[English] 日本語
Yorodumi
- PDB-2be6: 2.0 A crystal structure of the CaV1.2 IQ domain-Ca/CaM complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2be6
Title2.0 A crystal structure of the CaV1.2 IQ domain-Ca/CaM complex
Components
  • Calmodulin 2
  • Voltage-dependent L-type calcium channel alpha-1C subunit
KeywordsMEMBRANE PROTEIN / calmodulin / calcium channel / IQ domain / inactivation / facilitation / calcium-dependent / gating / voltage-gated
Function / homology
Function and homology information


Wnt signaling pathway, calcium modulating pathway / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / regulation of high voltage-gated calcium channel activity / positive regulation of adenylate cyclase activity / inositol phosphate metabolic process / regulation of opsin-mediated signaling pathway / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase ...Wnt signaling pathway, calcium modulating pathway / voltage-gated calcium channel activity involved in AV node cell action potential / voltage-gated calcium channel activity involved in cardiac muscle cell action potential / immune system development / regulation of high voltage-gated calcium channel activity / positive regulation of adenylate cyclase activity / inositol phosphate metabolic process / regulation of opsin-mediated signaling pathway / membrane depolarization during atrial cardiac muscle cell action potential / Phase 2 - plateau phase / calcium ion transmembrane transport via high voltage-gated calcium channel / platelet degranulation / regulation of nitric-oxide synthase activity / positive regulation of muscle contraction / membrane depolarization during AV node cell action potential / high voltage-gated calcium channel activity / : / : / positive regulation of cyclic-nucleotide phosphodiesterase activity / cardiac conduction / L-type voltage-gated calcium channel complex / : / membrane depolarization during cardiac muscle cell action potential / establishment of protein localization to mitochondrial membrane / cell communication by electrical coupling involved in cardiac conduction / type 3 metabotropic glutamate receptor binding / regulation of ventricular cardiac muscle cell action potential / camera-type eye development / NCAM1 interactions / cardiac muscle cell action potential involved in contraction / embryonic forelimb morphogenesis / glycogen catabolic process / calcium ion transport into cytosol / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / voltage-gated calcium channel complex / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / positive regulation of DNA binding / CaMK IV-mediated phosphorylation of CREB / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / Glycogen breakdown (glycogenolysis) / nitric-oxide synthase binding / CLEC7A (Dectin-1) induces NFAT activation / negative regulation of peptidyl-threonine phosphorylation / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / regulation of synaptic vesicle exocytosis / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / alpha-actinin binding / Fc-epsilon receptor signaling pathway / calcineurin-mediated signaling / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / regulation of synaptic vesicle endocytosis / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / calcium ion import across plasma membrane / Long-term potentiation / protein phosphatase activator activity / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / viral process / RHO GTPases activate IQGAPs / phosphatidylinositol 3-kinase binding / voltage-gated calcium channel activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / positive regulation of protein autophosphorylation / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / positive regulation of peptidyl-threonine phosphorylation / Ion homeostasis
Similarity search - Function
Calmodulin / Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain ...Calmodulin / Voltage-dependent calcium channel, L-type, alpha-1C subunit / Voltage-gated calcium channel subunit alpha, C-terminal / Voltage-gated calcium channel subunit alpha, C-term / Voltage-dependent calcium channel, L-type, alpha-1 subunit / Voltage-dependent calcium channel, alpha-1 subunit, IQ domain / Voltage gated calcium channel IQ domain / Voltage gated calcium channel IQ domain / Voltage-dependent calcium channel, alpha-1 subunit / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage-dependent L-type calcium channel, IQ-associated / : / Voltage-dependent channel domain superfamily / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Calmodulin-1 / Voltage-dependent L-type calcium channel subunit alpha-1C / Voltage-dependent L-type calcium channel subunit alpha-1C / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsVan Petegem, F. / Chatelain, F.C. / Minor Jr., D.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Insights into voltage-gated calcium channel regulation from the structure of the Ca(V)1.2 IQ domain-Ca(2+)/calmodulin complex
Authors: van Petegem, F. / Chatelain, F.C. / Minor Jr., D.L.
History
DepositionOct 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600HETEROGEN Calcium 501, 502, 503, 504 are associated with chain A, Ca 506, 507, 508, 509 with chain ...HETEROGEN Calcium 501, 502, 503, 504 are associated with chain A, Ca 506, 507, 508, 509 with chain B and Ca 511, 512, 513, 514 with chain C. Ni 505 is associated with chain A, 510 with chain B and 515 with chain C.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Calmodulin 2
D: Voltage-dependent L-type calcium channel alpha-1C subunit
B: Calmodulin 2
E: Voltage-dependent L-type calcium channel alpha-1C subunit
C: Calmodulin 2
F: Voltage-dependent L-type calcium channel alpha-1C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,67321
Polymers64,0166
Non-polymers65715
Water4,576254
1
A: Calmodulin 2
D: Voltage-dependent L-type calcium channel alpha-1C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5587
Polymers21,3392
Non-polymers2195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-87 kcal/mol
Surface area8860 Å2
MethodPISA
2
B: Calmodulin 2
E: Voltage-dependent L-type calcium channel alpha-1C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5587
Polymers21,3392
Non-polymers2195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-79 kcal/mol
Surface area8390 Å2
MethodPISA
3
C: Calmodulin 2
F: Voltage-dependent L-type calcium channel alpha-1C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5587
Polymers21,3392
Non-polymers2195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-83 kcal/mol
Surface area8310 Å2
MethodPISA
4
B: Calmodulin 2
E: Voltage-dependent L-type calcium channel alpha-1C subunit
C: Calmodulin 2
F: Voltage-dependent L-type calcium channel alpha-1C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,11614
Polymers42,6784
Non-polymers43810
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-163 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.731, 37.241, 86.860
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Calmodulin 2


