[English] 日本語
Yorodumi
- PDB-6fg8: Crystal structure of the BIR3 - SERK1 complex from Arabidopsis th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fg8
TitleCrystal structure of the BIR3 - SERK1 complex from Arabidopsis thaliana.
Components
  • Probable inactive receptor kinase At1g27190
  • Somatic embryogenesis receptor kinase 1
KeywordsPROTEIN BINDING / leucine rich repeat receptor / membrane receptor / pseudokinase / ectodomain / receptor complex / negative regulator
Function / homology
Function and homology information


microsporogenesis / floral organ abscission / pollen maturation / brassinosteroid mediated signaling pathway / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / Golgi organization / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase ...microsporogenesis / floral organ abscission / pollen maturation / brassinosteroid mediated signaling pathway / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / Golgi organization / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / signaling receptor binding / protein serine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Probable inactive receptor kinase At1g27190 / Somatic embryogenesis receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsHothorn, M. / Hohmann, U.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_176237 Switzerland
CitationJournal: Nat Plants / Year: 2018
Title: The SERK3 elongated allele defines a role for BIR ectodomains in brassinosteroid signalling.
Authors: Hohmann, U. / Nicolet, J. / Moretti, A. / Hothorn, L.A. / Hothorn, M.
History
DepositionJan 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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 / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Somatic embryogenesis receptor kinase 1
B: Probable inactive receptor kinase At1g27190
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,33413
Polymers54,8172
Non-polymers3,51711
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation, gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint46 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.173, 50.757, 77.425
Angle α, β, γ (deg.)90.00, 96.72, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Somatic embryogenesis receptor kinase 1 / AtSERK1 / Somatic embryogenesis receptor-like kinase 1


Mass: 28410.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: seedling / Gene: SERK1, At1g71830, F14O23.21, F14O23_24 / Cell line (production host): 38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q94AG2, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Protein Probable inactive receptor kinase At1g27190


Mass: 26406.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: seedling / Gene: At1g27190, T7N9.25 / Cell line (production host): 38 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O04567

-
Sugars , 3 types, 6 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 438 molecules

#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 1.86 Å3/Da / Density % sol: 33.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19% PEG 3,350, 1 M LiCl, 0.1 M sodium acetate pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.25→40.81 Å / Num. obs: 109876 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 20.5 Å2 / CC1/2: 1 / Rrim(I) all: 0.058 / Rsym value: 0.056 / Net I/σ(I): 15.1
Reflection shellResolution: 1.25→1.33 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 17072 / CC1/2: 0.85 / Rrim(I) all: 1.1 / Rsym value: 1.16 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lsc, 6fg7

