880.5344-0.14010.13520.024-0.05090.25950.19060.266162.0381-24.239775.996
74.98220.6980.29985.47090.66316.1226-0.0168-1.0366-0.39890.74210.00820.4850.1108-0.18630.00860.1182-0.01110.06920.32030.14210.1423132.8127-2.230697.875
82.6171-0.91240.43126.4136-0.36145.7571-0.1631-0.88040.02550.73740.09480.0004-0.45540.32710.06840.2001-0.0615-0.00990.3880.01230.0347147.34649.6911100.4306
900000000000000-00.2527-0.1745-0.13220.3546-0.0320.2327186.82113.11395.891
1000000000000000-00.6043-0.04050.03210.2428-0.130.3422171.0779.104126.301
1100000000000000-00.37820.1229-0.01850.2-0.16420.1646181.1013.139118.257
1200000000000000-00.5852-0.3670.16170.6803-0.0720.3455195.75613.736102.189
1300000000000000-00.283-0.15860.07681.20520.18430.6608160.1646.42589.867
1400000000000000-00.18450.08120.08290.31920.05290.2781175.625-14.884122.706
1500000000000000-00.0843-0.1037-0.15640.64010.06980.3193169.128-14.027113.588
1600000000000000-00.1352-0.0061-0.13790.2508-0.0080.1415199.551-10.43497.289
1700000000000000-00.11120.1349-0.08540.1751-0.09360.141191.685-4.295107.556
1800000000000000-00.8339-0.6120.02631.1616-0.18610.494163.212-6.86186.525
1900000000000000-00.3162-0.16520.17060.28790.05120.503129.242-45.17104.037
2000000000000000-00.34510.06550.05310.14180.13770.232153.024-43.342108.405
2100000000000000-00.1056-0.11270.0010.30320.27520.5602131.714-37.16496.838
2200000000000000-00.30920.2325-0.20770.22930.01270.6643163.867-49.054100.897
2300000000000000-00.94910.0353-0.49720.72850.36040.7648147.295-19.74982.774
2400000000000000-00.46610.4422-0.28840.7673-0.20290.4443165.289-31.525118.246
2500000000000000-00.33510.15530.09550.39580.24340.3133141.265-35.062116.37
2600000000000000-00.4113-0.00340.02560.6817-0.1140.1167163.043-23.904110.467
2700000000000000-00.73780.28060.41070.34760.25390.48130.689-26.844122.091
2800000000000000-00.9022-0.14630.39040.73350.31321.0086147.178-8.88893.112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 173
2X-RAY DIFFRACTION2B1 - 173
3X-RAY DIFFRACTION3C1 - 173
4X-RAY DIFFRACTION4D1 - 173
5X-RAY DIFFRACTION5E1 - 65
6X-RAY DIFFRACTION6F1 - 65
7X-RAY DIFFRACTION7G1 - 65
8X-RAY DIFFRACTION8H1 - 65
9X-RAY DIFFRACTION9A201
10X-RAY DIFFRACTION10A206
11X-RAY DIFFRACTION11A211
12X-RAY DIFFRACTION12A216
13X-RAY DIFFRACTION13A221
14X-RAY DIFFRACTION14B201
15X-RAY DIFFRACTION15B206
16X-RAY DIFFRACTION16B211
17X-RAY DIFFRACTION17B216
18X-RAY DIFFRACTION18B221
19X-RAY DIFFRACTION19C201
20X-RAY DIFFRACTION20C206
21X-RAY DIFFRACTION21C211
22X-RAY DIFFRACTION22C216
23X-RAY DIFFRACTION23C221
24X-RAY DIFFRACTION24D201
25X-RAY DIFFRACTION25D206
26X-RAY DIFFRACTION26D211
27X-RAY DIFFRACTION27D216
28X-RAY DIFFRACTION28D221

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