[English] 日本語
Yorodumi
- PDB-6g3w: Crystal structure of the BIR3 - SERK2 complex from Arabidopsis th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g3w
TitleCrystal structure of the BIR3 - SERK2 complex from Arabidopsis thaliana.
Components
  • Probable inactive receptor kinase At1g27190
  • Somatic embryogenesis receptor kinase 2
KeywordsPROTEIN BINDING / leucine rich repeat receptor / membrane receptor / pseudokinase / ectodomain / receptor complex / negative regulator
Function / homology
Function and homology information


microsporogenesis / pollen maturation / brassinosteroid mediated signaling pathway / receptor serine/threonine kinase binding / non-specific serine/threonine protein kinase / protein kinase activity / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding ...microsporogenesis / pollen maturation / brassinosteroid mediated signaling pathway / receptor serine/threonine kinase binding / non-specific serine/threonine protein kinase / protein kinase activity / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / ATP binding / nucleus / 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 ...: / 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 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: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Somatic embryogenesis receptor kinase 2
B: Probable inactive receptor kinase At1g27190
C: Somatic embryogenesis receptor kinase 2
D: Probable inactive receptor kinase At1g27190
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,93815
Polymers90,2084
Non-polymers2,73111
Water2,576143
1
A: Somatic embryogenesis receptor kinase 2
B: Probable inactive receptor kinase At1g27190
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8888
Polymers45,1042
Non-polymers1,7846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Somatic embryogenesis receptor kinase 2
D: Probable inactive receptor kinase At1g27190
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0517
Polymers45,1042
Non-polymers9475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.184, 52.155, 308.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPROPROAA30 - 2123 - 185
21ASNASNPROPROCC30 - 2123 - 185
12ASPASPGLYGLYBB26 - 2122 - 188
22ASPASPGLYGLYDD26 - 2122 - 188

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Somatic embryogenesis receptor kinase 2 / AtSERK2 / Somatic embryogenesis receptor-like kinase 2


Mass: 23975.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK2, At1g34210, F23M19.11 / Plasmid: pfastbac / Cell line (production host): Tnao38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9XIC7, non-specific serine/threonine protein kinase
#2: Protein Probable inactive receptor kinase At1g27190


Mass: 21127.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g27190, T7N9.25 / Plasmid: pfastbac / Cell line (production host): Tnao38 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O04567

-
Sugars , 2 types, 8 molecules

#3: 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.: 2
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
#4: 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.: 6
Source method: isolated from a genetically manipulated source
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 , 3 types, 146 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% (w/v) PEG 3,350, 0.2 M MgCl_2 x 6H_2O, 0.1 M Bis-Tris pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000027 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000027 Å / Relative weight: 1
ReflectionResolution: 2.2→49.41 Å / Num. obs: 42439 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.115 / Rsym value: 0.111 / Net I/σ(I): 17
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 13 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6697 / CC1/2: 0.71 / Rrim(I) all: 1.67 / Rsym value: 1.604 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6fg8, 4z61

