[English] 日本語
Yorodumi
- PDB-7ogq: Plant peptide hormone receptor H1I2S1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ogq
TitlePlant peptide hormone receptor H1I2S1
Components
  • Protein IDA-LIKE 2
  • 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 / 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
Protein IDA-like / : / 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 ...Protein IDA-like / : / 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 2 / 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: 2.2 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
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Receptor-like protein kinase HSL1
BBB: Somatic embryogenesis receptor kinase 1
CCC: Protein IDA-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,59322
Polymers90,0763
Non-polymers8,51719
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint45 kcal/mol
Surface area34730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.817, 88.078, 166.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11AAA-953-

HOH

21AAA-969-

HOH

-
Components

-
Protein , 2 types, 2 molecules AAABBB

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


Mass: 66569.797 Da / Num. of mol.: 1
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.: 1
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

-
Protein/peptide , 1 types, 1 molecules CCC

#3: Protein/peptide Protein IDA-LIKE 2


Mass: 1527.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IDL2, At5g64667, MUB3 / Production host: synthetic construct (others) / References: UniProt: Q6DUW9

-
Sugars , 7 types, 13 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-3][LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-2/a3-b1_a4-c1_a6-f1_c4-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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.: 3
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)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#8: 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.: 1
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)][a-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: 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.: 2
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
#10: 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.: 3 / 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

-
Non-polymers , 2 types, 324 molecules

#11: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2 M ammonium sulphate 0.1 M Bis-Tris 25 % w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.254716 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 21, 2020
RadiationMonochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.254716 Å / Relative weight: 1
ReflectionResolution: 2.2→46.973 Å / Num. obs: 65575 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
10.08-46.9312.10.03379310.0130.036
2.2-2.2510.71.99245740.4650.932.202

