[English] 日本語
Yorodumi
- PDB-4v0w: The crystal structure of mouse PP1G in complex with truncated hum... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v0w
TitleThe crystal structure of mouse PP1G in complex with truncated human PPP1R15B (631-669)
Components
  • PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
  • SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
KeywordsHYDROLASE/HYDROLASE REGULATOR / HYDROLASE-HYDROLASE REGULATOR COMPLEX
Function / homology
Function and homology information


Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 1 complex / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein phosphatase type 1 complex / regulation of nucleocytoplasmic transport / RHO GTPases Activate Formins / Separation of Sister Chromatids / protein phosphatase 1 binding / protein phosphatase regulator activity / lamin binding / protein serine/threonine phosphatase activity / glycogen metabolic process / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / ER overload response / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / negative regulation of PERK-mediated unfolded protein response / microtubule organizing center / phosphatase activity / cleavage furrow / blastocyst development / negative regulation of protein phosphorylation / protein dephosphorylation / positive regulation of glial cell proliferation / response to endoplasmic reticulum stress / circadian regulation of gene expression / regulation of circadian rhythm / response to hydrogen peroxide / neuron differentiation / kinetochore / regulation of translation / presynapse / midbody / spermatogenesis / dendritic spine / mitochondrial outer membrane / chromosome, telomeric region / nuclear speck / protein domain specific binding / cell division / protein-containing complex binding / protein kinase binding / nucleolus / glutamatergic synapse / endoplasmic reticulum / mitochondrion / metal ion binding
Similarity search - Function
Protein phosphatase 1, regulatory subunit 15B, N-terminal / eIF2-alpha phosphatase phosphorylation constitutive repressor / Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. ...Protein phosphatase 1, regulatory subunit 15B, N-terminal / eIF2-alpha phosphatase phosphorylation constitutive repressor / Protein phosphatase 1, regulatory subunit 15A/B, C-terminal / : / Phosphatase-1 catalytic subunit binding region / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Protein phosphatase 1 regulatory subunit 15B
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsChen, R. / Yan, Y. / Casado, A.C. / Ron, D. / Read, R.J.
CitationJournal: Elife / Year: 2015
Title: G-actin provides substrate-specificity to eukaryotic initiation factor 2 alpha holophosphatases.
Authors: Chen, R. / Rato, C. / Yan, Y. / Crespillo-Casado, A. / Clarke, H.J. / Harding, H.P. / Marciniak, S.J. / Read, R.J. / Ron, D.
History
DepositionSep 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / pdbx_database_proc / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval
Revision 1.2May 1, 2024Group: Data collection / Database references ...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 / struct_conn / 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_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.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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
C: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
D: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3598
Polymers78,1394
Non-polymers2204
Water10,971609
1
A: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
B: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1804
Polymers39,0702
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-25.7 kcal/mol
Surface area13400 Å2
MethodPISA
2
C: SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT
D: PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1804
Polymers39,0702
Non-polymers1102
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-25.2 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.010, 67.860, 156.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SERINE/THREONINE-PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PP-1G / PROTEIN PHOSPHATASE PP1-GAMMA CATALYTIC SUBUNIT / PROTEIN PHOSPHATASE 1C CATALYTIC SUBUNIT


Mass: 33921.035 Da / Num. of mol.: 2 / Fragment: RESIDUES 7-300
Source method: isolated from a genetically manipulated source
Details: TRUNCATED MOUSE PP1G INCLUDING RESIDUES OF 7- 300 / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21 (bacteria)
References: UniProt: P63087, protein-serine/threonine phosphatase
#2: Protein/peptide PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT 15B


Mass: 5148.678 Da / Num. of mol.: 2 / Fragment: RESIDUES 631-669
Source method: isolated from a genetically manipulated source
Details: TRUNCATED HUMAN PPP1R15B INCLUDING RESIDUES OF 631-669
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5SWA1
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMN A301 AND O A302 ARE MODELLED AS ALTERNATE CONFORMERS MN C301 AND O C302 ARE MODELLED AS ...MN A301 AND O A302 ARE MODELLED AS ALTERNATE CONFORMERS MN C301 AND O C302 ARE MODELLED AS ALTERNATE CONFORMERS