4lsc

6fg7


Resolution: 1.25→40.81 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.472 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18394 5491 5 %RANDOM
Rwork0.15145 ---
obs0.15308 104302 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.386 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å2-0.48 Å2
2---1.35 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.25→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 233 433 3504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193297
X-RAY DIFFRACTIONr_bond_other_d0.0020.023031
X-RAY DIFFRACTIONr_angle_refined_deg1.7452.0684535
X-RAY DIFFRACTIONr_angle_other_deg1.02737161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.98725.645124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36515532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1171515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213516
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02557
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_it1.7761.8411561
X-RAY DIFFRACTIONr_mcbond_other1.7591.8381560
X-RAY DIFFRACTIONr_mcangle_it2.2232.7621961
X-RAY DIFFRACTIONr_mcangle_other2.2262.7651962
X-RAY DIFFRACTIONr_scbond_it2.8832.7141736
X-RAY DIFFRACTIONr_scbond_other2.8722.7141736
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3073.9572550
X-RAY DIFFRACTIONr_long_range_B_refined4.41527.8783768
X-RAY DIFFRACTIONr_long_range_B_other4.41827.8963769
X-RAY DIFFRACTIONr_rigid_bond_restr1.97136328
X-RAY DIFFRACTIONr_sphericity_free35.7265253
X-RAY DIFFRACTIONr_sphericity_bonded13.89556416
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 385 -
Rwork0.308 7321 -
obs--94.11 %
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)
10.02190.002-0.01720.0324-0.01970.02360.0007-0.00230.00070.0004-0.0011-0.0012-0.00060.0030.00040.0166-0.00020.00670.02170.00010.0028-13.249-3.2862-5.2207
20.1308-0.07530.04550.46050.04310.0337-0.0042-0.0048-0.0039-0.00370.00310.0051-0.0055-0.00520.00120.0174-0.00040.00590.0222-0.00130.0031-19.25570.3885-15.9228
30.0254-0.0265-0.00280.0290.01580.1287-0.00210.00040.00030.0022-0.0008-0.00010.0034-0.00130.0030.0159-0.00110.00750.0207-0.00050.0037-14.3927-15.1834-7.5526
40.0596-0.09880.04690.5193-0.72551.2180.0065-0.0013-0.00680.00930.00220.0138-0.02870.0025-0.00870.0186-0.00150.00620.02290.00010.0035-25.0646-4.2571-5.6225
50.0028-0.00720.0030.0504-0.01350.02390.0005-0.0004-0.0001-0.00010.00160.00190.0003-0.0024-0.00210.0159-0.00020.00660.0217-0.00020.003-25.1611-14.1365-10.9019
60.02220.0075-0.00310.0608-0.00760.00970.00020.003-0.0002-0.00140.00240.002-0-0.0014-0.00270.0171-0.00030.00640.02190.00040.0031-32.2805-19.7464-15.9335
70.0708-0.0090.05770.0756-0.05930.17620.0018-0.00340.0060.0058-0.0064-0.0003-0.0103-0.00430.00460.01760.00010.00790.0207-0.00110.0041-35.0799-27.8407-19.2799
80.23950.1874-0.26991.3478-0.59351.003-0.0080.0085-0.0177-0.01870.00950.05170.0259-0.0164-0.00150.0129-0.00270.00260.0157-0.00240.0081-41.3658-35.6224-15.8199
90.03230.0173-0.05410.012-0.02760.0915-0.0001-0.0059-0.0042-0.0015-0.0064-0.00420.00060.00760.00650.0157-0.00010.00680.02270.00060.0044-13.0398-27.0252-39.6166
100.0115-0.00450.00440.0018-0.00130.2409-0.00780.00140.00020.0031-0.00170.0001-0.00670.0060.00940.0182-0.0010.0070.0221-0.00040.0043-18.5587-22.5142-29.1574
110.01240.0093-0.00050.00790.00270.0121-0.00110.0006-0.00090.0002-0.00020.0001-0.00040.00030.00130.016-00.00740.02120.00010.0036-27.8807-28.971-42.0988
120.44290.30630.49180.22570.41430.9415-0.0038-0.01020.00550.0031-0.010.00540.0234-0.02160.01380.01780.00140.00830.020.00080.004-38.1871-33.6715-33.9061
130.02950.0254-0.0420.0698-0.01290.2149-0.0047-0.0027-0.0014-0.002-0.0056-0.0081-0.0069-0.01190.01030.016-0.00130.00680.0175-0.00090.0068-39.3591-27.4647-45.4722
140.0490.0692-0.13560.25980.0370.6990.0013-0.00830.00680.0193-0.0260.04310.00430.01010.02470.01220.0010.00730.0299-0.00070.0094-43.1763-26.7789-34.2607
150.0886-0.05280.02240.1334-0.05780.0252-0.0147-0.0073-0.0025-0.00310.014-0.00210.0004-0.00740.00070.01750.00150.00730.0289-0.00170.0035-46.3581-26.0983-47.3822
160.0023-0.01020.01250.0666-0.08790.1172-0.0008-0.00360.00040.0171-0.0085-0.0056-0.02320.02050.00930.0174-0.00780.00630.03940.00040.0052-50.6755-22.0736-49.0914
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 66
2X-RAY DIFFRACTION2A67 - 74
3X-RAY DIFFRACTION3A75 - 85
4X-RAY DIFFRACTION4A86 - 93
5X-RAY DIFFRACTION5A94 - 138
6X-RAY DIFFRACTION6A139 - 183
7X-RAY DIFFRACTION7A184 - 204
8X-RAY DIFFRACTION8A205 - 212
9X-RAY DIFFRACTION9B25 - 57
10X-RAY DIFFRACTION10B58 - 78
11X-RAY DIFFRACTION11B79 - 140
12X-RAY DIFFRACTION12B141 - 146
13X-RAY DIFFRACTION13B147 - 165
14X-RAY DIFFRACTION14B166 - 173
15X-RAY DIFFRACTION15B174 - 190
16X-RAY DIFFRACTION16B191 - 212

+
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