6fg8

4z61


Resolution: 2.2→49.41 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 16.233 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.214 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 2122 5 %RANDOM
Rwork0.21698 ---
obs0.21852 40314 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.234 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2--1.96 Å2-0 Å2
3----3.17 Å2
Refinement stepCycle: 1 / Resolution: 2.2→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5634 0 176 143 5953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195934
X-RAY DIFFRACTIONr_bond_other_d0.0010.025445
X-RAY DIFFRACTIONr_angle_refined_deg1.4342.0258093
X-RAY DIFFRACTIONr_angle_other_deg0.808312756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9575744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.42725.641234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1715977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8231529
X-RAY DIFFRACTIONr_chiral_restr0.0740.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021042
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_it1.2143.4162982
X-RAY DIFFRACTIONr_mcbond_other1.2143.4162981
X-RAY DIFFRACTIONr_mcangle_it1.9775.1173721
X-RAY DIFFRACTIONr_mcangle_other1.9765.1173722
X-RAY DIFFRACTIONr_scbond_it1.6683.7792952
X-RAY DIFFRACTIONr_scbond_other1.6683.782953
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7855.6184372
X-RAY DIFFRACTIONr_long_range_B_refined6.07167.11624038
X-RAY DIFFRACTIONr_long_range_B_other6.06867.08424012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A56220.11
12C56220.11
21B52660.13
22D52660.13
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 154 -
Rwork0.361 2928 -
obs--99.32 %
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)
17.55140.23612.8342.8573-1.15336.51460.07270.50620.2271-0.73880.14840.0915-0.31310.2643-0.22110.3073-0.09080.03060.17660.05520.1157-1.934522.0522119.1556
25.92181.5582.29653.1157-0.38384.992-0.11420.67240.4622-0.35790.1463-0.2464-0.63980.6453-0.03210.2283-0.05640.08280.12590.01280.12531.343220.7859125.6341
34.89691.34930.73612.40441.02873.07490.08140.3301-0.2313-0.03850.0489-0.21930.22490.1204-0.13040.0480.0158-0.00780.0375-0.02510.0359-8.53237.6766127.416
48.3371.4588-1.60852.0773.27037.31440.2409-0.7558-1.00150.3338-0.1507-0.35640.44830.0324-0.09020.2394-0.0249-0.07820.12820.03950.1908-11.34031.5286136.5994
56.67871.1409-0.35396.4194-1.72645.01060.0502-0.2951-0.640.2358-0.0110.41070.8771-0.7241-0.03930.2255-0.112-0.00230.201-0.03280.1466-22.8121-1.1188133.6574
63.71430.25421.63652.77893.187317.4168-0.19020.18190.1633-0.2620.18520.064-0.3397-0.07920.00490.07650.00890.01920.1035-0.01250.2253-24.574419.898153.2013
71.4650.8622-0.20193.28010.73076.8695-0.03140.07340.2759-0.27720.10040.051-0.6054-0.2458-0.0690.06940.0202-0.00350.0416-0.02750.1397-17.340119.6451150.8444
81.78150.1180.23122.1189-0.54034.4822-0.13730.0079-0.0196-0.08860.0765-0.00380.4082-0.18880.06070.0555-0.02570.02710.0196-0.03450.1007-22.34163.4936158.4984
912.46677.1675-4.60448.7191-3.88694.85080.1418-0.2529-0.91020.3-0.1686-0.32520.5079-0.47220.02690.4304-0.0339-0.00070.2118-0.02530.3301-19.8993-8.7858150.926
102.71-0.3215-2.32584.6295-2.04458.5495-0.02410.1532-0.702-0.5231-0.0523-0.140.90060.3030.07630.38170.0685-0.0110.0432-0.07820.3663-17.7231-12.1033162.5051
119.6291.1414-0.964711.68080.91893.98270.26020.0955-0.87590.4307-0.3963-0.14290.4772-0.3420.13610.35170.01980.01660.09420.02090.3592-16.2928-17.4251168.6596
123.72680.10511.34086.2874-1.12482.4562-0.0284-0.0398-0.34780.01480.14740.11330.3539-0.0727-0.1190.2452-0.01190.01080.2904-0.02940.2243-26.5981-9.4112112.0342
132.40370.638-1.41354.79793.7158.4248-0.08350.1375-0.2370.1414-0.04960.53880.7153-0.58350.13310.1354-0.1203-0.04050.5071-0.06130.2873-34.0106-5.9488108.754
142.5131.72830.39554.3772.10376.2063-0.10450.4188-0.066-0.03330.03740.09520.35-0.44870.06710.0657-0.072-0.04130.3592-0.0120.0653-22.43670.3847105.3405
152.91551.4294-3.71216.013.03629.2129-0.0668-0.0104-0.4780.49530.028-0.83880.62750.15090.03880.23780.0357-0.04440.3703-0.07170.161-9.4236-0.4257102.7146
165.16283.3012-2.3385.9694-1.6226.8231-0.22630.92820.0415-0.84290.6087-0.5846-1.29950.496-0.38240.5586-0.23610.14720.5366-0.03820.1772-10.371210.092197.7121
176.89864.66271.951110.42164.99062.43230.9461-0.28190.66690.6465-0.7699-0.35270.1381-0.3255-0.17620.8518-0.1208-0.14020.75420.06570.3983-4.631915.2185100.5037
1810.6607-0.0536.82913.54193.91388.80230.1419-0.1168-0.10030.065-0.21640.22370.2479-0.22150.07450.41620.026-0.01890.43850.0030.3697-27.960520.611474.9585
196.2726-0.4829-0.01950.5168-1.58035.99040.01160.0610.11940.23530.1250.1466-0.5304-0.5074-0.13670.50950.06020.01620.7280.08130.3485-30.467314.121181.1608
204.20570.61591.55710.42660.655510.70720.2093-0.072-0.0920.3120.0909-0.01550.00150.1224-0.30030.26650.0901-0.00610.39160.11550.285-22.349615.264875.6842
213.5808-0.78840.0740.568-1.08174.74150.1631-0.16850.40050.3675-0.1877-0.1134-0.63670.63070.02460.5737-0.1205-0.03470.64110.18330.266-12.417818.300274.9467
222.59662.05871.01051.91481.23446.48920.24680.0032-0.06050.3443-0.0978-0.37080.45750.8184-0.14890.51550.03120.00690.8460.190.4683-0.295313.318568.7428
231.89130.9828-2.88660.9139-2.52877.0322-0.0657-0.123-0.82710.1092-0.2812-0.071-0.29220.71970.34690.5283-0.00570.06060.82320.0350.750910.32099.012861.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 52
2X-RAY DIFFRACTION2A53 - 89
3X-RAY DIFFRACTION3A90 - 164
4X-RAY DIFFRACTION4A165 - 176
5X-RAY DIFFRACTION5A177 - 213
6X-RAY DIFFRACTION6B25 - 37
7X-RAY DIFFRACTION7B38 - 76
8X-RAY DIFFRACTION8B77 - 165
9X-RAY DIFFRACTION9B166 - 173
10X-RAY DIFFRACTION10B174 - 196
11X-RAY DIFFRACTION11B197 - 213
12X-RAY DIFFRACTION12C30 - 39
13X-RAY DIFFRACTION13C40 - 71
14X-RAY DIFFRACTION14C72 - 135
15X-RAY DIFFRACTION15C136 - 144
16X-RAY DIFFRACTION16C145 - 207
17X-RAY DIFFRACTION17C208 - 214
18X-RAY DIFFRACTION18D30 - 38
19X-RAY DIFFRACTION19D39 - 71
20X-RAY DIFFRACTION20D72 - 91
21X-RAY DIFFRACTION21D92 - 153
22X-RAY DIFFRACTION22D154 - 204
23X-RAY DIFFRACTION23D205 - 213

+
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