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.49 % / Description: NONE
Crystal growpH: 7.5 / Details: 3 M NACL, 0.1 M HEPES, PH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.55→33.94 Å / Num. obs: 96347 / % possible obs: 92.6 % / Observed criterion σ(I): 1.8 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
MOSFLMdata reduction
Aimlessdata scaling
CCP4Iphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE CRYSTAL STRUCTURE OF MOUSE PP1G IN COMPLEX WITH TRUNCATED HUMAN PPP1R15B INCLUDING RESIDUES OF 631-660

Resolution: 1.55→33.936 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2029 4800 5 %
Rwork0.1727 --
obs0.1743 96347 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→33.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5047 0 4 609 5660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065204
X-RAY DIFFRACTIONf_angle_d1.0537029
X-RAY DIFFRACTIONf_dihedral_angle_d12.4431955
X-RAY DIFFRACTIONf_chiral_restr0.042753
X-RAY DIFFRACTIONf_plane_restr0.004915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.56760.27671750.25293236X-RAY DIFFRACTION99
1.5676-1.58610.27921550.24973243X-RAY DIFFRACTION99
1.5861-1.60540.25161520.23493241X-RAY DIFFRACTION99
1.6054-1.62570.24771600.22593270X-RAY DIFFRACTION99
1.6257-1.64710.24641920.22213246X-RAY DIFFRACTION99
1.6471-1.66970.25921740.20993254X-RAY DIFFRACTION100
1.6697-1.69350.22881910.20833177X-RAY DIFFRACTION99
1.6935-1.71880.22881700.20083277X-RAY DIFFRACTION100
1.7188-1.74570.22271530.19233283X-RAY DIFFRACTION100
1.7457-1.77430.23721600.18623263X-RAY DIFFRACTION100
1.7743-1.80490.24861560.18513284X-RAY DIFFRACTION100
1.8049-1.83770.22031730.17983287X-RAY DIFFRACTION100
1.8377-1.87310.23911860.1843247X-RAY DIFFRACTION99
1.8731-1.91130.23651080.20821962X-RAY DIFFRACTION60
1.9113-1.95280.2458810.20551401X-RAY DIFFRACTION48
1.9528-1.99830.18131350.16432420X-RAY DIFFRACTION100
1.9983-2.04820.19051680.16723262X-RAY DIFFRACTION100
2.0482-2.10360.1711280.16132302X-RAY DIFFRACTION70
2.1036-2.16550.20041710.1583306X-RAY DIFFRACTION100
2.1655-2.23540.19121630.17573265X-RAY DIFFRACTION99
2.2354-2.31520.23391310.19822257X-RAY DIFFRACTION69
2.3152-2.40790.17861860.16313294X-RAY DIFFRACTION100
2.4079-2.51750.22291690.16333314X-RAY DIFFRACTION100
2.5175-2.65020.20421670.17143315X-RAY DIFFRACTION100
2.6502-2.81610.23481170.18142868X-RAY DIFFRACTION85
2.8161-3.03340.1871800.17213313X-RAY DIFFRACTION100
3.0334-3.33850.19461800.16493346X-RAY DIFFRACTION99
3.3385-3.8210.17881600.14792843X-RAY DIFFRACTION85
3.821-4.81180.16631610.13663218X-RAY DIFFRACTION94
4.8118-33.94360.19461980.17413553X-RAY DIFFRACTION100
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)
14.3312.2608-1.5446.1386-0.61834.1269-0.1990.4142-0.1619-0.44060.13090.08960.01-0.09180.05060.17270.0184-0.08620.2728-0.03850.17864.055580.2407-4.8006
21.6168-0.3692-0.04451.73240.20491.5370.05660.0713-0.0575-0.10970.01280.11690.0514-0.1334-0.04810.0739-0.0068-0.03790.13050.0280.11688.456488.36426.386
31.0408-0.37310.1421.58660.33091.46260.02670.055-0.0985-0.03420.0648-0.03390.13480.1247-0.09260.0586-0.0124-0.02040.12640.00410.122714.79184.7488.2188
42.2820.1361-0.6812.1857-0.14953.5812-0.0136-0.23860.13350.19450.1201-0.2058-0.08970.3604-0.07120.08220.0061-0.04180.1591-0.04050.139920.176892.505723.8064
53.4569-2.5727-0.32494.77910.19743.846-0.2159-0.30360.04890.32370.20990.104-0.0943-0.04530.01630.0930.0158-0.03030.1776-0.03180.101914.927993.427731.9345
62.66051.10490.21425.03771.87333.295-0.1216-0.3495-0.06930.23220.07560.40210.0463-0.46940.09840.07370.02260.00260.23540.05030.18443.170591.223824.761
