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- PDB-7ogo: Plant peptide hormone receptor H1I1S1 -

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Basic information

Entry
Database: PDB / ID: 7ogo
TitlePlant peptide hormone receptor H1I1S1
Components
  • Protein IDA-LIKE 1
  • Receptor-like protein kinase HSL1
  • Somatic embryogenesis receptor kinase 1
KeywordsPEPTIDE BINDING PROTEIN / Plant receptor LRR pepide hormone
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 / phosphorylation / protein phosphorylation / protein serine kinase activity / signaling receptor binding / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / extracellular space / 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 / 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. ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / 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. / Protein kinase domain / 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
Similarity search - Domain/homology
Protein IDA-LIKE 1 / Somatic embryogenesis receptor kinase 1 / Receptor-like protein kinase HSL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsRoman, A.O. / Jimenez-Sandoval, P. / Santiago, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_173101 Switzerland
CitationJournal: Nat Commun / Year: 2022
Title: HSL1 and BAM1/2 impact epidermal cell development by sensing distinct signaling peptides.
Authors: Roman, A.O. / Jimenez-Sandoval, P. / Augustin, S. / Broyart, C. / Hothorn, L.A. / Santiago, J.
History
DepositionMay 7, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Receptor-like protein kinase HSL1
BBB: Somatic embryogenesis receptor kinase 1
CCC: Protein IDA-LIKE 1
DDD: Receptor-like protein kinase HSL1
EEE: Somatic embryogenesis receptor kinase 1
FFF: Protein IDA-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,99532
Polymers180,2416
Non-polymers10,75426
Water4,972276
1
AAA: Receptor-like protein kinase HSL1
BBB: Somatic embryogenesis receptor kinase 1
CCC: Protein IDA-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,35715
Polymers90,1203
Non-polymers5,23712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10010 Å2
ΔGint66 kcal/mol
Surface area32710 Å2
MethodPISA
2
DDD: Receptor-like protein kinase HSL1
EEE: Somatic embryogenesis receptor kinase 1
FFF: Protein IDA-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,63717
Polymers90,1203
Non-polymers5,51714
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10390 Å2
ΔGint70 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.735, 146.405, 169.645
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21DDD
32BBB
42EEE
53CCC
63FFF

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERGLYGLYAAAA13 - 5972 - 586
211SERSERGLYGLYDDDD13 - 5972 - 586
322ASNASNPROPROBBBB27 - 2118 - 192
422ASNASNPROPROEEEE27 - 2118 - 192
533TYRTYRASNASNCCCC65 - 781 - 14
633TYRTYRASNASNFFFF65 - 781 - 14

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Protein , 2 types, 4 molecules AAADDDBBBEEE

#1: Protein Receptor-like protein kinase HSL1 / Protein HAESA-LIKE1


Mass: 66569.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HSL1, At1g28440, F3M18.12 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9SGP2, non-specific serine/threonine protein kinase
#2: Protein Somatic embryogenesis receptor kinase 1 / AtSERK1 / Somatic embryogenesis receptor-like kinase 1


Mass: 21978.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK1, At1g71830, F14O23.21, F14O23_24 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q94AG2, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Protein/peptide / Non-polymers , 2 types, 278 molecules CCCFFF

#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
#3: Protein/peptide Protein IDA-LIKE 1


Mass: 1571.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IDL1, At3g25655, T5M7 / Production host: synthetic construct (others) / References: UniProt: Q29PV4

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Sugars , 6 types, 26 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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.: 10
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
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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
#9: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN

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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: 3.4 Å3/Da / Density meas: 63.89 Mg/m3 / Density % sol: 63.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M ammonium citrate pH 7.0 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2019
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.38→169.64 Å / Num. obs: 99190 / % possible obs: 100 % / Redundancy: 26 % / CC1/2: 0.998 / Rmerge(I) obs: 0.341 / Rpim(I) all: 0.096 / Rrim(I) all: 0.354 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
13.04-169.6423.20.077140.9990.0190.073
2.38-2.4225.73.66248900.6691.0433.809