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
xia2data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IXO
Resolution: 2.2→46.973 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.687 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.195 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2343 3215 4.907 %
Rwork0.198 62304 -
all0.2 --
obs-65519 99.98 %
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: 53.542 Å2
Baniso -1Baniso -2Baniso -3
1--1.989 Å20 Å2-0 Å2
2--3.249 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 0 558 318 6796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136655
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176029
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0340.197992
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.7389081
X-RAY DIFFRACTIONr_angle_other_deg1.3511.67113995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715.09996
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg47.0082049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.79625.249261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34515.5311065
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg14.959203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8751516
X-RAY DIFFRACTIONr_chiral_restr0.0610.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027207
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021285
X-RAY DIFFRACTIONr_nbd_refined0.1910.21202
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.25880
X-RAY DIFFRACTIONr_nbtor_refined0.1610.23334
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1110.23107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2273
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.211
X-RAY DIFFRACTIONr_nbd_other0.2220.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.215
X-RAY DIFFRACTIONr_mcbond_it1.5453.6113182
X-RAY DIFFRACTIONr_mcbond_other1.5453.6113181
X-RAY DIFFRACTIONr_mcangle_it2.2645.4153975
X-RAY DIFFRACTIONr_mcangle_other2.2635.4143976
X-RAY DIFFRACTIONr_scbond_it3.4464.9033473
X-RAY DIFFRACTIONr_scbond_other3.3714.8633449
X-RAY DIFFRACTIONr_scangle_it4.8087.1075106
X-RAY DIFFRACTIONr_scangle_other4.7047.0465070
X-RAY DIFFRACTIONr_lrange_it5.058140.32399033
X-RAY DIFFRACTIONr_lrange_other5.054140.34298997
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.3752370.3364560X-RAY DIFFRACTION100
2.257-2.3190.3051980.34466X-RAY DIFFRACTION100
2.319-2.3860.2862470.2724273X-RAY DIFFRACTION100
2.386-2.460.2662000.254211X-RAY DIFFRACTION100
2.46-2.540.2752300.2344041X-RAY DIFFRACTION100
2.54-2.6290.2751900.2393972X-RAY DIFFRACTION100
2.629-2.7290.252140.2133804X-RAY DIFFRACTION100
2.729-2.840.2511930.2043666X-RAY DIFFRACTION100
2.84-2.9660.2671620.2193516X-RAY DIFFRACTION100
2.966-3.1110.231750.2193376X-RAY DIFFRACTION100
3.111-3.2790.2561790.2113208X-RAY DIFFRACTION100
3.279-3.4780.2581740.2223046X-RAY DIFFRACTION100
3.478-3.7180.2461200.1942876X-RAY DIFFRACTION100
3.718-4.0160.1971280.1692710X-RAY DIFFRACTION99.9648
4.016-4.3990.1561280.1382475X-RAY DIFFRACTION100
4.399-4.9180.1541200.142257X-RAY DIFFRACTION100
4.918-5.6780.1861040.1691987X-RAY DIFFRACTION100
5.678-6.9520.297860.1961733X-RAY DIFFRACTION99.8902
6.952-9.8230.28790.2081347X-RAY DIFFRACTION100
9.823-46.930.247510.196781X-RAY DIFFRACTION98.8124
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)
11.3833-1.0512-0.05292.96850.82932.05070.02890.12530.05-0.2193-0.08220.0421-0.0305-0.15510.05330.14190.02730.02340.06240.01090.012126.4355192.0527-3.2963
20.91640.18250.87960.11850.07811.50070.0544-0.1012-0.02130.0235-0.06310.02850.135-0.15240.00870.2020.0340.01610.0931-0.05490.064635.0155202.779641.0998
33.3072-1.3268-3.7470.83441.62285.13320.0751-0.2470.6983-0.19230.26-0.674-0.48361.0743-0.33510.5315-0.1924-0.03650.90430.27991.051975.9217213.046654.2476
44.3534-0.6882-1.26811.90440.6042.83650.06910.1789-0.0469-0.20130.01950.0120.09650.0057-0.08860.15860.0632-0.01230.155-0.03340.03847.3349204.039732.9147
53.59331.2436-1.14340.6701-0.27251.98060.04620.41410.0932-0.15290.0458-0.05310.0890.167-0.0920.19530.14450.03290.22890.00060.060759.5152208.509930.0043
63.7235-0.20970.19832.71911.65985.1432-0.0381-0.00760.2855-0.0468-0.11420.0178-0.1172-0.03760.15230.14480.01310.03250.20770.0250.221163.7461219.952131.2214
73.5590.9601-1.64561.6746-0.54242.61870.06310.21340.31470.0695-0.1028-0.3544-0.09060.52110.03970.1290.0986-0.02090.44170.06050.207973.0675215.271828.9038
81.13151.1222-1.53956.85620.05783.1232-0.04430.0506-0.0598-0.0939-0.1783-0.3863-0.17090.18090.22260.19210.0312-0.03780.48470.00970.346882.4266215.572427.5429
95.0691-0.9167-3.38541.14712.55316.1888-0.08110.20650.00520.09340.1456-0.10680.26040.2256-0.06450.19250.03780.01310.21550.01450.274231.1748198.762818.8472
107.76952.09090.34720.79430.73971.8562-0.10260.3959-0.39290.08210.2105-0.14330.38340.3009-0.10790.24640.07240.00730.1752-0.04270.15632.934204.105233.9169
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA12 - 165
2X-RAY DIFFRACTION2ALLAAA166 - 577
3X-RAY DIFFRACTION3ALLAAA578 - 606
4X-RAY DIFFRACTION4ALLBBB27 - 69
5X-RAY DIFFRACTION5ALLBBB70 - 133
6X-RAY DIFFRACTION6ALLBBB134 - 144
7X-RAY DIFFRACTION7ALLBBB145 - 185
8X-RAY DIFFRACTION8ALLBBB186 - 211
9X-RAY DIFFRACTION9ALLCCC70 - 78
10X-RAY DIFFRACTION10ALLCCC79 - 83

+
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://pdbjlc1.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