73.36172.1904-0.09593.35971.52832.89960.0837-0.1054-0.3884-0.09-0.11030.4220.2483-0.39510.01110.1245-0.0212-0.0340.2980.06210.3009-3.078388.009817.6991
82.00344.1152-1.16778.996-3.50218.7965-0.26180.00250.28620.3376-0.0145-0.0972-0.33670.14140.30850.23050.1337-0.01220.42230.03040.3913-0.6517105.645722.5402
95.96345.54273.05717.43281.46962.3908-0.107-0.97310.51740.0949-0.51962.0538-0.2529-1.71290.58130.25750.0495-0.02890.80650.01480.6115-10.997995.948620.8287
103.0791-2.3145-1.28541.75931.18543.71520.0308-0.397-0.24630.1686-0.30150.4380.4583-0.77310.25490.399-0.2151-0.15710.76960.15570.9835-11.134382.768514.6758
110.93910.0510.58732.383-0.87160.7802-0.0428-0.4352-0.08060.52420.08120.34640.3403-0.4207-0.45750.9207-0.06660.14990.30840.12790.084429.05759.00446.2266
122.1989-0.2491-0.18322.0931-0.11182.19810.077-0.0526-0.00640.28330.00590.0255-0.08830.0493-0.06990.1868-0.0321-0.01680.08760.02340.081535.868260.508433.0187
132.3022-0.42860.27121.8965-0.87222.56990.074-0.09730.01260.24220.07770.1933-0.2455-0.2398-0.13820.1907-0.00330.02220.07650.00950.094229.174566.315932.797
145.2592-2.3546-2.91893.44781.43374.14110.1738-0.10150.30190.1250.0494-0.1471-0.45910.1067-0.2140.1771-0.017-0.01860.0840.0260.0937.392568.98328.1592
152.14150.6164-0.5983.49851.23363.82920.1910.10090.26460.0482-0.0476-0.2134-0.72630.2819-0.12810.2793-0.05610.02780.16010.04850.194941.841274.476917.927
164.4676-1.0376-1.29513.0388-0.16893.77950.12160.2013-0.0593-0.3667-0.09640.0235-0.08750.0363-0.02910.1755-0.01030.01470.07860.02310.096337.84165.64058.0825
174.3433-0.0657-2.14453.1004-0.34574.4836-0.00310.1069-0.2309-0.2849-0.0893-0.02290.32740.06570.08390.16110.014-0.03130.08690.00370.102138.173654.658115.0785
181.82381.9935-1.58973.81220.02483.42660.02950.0185-0.1697-0.0477-0.07590.31560.2331-0.14120.01390.1771-0.011-0.03160.09120.00270.176334.610348.512122.6064
194.84094.3804-4.67835.0237-3.2965.6174-0.42510.3837-0.8154-0.3626-0.0687-0.4090.7009-0.07240.35040.25860.0243-0.01410.1703-0.01810.300240.606443.658321.2238
201.8078-0.31070.94552.8235-2.84696.6874-0.09770.7206-0.89360.78911.01532.40330.5864-1.9653-0.87420.7756-0.32540.19511.3404-0.02770.810317.696550.395429.0975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 31 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 32 THROUGH 99 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 100 THROUGH 172 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 173 THROUGH 215 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 216 THROUGH 239 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 240 THROUGH 271 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 272 THROUGH 300 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 639 THROUGH 643 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 644 THROUGH 648 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 649 THROUGH 653 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 6 THROUGH 31 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 32 THROUGH 99 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 100 THROUGH 145 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 146 THROUGH 172 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 173 THROUGH 199 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 200 THROUGH 238 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 239 THROUGH 271 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 272 THROUGH 300 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 639 THROUGH 653 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 654 THROUGH 660 )

+
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