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
xia2data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IXO

5ixo


Resolution: 2.38→111.083 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.482 / SU ML: 0.213 / Cross valid method: FREE R-VALUE / ESU R: 0.309 / ESU R Free: 0.221
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2476 4974 5.019 %
Rwork0.2343 94121 -
all0.235 --
obs-99095 99.993 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.014 Å2
Baniso -1Baniso -2Baniso -3
1-5.042 Å2-0 Å20 Å2
2---1.347 Å2-0 Å2
3----3.695 Å2
Refinement stepCycle: LAST / Resolution: 2.38→111.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11770 0 707 276 12753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01312801
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711779
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1160.1201106
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.70617510
X-RAY DIFFRACTIONr_angle_other_deg1.2951.63927282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4425.1161817
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg28.8082066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.71625.105525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03115.4052063
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg6.173202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7011534
X-RAY DIFFRACTIONr_chiral_restr0.0580.21804
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214283
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022573
X-RAY DIFFRACTIONr_nbd_refined0.1740.22279
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.211385
X-RAY DIFFRACTIONr_nbtor_refined0.1550.26398
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.25702
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2349
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1120.212
X-RAY DIFFRACTIONr_nbd_other0.1830.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.212
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_mcbond_it1.7054.4896286
X-RAY DIFFRACTIONr_mcbond_other1.7054.4896285
X-RAY DIFFRACTIONr_mcangle_it2.7756.7337849
X-RAY DIFFRACTIONr_mcangle_other2.7756.7337850
X-RAY DIFFRACTIONr_scbond_it2.3894.9626515
X-RAY DIFFRACTIONr_scbond_other2.3894.9626515
X-RAY DIFFRACTIONr_scangle_it3.4827.3399657
X-RAY DIFFRACTIONr_scangle_other3.4827.349657
X-RAY DIFFRACTIONr_lrange_it5.908167.92202566
X-RAY DIFFRACTIONr_lrange_other5.908167.926202548
X-RAY DIFFRACTIONr_ncsr_local_group_10.0630.0518269
X-RAY DIFFRACTIONr_ncsr_local_group_20.0630.055875
X-RAY DIFFRACTIONr_ncsr_local_group_30.0790.05273
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.062820.0501
12DDDX-RAY DIFFRACTIONLocal ncs0.062820.0501
23BBBX-RAY DIFFRACTIONLocal ncs0.06330.05011
24EEEX-RAY DIFFRACTIONLocal ncs0.06330.05011
35CCCX-RAY DIFFRACTIONLocal ncs0.079440.05006
36FFFX-RAY DIFFRACTIONLocal ncs0.079440.05006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.442-2.5090.3593530.3526714X-RAY DIFFRACTION99.9858
2.509-2.5810.3273370.3276536X-RAY DIFFRACTION99.9855
2.661-2.7480.3013220.2916129X-RAY DIFFRACTION99.9845
2.748-2.8450.3273400.2855949X-RAY DIFFRACTION100
2.952-3.0720.3092650.2845591X-RAY DIFFRACTION100
3.072-3.2090.3252820.265331X-RAY DIFFRACTION100
3.209-3.3660.272850.255059X-RAY DIFFRACTION100
3.366-3.5480.2792290.2414899X-RAY DIFFRACTION99.9805
3.548-3.7630.222470.2134599X-RAY DIFFRACTION100
3.763-4.0220.2352400.2024326X-RAY DIFFRACTION100
4.022-4.3440.1662190.1634052X-RAY DIFFRACTION99.9766
4.344-4.7590.161990.1453731X-RAY DIFFRACTION100
4.759-5.320.1811590.1563425X-RAY DIFFRACTION100
5.32-6.1420.2111710.1973000X-RAY DIFFRACTION100
6.142-7.520.1861000.1812619X-RAY DIFFRACTION100
7.52-10.6240.2111310.2022011X-RAY DIFFRACTION100

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