Mass: 16965.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM2 / Plasmid: pEGST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q53S29, UniProt: P0DP23*PLUS
#2: Protein/peptide Voltage-dependent L-type calcium channel alpha-1C subunit / Voltage-gated calcium channel alpha subunit Cav1.2 / Calcium channel / L type / alpha-1 polypeptide ...Voltage-gated calcium channel alpha subunit Cav1.2 / Calcium channel / L type / alpha-1 polypeptide / isoform 1 / cardiac muscle


Mass: 4373.104 Da / Num. of mol.: 3 / Fragment: IQ domain, residues 1659-1692
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CACNA1C, CACH2, CACN2, CACNL1A1, CCHL1A1 / Plasmid: pEGST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q13933, UniProt: Q13936*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 284 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M Bis-Tris, pH 6.5, 10-15% PEG4000, 0.25mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 284K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111.116
SYNCHROTRONALS 8.3.120.97972
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 11, 2004
ADSC QUANTUM 2102CCDNov 21, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.1161
20.979721
Reflection
IDNumberRmerge(I) obsΧ2D res high (Å)D res low (Å)% possible obs
1253770.0740.6362.83099.9
2405150.0841.0212.43099.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
6.023098.710.0291.005
4.786.0210010.0540.859
4.184.7810010.060.849
3.84.1810010.0730.76
3.533.810010.0970.688
3.323.5310010.1140.537
3.153.3210010.1570.455
3.023.1510010.2040.409
2.93.0210010.2850.391
2.82.910010.4010.408
5.163099.620.0361.698
4.15.1610020.0621.706
3.584.110020.081.617
3.263.5810020.1031.323
3.023.2610020.1360.966
2.853.0210020.1850.71
2.72.8510020.2570.611
2.592.799.920.3440.528
2.492.5999.720.4990.492
2.42.4999.620.6560.467
ReflectionResolution: 1.95→40.6 Å / Num. all: 39554 / Num. obs: 38548 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Χ2: 1.242
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 98.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.464 / Num. measured obs: 3838 / Χ2: 0.565 / % possible all: 98.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.165 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1810 5 %RANDOM
Rwork0.202 ---
all0.205 35999 --
obs0.205 35999 97.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20.51 Å2
2---1.76 Å20 Å2
3---1.04 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 15 254 4042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223901
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9565243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8045481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21425.64211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98915708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6761521
X-RAY DIFFRACTIONr_chiral_restr0.0950.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022973
X-RAY DIFFRACTIONr_nbd_refined0.2290.22124
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2268
X-RAY DIFFRACTIONr_metal_ion_refined0.2060.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.221
X-RAY DIFFRACTIONr_mcbond_it0.8061.52488
X-RAY DIFFRACTIONr_mcangle_it1.17123852
X-RAY DIFFRACTIONr_scbond_it2.05231565
X-RAY DIFFRACTIONr_scangle_it3.0894.51391
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 144 -
Rwork0.219 2553 -
all-2697 -
obs--98.9 %
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)
16.166-0.6429-4.53263.278-0.24138.7864-0.0886-0.4732-0.05960.2125-0.0015-0.2601-0.28270.4880.09010.13710.01740.02970.0520.0229-0.1193-42.258-1.835-19.449
212.247-1.702810.98092.7234-6.655920.4256-0.2858-0.29290.41110.76460.17830.4085-0.8627-0.93590.10750.25060.0670.11780.036-0.034-0.1066-48.1338.716-29.642
31.9770.4544-0.04655.67830.13722.62550.1213-0.06410.02240.4667-0.06860.05120.0343-0.1763-0.0527-0.1009-0.00820.01610.0012-0.0005-0.1424-40.85713.81-35.733
46.8335-1.049-5.53666.5426-6.003211.84530.00890.2281-0.44190.0184-0.807-1.08770.05710.08670.79810.173-0.0250.07630.10710.0131-0.0389-24.55816.4643.898
537.2406-4.0968-12.664810.65772.21598.7286-0.43730.3203-1.3392-0.67810.2099-0.23680.60040.14670.22730.3967-0.02070.18810.2117-0.02310.1935-21.9748.0212.145
611.52840.5343.19296.6175-0.3873.3117-0.07-0.98750.17630.46620.07580.5749-0.1433-0.296-0.00580.17140.0218-0.05580.18960.07830.1765-7.430.8983.185
73.4349-1.4486-0.85822.796-0.81885.006-0.1507-0.37610.17570.42250.0598-0.4468-0.08220.03390.09090.02410.0292-0.11740.1073-0.03140.0119-14.92413.936-26.633
87.707-1.6796-2.26796.68870.45063.4329-0.2703-0.532-0.2570.2672-0.0111-0.23220.10710.25690.2815-0.11060.01210.01840.03170.02130.09150.0771.729-37.042
925.1901-4.5688-2.39475.15310.10248.1294-0.4993-2.6045-0.19790.33260.5351-0.457-0.08230.9729-0.0358-0.00110.0373-0.0530.3058-0.01750.1331-4.0586.729-28.114
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA3 - 774 - 78
22DB1612 - 16405 - 33
33AA81 - 14682 - 147
44BC4 - 785 - 79
55ED1612 - 16255 - 18
66BC82 - 14683 - 147
77CE4 - 755 - 76
88CE82 - 14683 - 147
99FF1615 - 16368 - 29

+
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